From 47f2515cb9a06dbf39877d4648fce3e571e92456 Mon Sep 17 00:00:00 2001 From: xzy Date: Mon, 13 Jan 2025 11:00:42 +0800 Subject: [PATCH] update ans --- examples/atlas/sweep_results/Blood_ans.csv | 2298 ++++++++-- examples/atlas/sweep_results/Brain_ans.csv | 3930 ++++++++++++----- examples/atlas/sweep_results/Heart_ans.csv | 3119 +++++++++++-- .../atlas/sweep_results/Intestine_ans.csv | 316 +- examples/atlas/sweep_results/Kidney_ans.csv | 1206 ++++- examples/atlas/sweep_results/Lung_ans.csv | 2487 +++++++++-- examples/atlas/sweep_results/Pancreas_ans.csv | 874 +++- 7 files changed, 12148 insertions(+), 2082 deletions(-) diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index 70470681..cbbb8812 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0rvmzkia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e9ndxdji,https://wandb.ai/xzy11632/dance-dev/sweeps/6lndzud2,https://wandb.ai/xzy11632/dance-dev/sweeps/kboc5b0g","- type: filter.gene target: FilterGenesPercentile params: {} @@ -91,7 +91,69 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.2874999940395355,,,,,,, +",0.2874999940395355,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/965m42b6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2yalgnau,https://wandb.ai/xzy11632/dance-dev/sweeps/8t32838i,https://wandb.ai/xzy11632/dance-dev/sweeps/vudu58gr","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.289000004529953,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.289000004529953 fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lx05p3vr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iuazawqt,https://wandb.ai/xzy11632/dance-dev/sweeps/s9ckkiye,https://wandb.ai/xzy11632/dance-dev/sweeps/kval7p9y","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -220,7 +282,69 @@ fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.9113029837608336,,,,,,, +",0.9113029837608336,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lfanvedj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zwqjgnrk,https://wandb.ai/xzy11632/dance-dev/sweeps/x274423x,https://wandb.ai/xzy11632/dance-dev/sweeps/di5fcyua","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9215070605278016,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9215070605278016 c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/igxg3cvm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0fxcrj2d,https://wandb.ai/xzy11632/dance-dev/sweeps/ldrt5co9,https://wandb.ai/xzy11632/dance-dev/sweeps/f375yojf","- type: filter.gene target: FilterGenesPercentile params: @@ -313,7 +437,7 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27149999141693115,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene +",0.2714999914169311,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -347,7 +471,49 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27149999141693115,,,,,,, +",0.2714999914169311,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kk54kotc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fzgwbupw,https://wandb.ai/xzy11632/dance-dev/sweeps/2ut6s0zd,https://wandb.ai/xzy11632/dance-dev/sweeps/it9r1cru","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2879999876022339,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2879999876022339 b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mz273ff5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gm5ga5mm,https://wandb.ai/xzy11632/dance-dev/sweeps/gh2p49n8,https://wandb.ai/xzy11632/dance-dev/sweeps/2w6dihtz","- type: filter.gene target: FilterGenesPercentile params: @@ -433,7 +599,7 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.17249999940395355,all_total_runs:210|all_finished_runs:106|step2_total_runs:150|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:50.48%,True,"- type: filter.gene +",0.1724999994039535,all_total_runs:210|all_finished_runs:106|step2_total_runs:150|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:50.48%,True,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -458,7 +624,59 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.17249999940395355,,,,,,, +",0.1724999994039535,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypvuawcw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jw4epusa,https://wandb.ai/xzy11632/dance-dev/sweeps/6svq2ooy,https://wandb.ai/xzy11632/dance-dev/sweeps/rga0qr47","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 2 + max_val: 95 + mode: rv +- type: normalize + target: NormalizeTotal + params: + target_sum: 100000 + max_fraction: 0.01 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 230 + top: true + mode: rv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 842 + feat_norm_mode: minmax +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1675000041723251,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1665000021457672 d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgjtmzk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4lc9v41j,https://wandb.ai/xzy11632/dance-dev/sweeps/qgpqm3rx,https://wandb.ai/xzy11632/dance-dev/sweeps/l6uoduzp","- type: filter.gene target: FilterGenesPercentile params: {} @@ -536,7 +754,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.18799999356269836,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene +",0.1879999935626983,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -561,47 +779,38 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.17649999260902405,,,,,,, -84230ea4-998d-4aa8-8456-81dd54ce23af,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4lhkspy4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v3i9xvkp,https://wandb.ai/xzy11632/dance-dev/sweeps/4kznqqwz,https://wandb.ai/xzy11632/dance-dev/sweeps/ntv3k0kl","- type: filter.gene +",0.176499992609024,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/khimppcz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7dum9r3k,https://wandb.ai/xzy11632/dance-dev/sweeps/ecn9djtg,https://wandb.ai/xzy11632/dance-dev/sweeps/ncce9e88","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - min_cells - min_counts + - min_cells - max_counts - max_cells - min_counts: 28 - min_cells: 0.01009194186360022 - max_counts: 0.9387079584289736 - max_cells: 0.9674538063359476 + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: 4 - gmean_eps: 1 - n_genes: 2153 - n_cells: 100 - bin_size: 778 - bw_adjust: 4.348275785008059 + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: - n_top_genes: 4617 - n_bins: 12 - flavor: seurat + n_top_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7798573970794678,all_total_runs:510|all_finished_runs:358|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.20%,False,"- type: filter.gene +",0.1655000001192093,all_total_runs:601|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:21|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:84.53%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -614,11 +823,10 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -626,23 +834,95 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7673797011375427,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sjqz38be|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9nzex39q,https://wandb.ai/xzy11632/dance-dev/sweeps/w8vhof6g,https://wandb.ai/xzy11632/dance-dev/sweeps/hy70jugh","- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: NormalizeTotal - params: {} -- type: filter.gene - target: FilterGenesTopK +",0.1655000001192093 +84230ea4-998d-4aa8-8456-81dd54ce23af,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4lhkspy4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v3i9xvkp,https://wandb.ai/xzy11632/dance-dev/sweeps/4kznqqwz,https://wandb.ai/xzy11632/dance-dev/sweeps/ntv3k0kl","- type: filter.gene + target: FilterGenesScanpyOrder params: - num_genes: 3000 + order: + - min_cells + - min_counts + - max_counts + - max_cells + min_counts: 28 + min_cells: 0.01009194186360022 + max_counts: 0.9387079584289736 + max_cells: 0.9674538063359476 +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 4 + gmean_eps: 1 + n_genes: 2153 + n_cells: 100 + bin_size: 778 + bw_adjust: 4.348275785008059 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 4617 + n_bins: 12 + flavor: seurat +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7798573970794678,all_total_runs:510|all_finished_runs:358|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.20%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7673797011375427,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sjqz38be|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9nzex39q,https://wandb.ai/xzy11632/dance-dev/sweeps/w8vhof6g,https://wandb.ai/xzy11632/dance-dev/sweeps/hy70jugh","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -731,7 +1011,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.7700534759358288 +",0.7700534759358288,,,,,,, d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/68dze8s6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9p2fidft,https://wandb.ai/xzy11632/dance-dev/sweeps/gfb4afks,https://wandb.ai/xzy11632/dance-dev/sweeps/rfgdltml","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -909,7 +1189,7 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3631910426871938 +",0.3631910426871938,,,,,,, 71be997d-ff75-41b9-8a9f-1288c865f921,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3hrf2wbb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d6vpumby,https://wandb.ai/xzy11632/dance-dev/sweeps/4ewws3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/iuubdwht","- type: filter.gene target: FilterGenesPercentile params: {} @@ -952,8 +1232,7 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4636363685131073,,,,,,,,,,,,,, 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target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1062,16 +1349,17 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20100000500679016,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.29%,False,"- type: filter.gene +",0.4339622557163238,all_total_runs:510|all_finished_runs:355|step2_total_runs:450|step2_finished_runs:322|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:69.61%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizeTotal - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1083,67 +1371,18 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20100000500679016,,,,,,,,,,,,,, -738942eb-ac72-44ff-a64b-8943b5ecd8d9,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pk55qst3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ikkth34p,https://wandb.ai/xzy11632/dance-dev/sweeps/33eivzhs,https://wandb.ai/xzy11632/dance-dev/sweeps/0iyvi4uj","- type: filter.gene 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feature.cell + target: CellPCA - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.21250000596046448,,,,,,, -2a498ace-872a-4935-984b-1afa70fd9886,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51z2kmba|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/exnltfk3,https://wandb.ai/xzy11632/dance-dev/sweeps/l5tne1kz,https://wandb.ai/xzy11632/dance-dev/sweeps/5v2hyx8m","- type: filter.gene - target: FilterGenesPercentile +",0.4226415157318115 +c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y14kg9m4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zxn6dvhn,https://wandb.ai/xzy11632/dance-dev/sweeps/sw3khaut,https://wandb.ai/xzy11632/dance-dev/sweeps/9h4fnk3e","- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: NormalizePlaceHolder params: {} - type: filter.gene target: FilterGenesTopK @@ -1260,22 +1494,18 @@ 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-3faad104-2ab8-4434-816d-474d8d2641db,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j9vqmqzc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/78oimcb2,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bv7omo,https://wandb.ai/xzy11632/dance-dev/sweeps/v818bxqg","- type: filter.gene - target: FilterGenesPercentile +",0.1835000067949295,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/a37nb7n4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/krzjdm8h,https://wandb.ai/xzy11632/dance-dev/sweeps/kzfqbn9t,https://wandb.ai/xzy11632/dance-dev/sweeps/gtf2j5hu","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 4 - max_val: 95 - mode: cv + order: + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 202 + min_cells: 0.03326649451848795 + max_counts: 0.91293116819139 + max_cells: 0.9561302093475796 - type: normalize - target: Log1P + target: ScaleFeature params: - base: 3.32067047306569 + mode: normalize + eps: 0.3 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: - n_top_genes: 9665 - n_bins: 29 - flavor: cell_ranger + n_top_genes: 9344 + span: 0.16241092053064884 - type: feature.cell - target: WeightedFeatureSVD + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 106 + n_components: 593 feat_norm_mode: minmax - type: graph.cell target: CellFeatureGraph @@ -1329,7 +1560,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,"- type: filter.gene +",0.19449999928474423,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:108|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:77.62%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1342,10 +1573,10 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -1353,7 +1584,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -1363,141 +1594,115 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.23999999463558197,,,,,,, -4c4cd77c-8fee-4836-9145-16562a8782fe,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9despcsl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ezmsqc0q,https://wandb.ai/xzy11632/dance-dev/sweeps/wplvjtme,https://wandb.ai/xzy11632/dance-dev/sweeps/c3we0q6d","- type: filter.gene - target: FilterGenesPercentile +",0.1940000057220459,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y31tzbnv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d9z4c1q0,https://wandb.ai/xzy11632/dance-dev/sweeps/x570y2uo,https://wandb.ai/xzy11632/dance-dev/sweeps/0f3z54y5","- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.27300000190734863,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:10|finished_rate:78.57%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.20600000023841855,all_total_runs:600|all_finished_runs:429|step2_total_runs:540|step2_finished_runs:370|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:71.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.27300000190734863,,,,,,, -ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58nyk24l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lv24d8vj,https://wandb.ai/xzy11632/dance-dev/sweeps/ad02sli6,https://wandb.ai/xzy11632/dance-dev/sweeps/735gpode","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.20600000023841855 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-",0.3179999887943268,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.2010000050067901,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.29%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3179999887943268,,,,,,, -bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bjkz4jyd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/u1a19m75,https://wandb.ai/xzy11632/dance-dev/sweeps/gfs40k7c,https://wandb.ai/xzy11632/dance-dev/sweeps/nrb4cgnm","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.2010000050067901,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51cpr0d9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/95hn1egh,https://wandb.ai/xzy11632/dance-dev/sweeps/peld3u5u,https://wandb.ai/xzy11632/dance-dev/sweeps/on2ik08p","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 95 + mode: sum - type: normalize - target: ScaleFeature - params: {} + target: Log1P + params: + base: 9.417934904058548 - type: filter.gene target: HighlyVariableGenesRawCount params: - n_top_genes: 3000 + n_top_genes: 9808 + span: 0.19479949862140847 - type: feature.cell + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + n_components: 505 + feat_norm_mode: l2 - type: graph.cell target: CellFeatureGraph params: @@ -1507,16 +1712,16 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.32850000262260437,all_total_runs:210|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:67.62%,False,"- type: filter.gene +",0.23399999737739563,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:83.33%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1532,43 +1737,36 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.32850000262260437,,,,,,, -bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gih5b907|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3h8b4ia7,https://wandb.ai/xzy11632/dance-dev/sweeps/nqd9ry7o,https://wandb.ai/xzy11632/dance-dev/sweeps/vkrxl804","- type: filter.gene +",0.2335000038146973,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w9issa4d|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/b06p6hx8,https://wandb.ai/xzy11632/dance-dev/sweeps/1i8tao7g,https://wandb.ai/xzy11632/dance-dev/sweeps/5l53xzqj","- type: filter.gene target: FilterGenesPlaceHolder + params: {} - type: normalize - target: ScaleFeature - params: - mode: minmax - eps: 0.3 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 2457 - span: 0.4560040203055745 + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 963 - feat_norm_mode: minmax -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:76.19%,False,"- type: filter.gene +",0.2345000058412552,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -1576,27 +1774,88 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,,,"step2:https://wandb.ai/xzy11632/dan out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph + target: WeightedFeatureSVD +- type: misc + target: SetConfig params: - cell_feature_channel: feature.cell + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2345000058412552 +738942eb-ac72-44ff-a64b-8943b5ecd8d9,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pk55qst3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ikkth34p,https://wandb.ai/xzy11632/dance-dev/sweeps/33eivzhs,https://wandb.ai/xzy11632/dance-dev/sweeps/0iyvi4uj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_counts + - min_cells + - max_counts + min_counts: 78 + min_cells: 0.010918863730631823 + max_counts: 0.9529126141448788 + max_cells: 0.9571952580883056 +- type: normalize + target: NormalizeTotal + params: + target_sum: 100000 + max_fraction: 0.5 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8304 + top: false + mode: var +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.23849999904632568,,,,,,, -d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/en37dusf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mc3gybd1,https://wandb.ai/xzy11632/dance-dev/sweeps/mo1fgrq0,https://wandb.ai/xzy11632/dance-dev/sweeps/algcvv9n","- type: filter.gene +",0.3030000030994415,all_total_runs:510|all_finished_runs:378|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.12%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: FilterGenesTopK params: num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.289000004529953,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xo0nl62w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8mbj6ni4,https://wandb.ai/xzy11632/dance-dev/sweeps/z5plqd2c,https://wandb.ai/xzy11632/dance-dev/sweeps/8yrbdg1z","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell @@ -1612,16 +1871,24 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.4535000026226044,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.62%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.32600000500679016,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.10%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell @@ -1637,4 +1904,1433 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.4535000026226044,,,,,,, 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+",0.33550000190734863,all_total_runs:600|all_finished_runs:448|step2_total_runs:540|step2_finished_runs:388|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33550000190734863 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feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4641327559947967,all_total_runs:510|all_finished_runs:337|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:66.08%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4641327559947967,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7bo3ceh1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dtijfdv0,https://wandb.ai/xzy11632/dance-dev/sweeps/hdzrhugh,https://wandb.ai/xzy11632/dance-dev/sweeps/41dsr5zv","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 2.104951608085805 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3803 + top: true + mode: cv +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 127 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5187366167023555,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rf2i7twp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/85j5c24x,https://wandb.ai/xzy11632/dance-dev/sweeps/kwna8mqg,https://wandb.ai/xzy11632/dance-dev/sweeps/8tvxcuym","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5251606106758118,all_total_runs:600|all_finished_runs:492|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5251606106758118 diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index 549fb1f6..f9a8e694 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 0bc7235a-ae5a-479d-a487-510435377e55,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q8thzcku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/67icoeh5,https://wandb.ai/xzy11632/dance-dev/sweeps/2yzyyprb,https://wandb.ai/xzy11632/dance-dev/sweeps/l4guxas3","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -95,7 +95,123 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5544999837875366 +",0.5544999837875366,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/oxjgrsrd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w5pscp3d,https://wandb.ai/xzy11632/dance-dev/sweeps/s6b7bfmw,https://wandb.ai/xzy11632/dance-dev/sweeps/x51l7r3s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5509999990463257,all_total_runs:600|all_finished_runs:504|step2_total_runs:540|step2_finished_runs:445|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5509999990463257,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xuu3n6fc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fin2t33m,https://wandb.ai/xzy11632/dance-dev/sweeps/77fw5o6f,https://wandb.ai/xzy11632/dance-dev/sweeps/aqsvve2s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5315,all_total_runs:150|all_finished_runs:61|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:40.67%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5315 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Brain),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0fw2so56|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmr1g5de,https://wandb.ai/xzy11632/dance-dev/sweeps/7izot7qs,https://wandb.ai/xzy11632/dance-dev/sweeps/jlmorjb4","- type: filter.gene target: FilterGenesPercentile params: {} @@ -203,7 +319,89 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3675000071525574 +",0.3675000071525574,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q84d43mh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7kx3k7oq,https://wandb.ai/xzy11632/dance-dev/sweeps/euoz4xtn,https://wandb.ai/xzy11632/dance-dev/sweeps/2mr5ac2i","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.382999986410141,all_total_runs:600|all_finished_runs:506|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.382999986410141,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o748tsyg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/py2yh3r8,https://wandb.ai/xzy11632/dance-dev/sweeps/cdz2iob0,https://wandb.ai/xzy11632/dance-dev/sweeps/ax6j7ylt","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3795,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3795 9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tjo2gadd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0h9izpy1,https://wandb.ai/xzy11632/dance-dev/sweeps/i8ghsgev,https://wandb.ai/xzy11632/dance-dev/sweeps/h1l9teot","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -268,22 +466,26 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5149999856948853,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lm5mwxkq,https://wandb.ai/xzy11632/dance-dev/sweeps/ortq51x9,https://wandb.ai/xzy11632/dance-dev/sweeps/lakwxgnu","- type: filter.gene +",0.5149999856948853,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ml42ca0j,https://wandb.ai/xzy11632/dance-dev/sweeps/nsx84eyz,https://wandb.ai/xzy11632/dance-dev/sweeps/3k71zgrp","- type: filter.gene target: FilterGenesPlaceHolder - params: {} - type: normalize target: ScaleFeature - params: {} + params: + mode: normalize + eps: 0.7 - type: filter.gene target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 3000 + n_top_genes: 2467 + n_bins: 23 + flavor: cell_ranger - type: feature.cell + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + n_components: 490 + feat_norm_mode: null - type: graph.cell target: CellFeatureGraph params: @@ -293,7 +495,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5440000295639038,all_total_runs:182|all_finished_runs:114|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.64%,False,"- type: filter.gene +",0.5460000038146973,all_total_runs:215|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:26|step3_1_finished_runs:20|step3_2_total_runs:19|step3_2_finished_runs:15|finished_rate:76.74%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -318,18 +520,25 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5440000295639038 -52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5awnfxur|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3bspph5d,https://wandb.ai/xzy11632/dance-dev/sweeps/4wkwaao0,https://wandb.ai/xzy11632/dance-dev/sweeps/gosfxkg9","- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: ScTransform +",0.5440000295639038,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/updcwamn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ohu0gf1,https://wandb.ai/xzy11632/dance-dev/sweeps/90jvnxg4,https://wandb.ai/xzy11632/dance-dev/sweeps/wuc8ylei","- type: filter.gene + target: FilterGenesScanpyOrder params: - processes_num: 8 + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -342,17 +551,25 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5485000014305115,all_total_runs:476|all_finished_runs:348|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:73.11%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: ScTransform +",0.5335000157356262,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:444|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder params: - processes_num: 8 + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -365,20 +582,121 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5485000014305115,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzh51eku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t7mnkajx,https://wandb.ai/xzy11632/dance-dev/sweeps/4n8979b9,https://wandb.ai/xzy11632/dance-dev/sweeps/pfvyypow","- type: filter.gene +",0.5335000157356262,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w0h5fqbq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pw550ttt,https://wandb.ai/xzy11632/dance-dev/sweeps/0zjzlktf,https://wandb.ai/xzy11632/dance-dev/sweeps/mzcibev2","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - max_cells - - max_counts - min_counts - min_cells - min_counts: 417 - min_cells: 0.0672634037707255 - max_counts: 0.9623011565598958 - max_cells: 0.9539584138468586 + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5295,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5295 +52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5awnfxur|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3bspph5d,https://wandb.ai/xzy11632/dance-dev/sweeps/4wkwaao0,https://wandb.ai/xzy11632/dance-dev/sweeps/gosfxkg9","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5485000014305115,all_total_runs:476|all_finished_runs:348|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:73.11%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5485000014305115,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzh51eku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t7mnkajx,https://wandb.ai/xzy11632/dance-dev/sweeps/4n8979b9,https://wandb.ai/xzy11632/dance-dev/sweeps/pfvyypow","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 417 + min_cells: 0.0672634037707255 + max_counts: 0.9623011565598958 + max_cells: 0.9539584138468586 +- type: normalize + target: ScaleFeature params: mode: minmax eps: 0.1 @@ -437,7 +755,114 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5889999866485596 +",0.5889999866485596,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h5sox1qq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tkk37137,https://wandb.ai/xzy11632/dance-dev/sweeps/8kuofdmo,https://wandb.ai/xzy11632/dance-dev/sweeps/v8plc2lh","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5895000100135803,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5895000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/obu7ohqs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuwhe23l,https://wandb.ai/xzy11632/dance-dev/sweeps/mje7v676,https://wandb.ai/xzy11632/dance-dev/sweeps/30rb0den","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 9.81581694983002 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 8533 + span: 0.5476309362757072 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5825,all_total_runs:150|all_finished_runs:121|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:80.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.582 56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/om1u72x5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bfpl63bz,https://wandb.ai/xzy11632/dance-dev/sweeps/h86ptqve,https://wandb.ai/xzy11632/dance-dev/sweeps/hoc145hn","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -452,54 +877,1594 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c top: false mode: rv - type: feature.cell - target: GaussRandProjFeature + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 992 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3549999892711639,all_total_runs:510|all_finished_runs:396|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.65%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.340499997138977,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0xq25wc4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vmop7pif,https://wandb.ai/xzy11632/dance-dev/sweeps/8tn7yvjs,https://wandb.ai/xzy11632/dance-dev/sweeps/1dpu33ih","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3544999957084656,all_total_runs:600|all_finished_runs:502|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3544999957084656,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpa8itbf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yxhw6hrg,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwvhde7,https://wandb.ai/xzy11632/dance-dev/sweeps/1mzn11g0","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.373,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:71|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:61.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.373 +43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njrfx2sd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d0qeq1ft,https://wandb.ai/xzy11632/dance-dev/sweeps/ao28i16e,https://wandb.ai/xzy11632/dance-dev/sweeps/1tkopoue","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 99 + mode: var +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: + min: 1 + max: 10 + gmean_eps: + min: 1 + max: 10 + n_genes: + min: 1000 + max: 3000 + n_cells: + values: + - null + - 1 + - 10 + - 100 + bin_size: + min: 300 + max: 800 + bw_adjust: + min: 1.0 + max: 5.0 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: + min: 0.05 + max: 0.5 + max_disp: + min: 1.0 + max: 100.0 + min_mean: + min: 0.0 + max: 0.0125 + max_mean: + min: 3.0 + max: 20.0 + n_bins: + min: 10 + max: 30 + flavor: + values: + - seurat + - cell_ranger +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: + min: 100 + max: 1000 + feat_norm_mode: + values: + - null + - normalize + - standardize + - minmax + - l2 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8744999766349792,all_total_runs:510|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8654999732971191,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i9nym2ro|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ugip15uh,https://wandb.ai/xzy11632/dance-dev/sweeps/azouushu,https://wandb.ai/xzy11632/dance-dev/sweeps/fdz2z220","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033,all_total_runs:210|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:67.14%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1t63xurp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uvq676zh,https://wandb.ai/xzy11632/dance-dev/sweeps/mfu80ue4,https://wandb.ai/xzy11632/dance-dev/sweeps/czug79hi","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8619999885559082,all_total_runs:600|all_finished_runs:500|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8619999885559082,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/887k1rjt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/oioj5d4q,https://wandb.ai/xzy11632/dance-dev/sweeps/i59rya2f,https://wandb.ai/xzy11632/dance-dev/sweeps/j210fgqq","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.873,all_total_runs:150|all_finished_runs:125|step2_total_runs:90|step2_finished_runs:68|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.873 +22658f4f-9268-41ad-8828-cc53f4baa9fa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/aio76f5y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4igc6uwy,https://wandb.ai/xzy11632/dance-dev/sweeps/c21dzyzr,https://wandb.ai/xzy11632/dance-dev/sweeps/tesqknws","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7515000104904175,all_total_runs:510|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:63.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7515000104904175,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7710000276565552,all_total_runs:182|all_finished_runs:122|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:67.03%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7710000276565552,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/iimj1dz0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yrrc1i9f,https://wandb.ai/xzy11632/dance-dev/sweeps/pqzc3r5k,https://wandb.ai/xzy11632/dance-dev/sweeps/fdwokoxq","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: + min: 100 + max: 1000 + feat_norm_mode: + values: + - null + - normalize + - standardize + - minmax + - l2 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4715000092983246,all_total_runs:486|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:309|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:4|step3_1_finished_runs:3|step3_2_total_runs:12|step3_2_finished_runs:11|finished_rate:66.46%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + 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+",0.4639999866485596,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:342|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:71.18%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4639999866485596,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nmy20c1k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vk37x3sb,https://wandb.ai/xzy11632/dance-dev/sweeps/2ygn08c2,https://wandb.ai/xzy11632/dance-dev/sweeps/0omklbn8","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4934999942779541,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:78.10%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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type: filter.gene - target: FilterGenesPercentile +",0.4510000050067901,all_total_runs:459|all_finished_runs:372|step2_total_runs:450|step2_finished_runs:372|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:81.05%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizeTotal - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.340499997138977,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene +",0.4510000050067901,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uc3r74ot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s3l0vrwm,https://wandb.ai/xzy11632/dance-dev/sweeps/9vj7bbi4,https://wandb.ai/xzy11632/dance-dev/sweeps/mwg2kekc","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -509,22 +2474,22 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"- type: filter.gene +",0.5055000185966492,all_total_runs:182|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.48%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -534,104 +2499,52 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3580000102519989 -43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njrfx2sd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d0qeq1ft,https://wandb.ai/xzy11632/dance-dev/sweeps/ao28i16e,https://wandb.ai/xzy11632/dance-dev/sweeps/1tkopoue","- type: filter.gene +",0.5055000185966492,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4bmyn7k4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ylbgm0wn,https://wandb.ai/xzy11632/dance-dev/sweeps/4fpuzvk1,https://wandb.ai/xzy11632/dance-dev/sweeps/3pqtwqki","- type: filter.gene target: FilterGenesPercentile - params: - min_val: 9 - max_val: 99 - mode: var + params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: - min: 1 - max: 10 - gmean_eps: - min: 1 - max: 10 - n_genes: - min: 1000 - max: 3000 - n_cells: - values: - - null - - 1 - - 10 - - 100 - bin_size: - min: 300 - max: 800 - bw_adjust: - min: 1.0 - max: 5.0 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: FilterGenesRegression params: - min_disp: - min: 0.05 - max: 0.5 - max_disp: - min: 1.0 - max: 100.0 - min_mean: - min: 0.0 - max: 0.0125 - max_mean: - min: 3.0 - max: 20.0 - n_bins: - min: 10 - max: 30 - flavor: - values: - - seurat - - cell_ranger + num_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: - min: 100 - max: 1000 - feat_norm_mode: - values: - - null - - normalize - - standardize - - minmax - - l2 + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8744999766349792,all_total_runs:510|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene +",0.5214999914169312,all_total_runs:600|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.67%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: Log1P params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8654999732971191,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i9nym2ro|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ugip15uh,https://wandb.ai/xzy11632/dance-dev/sweeps/azouushu,https://wandb.ai/xzy11632/dance-dev/sweeps/fdz2z220","- type: filter.gene +",0.5214999914169312,,,,,,, +c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w1v0bvs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8s7p9moq,https://wandb.ai/xzy11632/dance-dev/sweeps/on8m4hqo,https://wandb.ai/xzy11632/dance-dev/sweeps/ssor6fhj","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -644,28 +2557,25 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.8740000128746033,all_total_runs:210|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:67.14%,False,"- type: filter.gene 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+",0.6100000143051147,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ojpcn5g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z9bpiv2r,https://wandb.ai/xzy11632/dance-dev/sweeps/d3yy3133,https://wandb.ai/xzy11632/dance-dev/sweeps/pbn9c42i","- type: filter.gene + target: FilterGenesPlaceHolder params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -689,7 +2622,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -699,121 +2632,122 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.8740000128746033 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type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.7515000104904175,all_total_runs:510|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:63.33%,False,"- type: filter.gene +",0.6389999985694885,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sj7b58nh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nwnyv0md,https://wandb.ai/xzy11632/dance-dev/sweeps/63eiq8x8","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: NormalizeTotal params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7515000104904175,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.640999972820282,all_total_runs:580|all_finished_runs:460|step2_total_runs:540|step2_finished_runs:420|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|finished_rate:79.31%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.7710000276565552,all_total_runs:182|all_finished_runs:122|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:67.03%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 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-421e5f54-5de7-425f-b399-34ead0651ce1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/u41n43km|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cidz8sry,https://wandb.ai/xzy11632/dance-dev/sweeps/xv6wv8e5,https://wandb.ai/xzy11632/dance-dev/sweeps/g8l71hnl","- type: filter.gene +",0.7944999933242798,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pnrn8w7g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bpgm4640,https://wandb.ai/xzy11632/dance-dev/sweeps/8y4as678,https://wandb.ai/xzy11632/dance-dev/sweeps/9s7cwjsk","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -829,21 +2763,25 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.92849999666214,all_total_runs:510|all_finished_runs:383|step2_total_runs:450|step2_finished_runs:325|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.10%,False,"- type: filter.gene +",0.8090000152587891,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -859,21 +2797,25 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.92849999666214,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2v3pfqs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/exctgkg7,https://wandb.ai/xzy11632/dance-dev/sweeps/0ilextij,https://wandb.ai/xzy11632/dance-dev/sweeps/hxwj0qn7","- type: filter.gene +",0.8090000152587891,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7v3lwalo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kw2ikhb8,https://wandb.ai/xzy11632/dance-dev/sweeps/0m9yh1l4,https://wandb.ai/xzy11632/dance-dev/sweeps/6qay03k2","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -886,10 +2828,10 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -898,16 +2840,13 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.92849999666214,all_total_runs:208|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:7|step3_2_total_runs:19|step3_2_finished_runs:8|finished_rate:57.69%,True,"- type: filter.gene +",0.7954999804496765,all_total_runs:600|all_finished_runs:505|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -920,10 +2859,10 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -932,71 +2871,45 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.92849999666214 -595c9010-99ec-462d-b6a1-2b2fe5407871,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9kbd9qot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qx1jjjzk,https://wandb.ai/xzy11632/dance-dev/sweeps/o52320x4,https://wandb.ai/xzy11632/dance-dev/sweeps/ti1xb207","- type: filter.gene +",0.7954999804496765,,,,,,, +364348b4-bc34-4fe1-a851-60d99e36cafa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vwy5n0wm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/07fioida,https://wandb.ai/xzy11632/dance-dev/sweeps/xufvszgy,https://wandb.ai/xzy11632/dance-dev/sweeps/0yezlkrd","- type: filter.gene target: FilterGenesPercentile - params: - min_val: 6 - max_val: 97 - mode: sum + params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: 6 - gmean_eps: 1 - n_genes: 2719 - n_cells: null - bin_size: 341 - bw_adjust: 4.188156564910177 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesRegression params: - n_top_genes: 4529 - n_bins: 28 - flavor: seurat + num_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 127 - feat_norm_mode: l2 + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7764999866485596,all_total_runs:510|all_finished_runs:344|step2_total_runs:450|step2_finished_runs:340|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:67.45%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.4550000131130218,all_total_runs:493|all_finished_runs:322|step2_total_runs:450|step2_finished_runs:301|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.31%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesRegression params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1009,31 +2922,22 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7699999809265137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t969ysm5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lkr2r2zq,https://wandb.ai/xzy11632/dance-dev/sweeps/kpnyhd83,https://wandb.ai/xzy11632/dance-dev/sweeps/tzy3vv3w","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.4550000131130218,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rtybof1t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8i4spm76,https://wandb.ai/xzy11632/dance-dev/sweeps/s2fldxlp,https://wandb.ai/xzy11632/dance-dev/sweeps/ew7a4p33","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -1043,31 +2947,22 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.7954999804496765,all_total_runs:179|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:17|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.27%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.4740000069141388,all_total_runs:182|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.53%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -1077,142 +2972,116 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.7954999804496765 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-",0.4169999957084656,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/17rooerg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k5eks81i,https://wandb.ai/xzy11632/dance-dev/sweeps/tjht44xq,https://wandb.ai/xzy11632/dance-dev/sweeps/jv70jolu","- type: filter.gene +",0.5084999799728394,all_total_runs:510|all_finished_runs:319|step2_total_runs:450|step2_finished_runs:297|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.55%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: + - min_counts - min_cells - max_counts - - min_counts - max_cells - min_counts: 396 - min_cells: 0.08114426717926743 - max_counts: 0.90410781757729 - max_cells: 0.9639650300380824 + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: ScTransform params: - mode: l2 - eps: 0.7 + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 2843 - span: 0.22156016971664047 + n_top_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 421 - feat_norm_mode: null -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.49549999833106995,all_total_runs:182|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.33%,False,"- type: filter.gene 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-",0.3400000035762787,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:73.47%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.5115000009536743,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6mib6vb3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rrbcza8h,https://wandb.ai/xzy11632/dance-dev/sweeps/84l9elo3,https://wandb.ai/xzy11632/dance-dev/sweeps/j16ha10r","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -1350,18 +3174,14 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3395000100135803 -9372df2d-13d6-4fac-980b-919a5b7eb483,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p5149kgi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0r0wmg1f,https://wandb.ai/xzy11632/dance-dev/sweeps/549m8ddo,https://wandb.ai/xzy11632/dance-dev/sweeps/envt6ozk","- type: filter.gene 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-",0.4639999866485596,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:342|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:71.18%,False,"- type: filter.gene +",0.5139999985694885,,,,,,, +d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/996q4lqs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/itvecyve,https://wandb.ai/xzy11632/dance-dev/sweeps/b8xy9cpt,https://wandb.ai/xzy11632/dance-dev/sweeps/4vxpqar7","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - min_counts - min_cells - max_counts + - min_counts - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + min_counts: 250 + min_cells: 0.0855746910666821 + max_counts: 0.9536696418259212 + max_cells: 0.9763833874910646 - type: normalize target: ScTransform params: processes_num: 8 + min_cells: 2 + gmean_eps: 1 + n_genes: 2008 + n_cells: null + bin_size: 501 + bw_adjust: 1.1228665082399538 - type: filter.gene target: FilterGenesRegression params: - num_genes: 3000 + method: enclasc + num_genes: 9677 - type: feature.cell + target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4639999866485596,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nmy20c1k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vk37x3sb,https://wandb.ai/xzy11632/dance-dev/sweeps/2ygn08c2,https://wandb.ai/xzy11632/dance-dev/sweeps/0omklbn8","- type: filter.gene - target: FilterGenesPercentile 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-",0.4934999942779541,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:78.10%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.5693069100379944,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rl05x7ci|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zrcomei,https://wandb.ai/xzy11632/dance-dev/sweeps/bt85t5r6,https://wandb.ai/xzy11632/dance-dev/sweeps/pt4fsfec","- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize target: Log1P @@ -1465,7 +3289,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -1475,105 +3299,101 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.4934999942779541 -94c41723-b2c4-4b59-a49a-64c9b851903e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fxkuovhw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5je4ee5m,https://wandb.ai/xzy11632/dance-dev/sweeps/u8uc0m16,https://wandb.ai/xzy11632/dance-dev/sweeps/ljbofqhi","- type: filter.gene +",0.5748762488365173,all_total_runs:196|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.45%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.4510000050067901,all_total_runs:459|all_finished_runs:372|step2_total_runs:450|step2_finished_runs:372|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:81.05%,False,"- type: filter.gene +",0.5748762488365173,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58chvobl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qnjsie2l,https://wandb.ai/xzy11632/dance-dev/sweeps/nvedfna7,https://wandb.ai/xzy11632/dance-dev/sweeps/h3mv5jvv","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: CellSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4510000050067901,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uc3r74ot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s3l0vrwm,https://wandb.ai/xzy11632/dance-dev/sweeps/9vj7bbi4,https://wandb.ai/xzy11632/dance-dev/sweeps/mwg2kekc","- type: filter.gene +",0.5866336822509766,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.83%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: Log1P params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: CellSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.5055000185966492,all_total_runs:182|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.48%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.5866336822509766,,,,,,, +774c18c5-efa1-4dc5-9e5e-2c824bab2e34,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fj389gc1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ubgfkhxk,https://wandb.ai/xzy11632/dance-dev/sweeps/oqrx2u9d,https://wandb.ai/xzy11632/dance-dev/sweeps/f59m8oby","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 2 + max_val: 99 + mode: var - type: normalize - target: ScTransform + target: Log1P params: - processes_num: 8 + base: 1.0584452177046255 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 8584 + span: 0.3285327702328724 - type: feature.cell + target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.5055000185966492 -c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w1v0bvs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8s7p9moq,https://wandb.ai/xzy11632/dance-dev/sweeps/on8m4hqo,https://wandb.ai/xzy11632/dance-dev/sweeps/ssor6fhj","- type: filter.gene +",0.525801956653595,all_total_runs:493|all_finished_runs:327|step2_total_runs:450|step2_finished_runs:289|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:66.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1590,9 +3410,9 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesRegression params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1604,7 +3424,7 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6100000143051147,all_total_runs:493|all_finished_runs:322|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.31%,False,"- type: filter.gene +",0.5118549466133118,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2b6ovf5e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/p16tpv7x,https://wandb.ai/xzy11632/dance-dev/sweeps/3sk7tq5f,https://wandb.ai/xzy11632/dance-dev/sweeps/c2j4hpev","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1617,41 +3437,52 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.6100000143051147,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ojpcn5g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z9bpiv2r,https://wandb.ai/xzy11632/dance-dev/sweeps/d3yy3133,https://wandb.ai/xzy11632/dance-dev/sweeps/pbn9c42i","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform +",0.5355648398399353,all_total_runs:196|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:64.80%,False,"- type: filter.gene + target: FilterGenesScanpyOrder params: - processes_num: 8 + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -1661,43 +3492,60 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ params: 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WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6389999985694885 -e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gbqweu7x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eo0n8lpt,https://wandb.ai/xzy11632/dance-dev/sweeps/dtisosl6,https://wandb.ai/xzy11632/dance-dev/sweeps/c3h0t2hl","- type: filter.gene +",0.5299860239028931,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:389|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.83%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5299860239028931,,,,,,, +3d044b52-140a-4528-bf0d-a2dbef9e1f40,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9hu1w69n|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uirvntb0,https://wandb.ai/xzy11632/dance-dev/sweeps/vkaj6z6p,https://wandb.ai/xzy11632/dance-dev/sweeps/tyw2zheq","- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1710,16 +3558,17 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: 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params: out: feature.cell @@ -1823,16 +3662,25 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4550000131130218,all_total_runs:493|all_finished_runs:322|step2_total_runs:450|step2_finished_runs:301|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.31%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.3901515007019043,all_total_runs:600|all_finished_runs:482|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1845,87 +3693,91 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4550000131130218,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rtybof1t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8i4spm76,https://wandb.ai/xzy11632/dance-dev/sweeps/s2fldxlp,https://wandb.ai/xzy11632/dance-dev/sweeps/ew7a4p33","- type: filter.gene +",0.3901515007019043,,,,,,, +f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qphd8ocy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/x4rsitxd,https://wandb.ai/xzy11632/dance-dev/sweeps/4f2tamuu,https://wandb.ai/xzy11632/dance-dev/sweeps/y585p279","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.4740000069141388,all_total_runs:182|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.53%,False,"- type: filter.gene 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base: 9.78567214435452 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: - n_top_genes: 8640 - n_bins: 17 - flavor: cell_ranger + min_disp: 0.42152838507294543 + max_disp: 90.25784555274645 + min_mean: 0.003754725333592855 + max_mean: 13.674551723139253 + n_bins: 13 + flavor: seurat - type: feature.cell - target: FeatureCellPlaceHolder + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO + n_components: 484 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.5084999799728394,all_total_runs:510|all_finished_runs:319|step2_total_runs:450|step2_finished_runs:297|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.55%,False,"- type: filter.gene +",0.5167151093482971,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1938,25 +3790,28 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: NormalizeTotal + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.4819999933242798,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/aqfmsmpx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sxj7ndgn,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6pxhij,https://wandb.ai/xzy11632/dance-dev/sweeps/kfpas6cb","- type: filter.gene +",0.5130813717842102,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c6dubcot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6h51vv85,https://wandb.ai/xzy11632/dance-dev/sweeps/3wbf935e,https://wandb.ai/xzy11632/dance-dev/sweeps/eaxe9v47","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1969,28 +3824,25 @@ 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min_cells: 2 - gmean_eps: 1 - n_genes: 2008 - n_cells: null - bin_size: 501 - bw_adjust: 1.1228665082399538 + target: NormalizePlaceHolder - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: - method: enclasc - num_genes: 9677 + num_genes: 2921 + top: true + mode: cv - type: feature.cell - target: FeatureCellPlaceHolder + target: GaussRandProjFeature params: out: feature.cell log_level: INFO + n_components: 237 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5736386179924011,all_total_runs:493|all_finished_runs:342|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:69.37%,False,"- type: filter.gene 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params: @@ -2110,22 +3943,23 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5748762488365173,all_total_runs:196|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.45%,False,"- type: filter.gene +",0.6637080907821655,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:117|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:75.00%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -2135,53 +3969,82 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5748762488365173 -774c18c5-efa1-4dc5-9e5e-2c824bab2e34,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fj389gc1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ubgfkhxk,https://wandb.ai/xzy11632/dance-dev/sweeps/oqrx2u9d,https://wandb.ai/xzy11632/dance-dev/sweeps/f59m8oby","- type: filter.gene +",0.6637080907821655,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/983ind0g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jcaz6527,https://wandb.ai/xzy11632/dance-dev/sweeps/wfvyft6a,https://wandb.ai/xzy11632/dance-dev/sweeps/c947lcfl","- type: filter.gene target: FilterGenesPercentile + params: {} +- type: 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n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2193,20 +4056,36 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5118549466133118,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2b6ovf5e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/p16tpv7x,https://wandb.ai/xzy11632/dance-dev/sweeps/3sk7tq5f,https://wandb.ai/xzy11632/dance-dev/sweeps/c2j4hpev","- type: filter.gene - target: FilterGenesScanpyOrder +",0.4739454090595245,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zmxfvz4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5pamm1zp,https://wandb.ai/xzy11632/dance-dev/sweeps/a0z7ol9w,https://wandb.ai/xzy11632/dance-dev/sweeps/e3io8n98","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5260545611381531,all_total_runs:210|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.52%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -2227,42 +4106,52 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: 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log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5136476159095764,all_total_runs:600|all_finished_runs:493|step2_total_runs:540|step2_finished_runs:433|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: 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+ split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5130813717842102,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e8vlk083,https://wandb.ai/xzy11632/dance-dev/sweeps/mwggo6ee,https://wandb.ai/xzy11632/dance-dev/sweeps/33pi0zc3","- type: filter.gene +",0.5026239156723022,,,,,,, +07760522-707a-4a1c-8891-dbd1226d6b27,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/flsm88dc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ggwltzko,https://wandb.ai/xzy11632/dance-dev/sweeps/6o4yy577,https://wandb.ai/xzy11632/dance-dev/sweeps/rq6r99by","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2414,12 +4303,11 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell @@ -2435,7 +4323,7 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5130813717842102,all_total_runs:182|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.27%,False,"- type: filter.gene +",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2448,12 +4336,11 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell @@ -2469,132 +4356,52 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5130813717842102 -f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xzxk78ak|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n3z93yct,https://wandb.ai/xzy11632/dance-dev/sweeps/4arisd9h,https://wandb.ai/xzy11632/dance-dev/sweeps/u8gs5iqg","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: NormalizePlaceHolder -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 2921 - top: true - mode: cv -- type: feature.cell - target: GaussRandProjFeature - params: - out: feature.cell - log_level: INFO - n_components: 237 -- type: misc - target: SetConfig +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d0dp8leo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/clti5xmd,https://wandb.ai/xzy11632/dance-dev/sweeps/gwwbfyoy,https://wandb.ai/xzy11632/dance-dev/sweeps/bji8pgf5","- type: filter.gene + target: FilterGenesScanpyOrder params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.6538461446762085,all_total_runs:493|all_finished_runs:370|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:75.05%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: GaussRandProjFeature -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.64891517162323,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4voqq7a0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6para2wq,https://wandb.ai/xzy11632/dance-dev/sweeps/cabldqak,https://wandb.ai/xzy11632/dance-dev/sweeps/s2xpuetf","- type: filter.gene - target: FilterGenesPlaceHolder + target: ScaleFeature params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6637080907821655,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:117|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:75.00%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:81.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder params: - config_dict: - label_channel: cell_type -",0.6637080907821655 -576f193c-75d0-4a11-bd25-8676587e6dc2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5wuups73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6py3oklg,https://wandb.ai/xzy11632/dance-dev/sweeps/dktteowl,https://wandb.ai/xzy11632/dance-dev/sweeps/smtg82tq","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.4739454090595245,all_total_runs:476|all_finished_runs:347|step2_total_runs:450|step2_finished_runs:347|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:72.90%,False,"- type: filter.gene - target: FilterGenesPlaceHolder + target: ScaleFeature params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 - type: filter.gene target: HighlyVariableGenesRawCount params: @@ -2603,160 +4410,200 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4739454090595245,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zmxfvz4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5pamm1zp,https://wandb.ai/xzy11632/dance-dev/sweeps/a0z7ol9w,https://wandb.ai/xzy11632/dance-dev/sweeps/e3io8n98","- type: filter.gene - target: FilterGenesPercentile - params: {} +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kygmspb8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lgj6yg3p,https://wandb.ai/xzy11632/dance-dev/sweeps/2kgqnf6r,https://wandb.ai/xzy11632/dance-dev/sweeps/j7yqtdud","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.5260545611381531,all_total_runs:210|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.52%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",1.0,all_total_runs:150|all_finished_runs:15|step2_total_runs:90|step2_finished_runs:7|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:10.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.5260545611381531 -ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9sbul8yi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/csltl4qv,https://wandb.ai/xzy11632/dance-dev/sweeps/vevuukvb,https://wandb.ai/xzy11632/dance-dev/sweeps/yky0bz21","- type: filter.gene - target: FilterGenesPercentile - params: {} +",1.0 +146216e1-ec30-4fee-a1fb-25defe801e2d,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.468804657459259,all_total_runs:493|all_finished_runs:368|step2_total_runs:450|step2_finished_runs:345|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.65%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.468804657459259,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xghzky,https://wandb.ai/xzy11632/dance-dev/sweeps/pwxoaixd,https://wandb.ai/xzy11632/dance-dev/sweeps/1yosmcdd","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/94jlkvhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pwo0mfuv,https://wandb.ai/xzy11632/dance-dev/sweeps/d1zcq1f3,https://wandb.ai/xzy11632/dance-dev/sweeps/45ment3z","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.48571428656578064,all_total_runs:210|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.67%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - 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-",0.48571428656578064 -07760522-707a-4a1c-8891-dbd1226d6b27,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/flsm88dc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ggwltzko,https://wandb.ai/xzy11632/dance-dev/sweeps/6o4yy577,https://wandb.ai/xzy11632/dance-dev/sweeps/rq6r99by","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pwpb4rfm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/smon44r5,https://wandb.ai/xzy11632/dance-dev/sweeps/rzc9i7hm,https://wandb.ai/xzy11632/dance-dev/sweeps/hdlybnl7","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2769,27 +4616,21 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph + target: FilterGenesRegression params: - cell_feature_channel: feature.cell + num_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:18|step2_total_runs:90|step2_finished_runs:14|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:12.00%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2802,28 +4643,22 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph + target: FilterGenesRegression params: - cell_feature_channel: feature.cell + num_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type ",1.0 -146216e1-ec30-4fee-a1fb-25defe801e2d,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene +700aed19-c16e-4ba8-9191-07da098a8626,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9vvinymt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0f6156l,https://wandb.ai/xzy11632/dance-dev/sweeps/fmt50h6n,https://wandb.ai/xzy11632/dance-dev/sweeps/pbhkpdsh","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2836,18 +4671,18 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: ScaleFeature params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -2857,7 +4692,7 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"- type: filter.gene +",1.0,all_total_runs:194|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:18|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:74.74%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2870,18 +4705,18 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: ScaleFeature params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -2891,8 +4726,7 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 -700aed19-c16e-4ba8-9191-07da098a8626,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9vvinymt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0f6156l,https://wandb.ai/xzy11632/dance-dev/sweeps/fmt50h6n,https://wandb.ai/xzy11632/dance-dev/sweeps/pbhkpdsh","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/15mt3eq3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3pcc3teq,https://wandb.ai/xzy11632/dance-dev/sweeps/vsssu6xu,https://wandb.ai/xzy11632/dance-dev/sweeps/k69a11h0","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2917,16 +4751,13 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:194|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:18|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:74.74%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2951,16 +4782,13 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0 +",1.0,,,,,,, 9813a1d4-d107-459e-9b2e-7687be935f69,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/piw9m0r4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/83fzgznu,https://wandb.ai/xzy11632/dance-dev/sweeps/k12d4bb4,https://wandb.ai/xzy11632/dance-dev/sweeps/elc05kea","- type: filter.gene target: FilterGenesPercentile params: {} @@ -3011,4 +4839,66 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lqheset7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxs7x3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/zlciejor,https://wandb.ai/xzy11632/dance-dev/sweeps/x840lvth","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:478|step2_total_runs:540|step2_finished_runs:430|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:79.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,,,,,,, diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index ba701e5d..eb3c6ef5 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 5a11f879-d1ef-458a-910c-9b0bdfca5ebf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzv8jp6b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hcdwfsqe,https://wandb.ai/xzy11632/dance-dev/sweeps/hr9dvt9y,https://wandb.ai/xzy11632/dance-dev/sweeps/vw8htm3n","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -109,7 +109,105 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.9506173133850098 +",0.9506173133850098,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vzuxzpj3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d7f23zg1,https://wandb.ai/xzy11632/dance-dev/sweeps/uzh7wc9b,https://wandb.ai/xzy11632/dance-dev/sweeps/675mh1vq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9365079402923584,all_total_runs:586|all_finished_runs:391|step2_total_runs:540|step2_finished_runs:353|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:66.72%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9365079402923584,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wl63ncu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tyhv65th,https://wandb.ai/xzy11632/dance-dev/sweeps/0d2njqgp,https://wandb.ai/xzy11632/dance-dev/sweeps/nmhbwu4c","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9435626102292768,all_total_runs:150|all_finished_runs:102|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:68.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9435626102292768 572f3f3e-d3e4-4d13-8e2b-88215e508481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/usfsqcao|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fn99c0s6,https://wandb.ai/xzy11632/dance-dev/sweeps/uff7y5g5,https://wandb.ai/xzy11632/dance-dev/sweeps/vgjmwbae","- type: filter.gene target: FilterGenesPercentile params: @@ -216,7 +314,94 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3995000123977661 +",0.3995000123977661,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dllmfk0t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pdu1htvk,https://wandb.ai/xzy11632/dance-dev/sweeps/9mfsvnog,https://wandb.ai/xzy11632/dance-dev/sweeps/fohrpha2","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3944999873638153,all_total_runs:558|all_finished_runs:349|step2_total_runs:540|step2_finished_runs:349|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.54%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3944999873638153,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uwriv450|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9hfqgivj,https://wandb.ai/xzy11632/dance-dev/sweeps/hp8z8z34,https://wandb.ai/xzy11632/dance-dev/sweeps/ejfw0jpu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_counts + - max_counts + - min_cells + min_counts: 346 + min_cells: 0.0694734963763344 + max_counts: 0.9289519358097762 + max_cells: 0.9793397916743596 +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.5 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.386,all_total_runs:150|all_finished_runs:102|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:68.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.367 9434b020-de42-43eb-bcc4-542b2be69015,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/scbko4h4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/aym16539,https://wandb.ai/xzy11632/dance-dev/sweeps/4cex2w1l,https://wandb.ai/xzy11632/dance-dev/sweeps/al84eum0","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -345,7 +530,109 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.9725000262260436 +",0.9725000262260436,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ljcbdxpa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cd3jmhod,https://wandb.ai/xzy11632/dance-dev/sweeps/iuk576pz,https://wandb.ai/xzy11632/dance-dev/sweeps/xgyejfld","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - max_cells + - min_cells + - min_counts + min_counts: 464 + min_cells: 0.03355997076275901 + max_counts: 0.9675911149628488 + max_cells: 0.956159811249128 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4104 + span: 0.5225329617640444 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 662 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9670000076293944,all_total_runs:600|all_finished_runs:419|step2_total_runs:540|step2_finished_runs:371|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:69.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9664999842643738,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cyx8x2ef|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cm2y2e85,https://wandb.ai/xzy11632/dance-dev/sweeps/znjdtv6p,https://wandb.ai/xzy11632/dance-dev/sweeps/46gbjbvk","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9405,all_total_runs:150|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:59.33%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9405 a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1128huxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/98s1vpgx,https://wandb.ai/xzy11632/dance-dev/sweeps/dkxsnzmu,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6fvur7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -467,8 +754,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6399999856948853 -c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i94przah|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7ruaq9f1,https://wandb.ai/xzy11632/dance-dev/sweeps/o1o45k7l,https://wandb.ai/xzy11632/dance-dev/sweeps/lnl0snl5","- type: filter.gene +",0.6399999856948853,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xkh6yuxk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spekwsdz,https://wandb.ai/xzy11632/dance-dev/sweeps/6dh4dpk0,https://wandb.ai/xzy11632/dance-dev/sweeps/i3do9zdc","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -476,9 +762,8 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: FilterGenesNumberPlaceHolder + params: {} - type: feature.cell params: out: feature.cell @@ -491,7 +776,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.836448609828949,all_total_runs:494|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:4|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.91%,False,"- type: filter.gene +",0.6345000267028809,all_total_runs:586|all_finished_runs:411|step2_total_runs:540|step2_finished_runs:371|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:70.14%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -499,8 +784,108 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression - params: + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6345000267028809,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/evq18crq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hlqtxu6d,https://wandb.ai/xzy11632/dance-dev/sweeps/ijgh3h21,https://wandb.ai/xzy11632/dance-dev/sweeps/pwgh6hr9","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6355,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6355 +c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i94przah|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7ruaq9f1,https://wandb.ai/xzy11632/dance-dev/sweeps/o1o45k7l,https://wandb.ai/xzy11632/dance-dev/sweeps/lnl0snl5","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.836448609828949,all_total_runs:494|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:4|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.91%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: num_genes: 3000 - type: feature.cell params: @@ -582,7 +967,87 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8317757248878479 +",0.8317757248878479,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/varlsjin|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/59ahqx3h,https://wandb.ai/xzy11632/dance-dev/sweeps/gbsb3rwm,https://wandb.ai/xzy11632/dance-dev/sweeps/tn2ract9","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.822429895401001,all_total_runs:586|all_finished_runs:433|step2_total_runs:540|step2_finished_runs:393|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.89%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.822429895401001,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x92janfg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cs9lr34q,https://wandb.ai/xzy11632/dance-dev/sweeps/b6e4q5lc,https://wandb.ai/xzy11632/dance-dev/sweeps/nbea554w","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8271028037383178,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8271028037383178 d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0kyb9nc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/px7yqntj,https://wandb.ai/xzy11632/dance-dev/sweeps/a1ye7fv1,https://wandb.ai/xzy11632/dance-dev/sweeps/vx4ibf72","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -711,7 +1176,85 @@ d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.25600001215934753 +",0.2560000121593475,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7a6dob4a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/oi1v8899,https://wandb.ai/xzy11632/dance-dev/sweeps/2uaewfha,https://wandb.ai/xzy11632/dance-dev/sweeps/6dyddwas","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2540000081062317,all_total_runs:600|all_finished_runs:500|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2540000081062317,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6wmjqpgy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n2e1k541,https://wandb.ai/xzy11632/dance-dev/sweeps/sa9ksi62,https://wandb.ai/xzy11632/dance-dev/sweeps/6j62a8fd","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2405,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2405 d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4raopmgl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tj8oqma7,https://wandb.ai/xzy11632/dance-dev/sweeps/j7f8tlxr,https://wandb.ai/xzy11632/dance-dev/sweeps/vo4w0lty","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -783,7 +1326,7 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29249998927116394,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False,"- type: filter.gene +",0.2924999892711639,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -808,25 +1351,116 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29249998927116394 -e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - max_cells - - min_cells - - max_counts - min_counts: 324 - min_cells: 0.0994897883945216 - max_counts: 0.9671792921176364 - max_cells: 0.952327145046576 +",0.2924999892711639,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hg8lr90w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bytbzr48,https://wandb.ai/xzy11632/dance-dev/sweeps/f12fqnz0,https://wandb.ai/xzy11632/dance-dev/sweeps/e7224vbc","- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize - target: NormalizePlaceHolder + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: - method: seurat3 + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3075000047683716,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:82.83%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3075000047683716,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gyyf7mvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uhzoul7q,https://wandb.ai/xzy11632/dance-dev/sweeps/gvcfxbmn,https://wandb.ai/xzy11632/dance-dev/sweeps/aenj1m4d","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 1941 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.276,all_total_runs:150|all_finished_runs:90|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:60.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2745 +e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 324 + min_cells: 0.0994897883945216 + max_counts: 0.9671792921176364 + max_cells: 0.952327145046576 +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 num_genes: 3947 - type: feature.cell target: GaussRandProjFeature @@ -938,7 +1572,116 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6290000081062317 +",0.6290000081062317,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ugaq0qoa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ce8bglci,https://wandb.ai/xzy11632/dance-dev/sweeps/7rk5gmih,https://wandb.ai/xzy11632/dance-dev/sweeps/r3xtjpfd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6230000257492065,all_total_runs:600|all_finished_runs:478|step2_total_runs:540|step2_finished_runs:418|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6230000257492065,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w5rpqy3q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ntx4v8m0,https://wandb.ai/xzy11632/dance-dev/sweeps/qcc4kp5w,https://wandb.ai/xzy11632/dance-dev/sweeps/wzg4qmk6","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 5497 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6275,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:70|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6265 f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/datmwta4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ri7gpq3f,https://wandb.ai/xzy11632/dance-dev/sweeps/6apaq3my,https://wandb.ai/xzy11632/dance-dev/sweeps/crgctmfi","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1035,8 +1778,7 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3880000114440918 -fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- type: filter.gene +",0.3880000114440918,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lhd5hw1j|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hkqqu13y,https://wandb.ai/xzy11632/dance-dev/sweeps/l8tuzebe,https://wandb.ai/xzy11632/dance-dev/sweeps/94g5yum1","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1049,13 +1791,12 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1068,7 +1809,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6654999852180481,all_total_runs:453|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:369|step3_0_total_runs:1|step3_0_finished_runs:0|step3_1_total_runs:1|step3_1_finished_runs:0|step3_2_total_runs:1|step3_2_finished_runs:0|finished_rate:81.46%,False,"- type: filter.gene +",0.3880000114440918,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:83.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1081,13 +1822,12 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1100,7 +1840,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6654999852180481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypo5xler|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/75anan67,https://wandb.ai/xzy11632/dance-dev/sweeps/js80dvkm,https://wandb.ai/xzy11632/dance-dev/sweeps/uqz1gvwh","- type: filter.gene +",0.3880000114440918,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lhd5hw1j|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/a006m2c5,https://wandb.ai/xzy11632/dance-dev/sweeps/0qg9p4iv,https://wandb.ai/xzy11632/dance-dev/sweeps/uf4gs6jq","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1116,24 +1856,18 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph + target: HighlyVariableGenesRawCount params: - cell_feature_channel: feature.cell + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.6775000095367432,all_total_runs:210|all_finished_runs:188|step2_total_runs:150|step2_finished_runs:128|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:89.52%,False,"- type: filter.gene +",0.3880000114440918,all_total_runs:600|all_finished_runs:442|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:73.67%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1149,25 +1883,19 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph + target: HighlyVariableGenesRawCount params: - cell_feature_channel: feature.cell + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.6775000095367432 -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Heart),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3qs9s7s9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m84q60x9,https://wandb.ai/xzy11632/dance-dev/sweeps/wu90yl9e,https://wandb.ai/xzy11632/dance-dev/sweeps/t9t6we7t","- type: filter.gene +",0.3880000114440918 +fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1184,21 +1912,22 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2975000143051147,all_total_runs:459|all_finished_runs:352|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:76.69%,False,"- type: filter.gene +",0.6654999852180481,all_total_runs:453|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:369|step3_0_total_runs:1|step3_0_finished_runs:0|step3_1_total_runs:1|step3_1_finished_runs:0|step3_2_total_runs:1|step3_2_finished_runs:0|finished_rate:81.46%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1215,46 +1944,45 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2975000143051147,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nrlo0chb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/itw8aeyv,https://wandb.ai/xzy11632/dance-dev/sweeps/gpjulqb6,https://wandb.ai/xzy11632/dance-dev/sweeps/c1at5qua","- type: filter.gene - target: FilterGenesPercentile +",0.6654999852180481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypo5xler|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/75anan67,https://wandb.ai/xzy11632/dance-dev/sweeps/js80dvkm,https://wandb.ai/xzy11632/dance-dev/sweeps/uqz1gvwh","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 10 - max_val: 99 - mode: rv + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: Log1P - params: - base: 9.18544800269841 + params: {} - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: - min_disp: 0.4075238200301367 - max_disp: 41.50678547261833 - min_mean: 0.00843552051034461 - max_mean: 8.182103499798425 - n_bins: 29 - flavor: cell_ranger + params: {} - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 745 - feat_norm_mode: l2 + split_name: train + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -1264,9 +1992,18 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.34450000524520874,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.6775000095367432,all_total_runs:210|all_finished_runs:188|step2_total_runs:150|step2_finished_runs:128|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:89.52%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: Log1P params: {} @@ -1288,179 +2025,191 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3434999883174896 -65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n9pv9var|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uox7hj7b,https://wandb.ai/xzy11632/dance-dev/sweeps/lghef4b7,https://wandb.ai/xzy11632/dance-dev/sweeps/16q0x97m","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 6 - max_val: 96 - mode: rv +",0.6775000095367432,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/53f85d2t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mx5wisvh,https://wandb.ai/xzy11632/dance-dev/sweeps/3hgvwcnm,https://wandb.ai/xzy11632/dance-dev/sweeps/d3hegirq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: ScaleFeature - params: - mode: standardize - eps: 0.3 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: - num_genes: 8619 - top: false - mode: cv + num_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 703 - feat_norm_mode: standardize + target: CellPCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3454999923706054,all_total_runs:510|all_finished_runs:405|step2_total_runs:450|step2_finished_runs:346|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.41%,False,"- type: filter.gene +",0.6725000143051147,all_total_runs:600|all_finished_runs:511|step2_total_runs:540|step2_finished_runs:453|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:85.17%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: CellPCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3075000047683716,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s66g7ypd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kuznrzx4,https://wandb.ai/xzy11632/dance-dev/sweeps/t9vtfezo,https://wandb.ai/xzy11632/dance-dev/sweeps/adq7j7mn","- type: filter.gene - target: FilterGenesPlaceHolder +",0.6725000143051147,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/webizoum|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tmwothqs,https://wandb.ai/xzy11632/dance-dev/sweeps/53ld9d93,https://wandb.ai/xzy11632/dance-dev/sweeps/xbnf6ce4","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: Log1P - params: - base: 7.954575208692654 + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 1124 - top: false - mode: sum + n_top_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD - params: - out: feature.cell - log_level: INFO - n_components: 224 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.35499998927116394,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.90%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} 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HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6359999775886536,all_total_runs:476|all_finished_runs:354|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.37%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.2975000143051147,all_total_runs:459|all_finished_runs:352|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:76.69%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6359999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j4vz4ws5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tecc0rt6,https://wandb.ai/xzy11632/dance-dev/sweeps/jtni6g54,https://wandb.ai/xzy11632/dance-dev/sweeps/uu6v00z6","- type: filter.gene 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CellFeatureGraph params: @@ -1470,7 +2219,31 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6460000276565552,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:80.95%,False,"- type: filter.gene +",0.3445000052452087,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3434999883174896,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9gykotmw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/erompt6i,https://wandb.ai/xzy11632/dance-dev/sweeps/egu5uugr,https://wandb.ai/xzy11632/dance-dev/sweeps/mld787ay","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1483,90 +2256,1724 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 + target: FilterGenesNumberPlaceHolder + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6455000042915344 -ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fadl6x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f6na6k1n,https://wandb.ai/xzy11632/dance-dev/sweeps/1hwk0ec1,https://wandb.ai/xzy11632/dance-dev/sweeps/g73ajpao","- type: filter.gene +",0.3395000100135803,all_total_runs:600|all_finished_runs:501|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.50%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: - min_counts - - max_counts - min_cells + - max_counts - max_cells - min_counts: 413 - min_cells: 0.07306060707222754 - max_counts: 0.9906711226720064 - max_cells: 0.9967104990967668 -- type: normalize - target: ScTransform + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell params: - processes_num: 8 - min_cells: 4 - gmean_eps: 1 - n_genes: 2400 - n_cells: null - bin_size: 538 - bw_adjust: 2.433119961706298 + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3395000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qckzvsgm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0dzg8at,https://wandb.ai/xzy11632/dance-dev/sweeps/d1jd1aip,https://wandb.ai/xzy11632/dance-dev/sweeps/0riym8d4","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.353035738226729 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3613 + span: 0.5980502565579662 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3535,all_total_runs:150|all_finished_runs:135|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:90.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.351 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+",1.0 +1252c5fb-945f-42d6-b1a8-8a3bd864384b,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1579,12 +3986,12 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1600,7 +4007,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3409999907016754,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:10|finished_rate:77.14%,False,"- type: filter.gene +",1.0,all_total_runs:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1613,12 +4020,12 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1634,43 +4041,36 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3409999907016754 -1c739a3e-c3f5-49d5-98e0-73975e751201,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pe7wrxhx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bjghjlj5,https://wandb.ai/xzy11632/dance-dev/sweeps/wahyq279,https://wandb.ai/xzy11632/dance-dev/sweeps/33b4rte8","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gxfub92q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zwovjdz3,https://wandb.ai/xzy11632/dance-dev/sweeps/euthmoud,https://wandb.ai/xzy11632/dance-dev/sweeps/xiyyfe6c","- type: filter.gene target: FilterGenesPlaceHolder + params: {} - type: normalize - target: ScaleFeature - params: - mode: normalize - eps: 0.7 + target: NormalizeTotal + params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesRegression params: - n_top_genes: 2560 - span: 0.1528448051259105 + num_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 479 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3375000059604645,all_total_runs:210|all_finished_runs:155|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:73.81%,False,"- type: filter.gene - target: FilterGenesPercentile +",1.0,all_total_runs:558|all_finished_runs:168|step2_total_runs:540|step2_finished_runs:168|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:30.11%,True,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -1679,49 +4079,41 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3370000123977661 -4ed927e9-c099-49af-b8ce-a2652d069333,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gl8a9d5v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nrpkd1s1,https://wandb.ai/xzy11632/dance-dev/sweeps/i4ot3t4a,https://wandb.ai/xzy11632/dance-dev/sweeps/1off7yhe","- type: filter.gene - target: FilterGenesPercentile +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gw31w8jw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/byh0a3yl,https://wandb.ai/xzy11632/dance-dev/sweeps/44fxvkm1,https://wandb.ai/xzy11632/dance-dev/sweeps/qwzcemto","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 4 - max_val: 98 - mode: cv + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: ScTransform params: - mode: l2 - eps: 0.5 + processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - method: enclasc - num_genes: 6023 + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA - params: - out: feature.cell - log_level: INFO - n_components: 894 - feat_norm_mode: null -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.2824999988079071,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:76.19%,False,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:10|step2_total_runs:90|step2_finished_runs:5|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:6.67%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1734,29 +4126,23 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.2770000100135803 -83b5e943-a1d5-4164-b3f2-f7a37f01b524,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ozba1990|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/338v3aw4,https://wandb.ai/xzy11632/dance-dev/sweeps/ptrrovoq,https://wandb.ai/xzy11632/dance-dev/sweeps/uln7yltc","- type: filter.gene +",1.0 +bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/frisdu4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fywjox,https://wandb.ai/xzy11632/dance-dev/sweeps/dz23lu62,https://wandb.ai/xzy11632/dance-dev/sweeps/g0d29txd","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1790,7 +4176,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:156|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:74.29%,False,"- type: filter.gene +",1.0,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1824,8 +4210,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 -97a17473-e2b1-4f31-a544-44a60773e2dd,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5n3rvy41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/863btck9,https://wandb.ai/xzy11632/dance-dev/sweeps/2eikroc1,https://wandb.ai/xzy11632/dance-dev/sweeps/ga9o1zyj","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ker3hse1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/u2lungmk,https://wandb.ai/xzy11632/dance-dev/sweeps/dj0siwoj,https://wandb.ai/xzy11632/dance-dev/sweeps/drz0g4vw","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1850,16 +4235,13 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:64.80%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:413|step2_total_runs:540|step2_finished_runs:363|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:68.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1884,17 +4266,48 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph +- type: misc + target: SetConfig params: - cell_feature_channel: feature.cell + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ff1dw1c2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/97hw5ggv,https://wandb.ai/xzy11632/dance-dev/sweeps/dfg3m7qm,https://wandb.ai/xzy11632/dance-dev/sweeps/91mz09o5","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0,all_total_runs:150|all_finished_runs:18|step2_total_runs:90|step2_finished_runs:4|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:12.00%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type ",1.0 -1009f384-b12d-448e-ba9f-1b7d2ecfbb4e,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/amviyxfs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ix2rrweg,https://wandb.ai/xzy11632/dance-dev/sweeps/xapwqo4n,https://wandb.ai/xzy11632/dance-dev/sweeps/f4x92sq0","- type: filter.gene +f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/as6ivetf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/icsk75i5,https://wandb.ai/xzy11632/dance-dev/sweeps/vtlcraw8,https://wandb.ai/xzy11632/dance-dev/sweeps/qjov7ai7","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1928,7 +4341,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:127|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:81.12%,False,"- type: filter.gene +",1.0,all_total_runs:182|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.88%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1962,8 +4375,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 -1062c0f2-2a44-4cf9-a7c8-b5ed58b4728d,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6dw5iyg7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/06k4gi1t,https://wandb.ai/xzy11632/dance-dev/sweeps/le8r1zi4,https://wandb.ai/xzy11632/dance-dev/sweeps/ocpspe17","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5ueqmi7v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1qtlda25,https://wandb.ai/xzy11632/dance-dev/sweeps/ir5rr5hz,https://wandb.ai/xzy11632/dance-dev/sweeps/krbtx7e0","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1988,16 +4400,13 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:81.90%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:81.67%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2022,17 +4431,13 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0 -1252c5fb-945f-42d6-b1a8-8a3bd864384b,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/azji707t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wkrd46cp,https://wandb.ai/xzy11632/dance-dev/sweeps/snjn7ct3,https://wandb.ai/xzy11632/dance-dev/sweeps/m3aqfp6h","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2045,28 +4450,21 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:27|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:18.00%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2079,29 +4477,22 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type ",1.0 -bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/frisdu4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fywjox,https://wandb.ai/xzy11632/dance-dev/sweeps/dz23lu62,https://wandb.ai/xzy11632/dance-dev/sweeps/g0d29txd","- type: filter.gene +f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2135,7 +4526,7 @@ bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene +",1.0,all_total_runs:210|all_finished_runs:149|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.95%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2169,8 +4560,7 @@ bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",1.0 -f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/as6ivetf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/icsk75i5,https://wandb.ai/xzy11632/dance-dev/sweeps/vtlcraw8,https://wandb.ai/xzy11632/dance-dev/sweeps/qjov7ai7","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jv6l7zfb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1sctem2k,https://wandb.ai/xzy11632/dance-dev/sweeps/p40vryym,https://wandb.ai/xzy11632/dance-dev/sweeps/g0mqq7jx","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2195,16 +4585,13 @@ f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,,,"step2:https://wandb.ai/xzy11632/dan log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.88%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:489|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:81.50%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2229,17 +4616,13 @@ f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,,,"step2:https://wandb.ai/xzy11632/dan log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0 -f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/syusb3sn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rkq3icqq,https://wandb.ai/xzy11632/dance-dev/sweeps/x0txps05,https://wandb.ai/xzy11632/dance-dev/sweeps/3avow7ff","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2252,28 +4635,21 @@ f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,,,"step2:https://wandb.ai/xzy11632/dan min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:149|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.95%,False,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:17|step2_total_runs:90|step2_finished_runs:7|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:11.33%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2286,25 +4662,18 @@ f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,,,"step2:https://wandb.ai/xzy11632/dan min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type ",1.0 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index 7c8388f9..eef41b0d 100644 --- a/examples/atlas/sweep_results/Intestine_ans.csv +++ b/examples/atlas/sweep_results/Intestine_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cal53l43|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6qn8k6fz,https://wandb.ai/xzy11632/dance-dev/sweeps/bk4iumv7,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwnnypr","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -113,7 +113,49 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.44699999690055847 +",0.4469999969005584,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w85f0jr1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yvez2as1,https://wandb.ai/xzy11632/dance-dev/sweeps/3r5lt9pe,https://wandb.ai/xzy11632/dance-dev/sweeps/78288m6z","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4645000100135803,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4645000100135803 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/968ejhzy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4mpkufxm,https://wandb.ai/xzy11632/dance-dev/sweeps/68q8gvfj,https://wandb.ai/xzy11632/dance-dev/sweeps/f094n1hy","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -243,7 +285,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.4889999926090241 +",0.4889999926090241,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1h4jwpys|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iz2i7d43,https://wandb.ai/xzy11632/dance-dev/sweeps/zcebhj28,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bod1sy","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.48100000619888306,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.48100000619888306 e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o6y5gglv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7g1mezgk,https://wandb.ai/xzy11632/dance-dev/sweeps/rqw2mq80,https://wandb.ai/xzy11632/dance-dev/sweeps/h31q7gkk","- type: filter.gene target: FilterGenesPercentile params: {} @@ -360,7 +444,51 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36229634284973145 +",0.3622963428497314,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8izf00fq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/60jnxyqe,https://wandb.ai/xzy11632/dance-dev/sweeps/oi5dwmnr,https://wandb.ai/xzy11632/dance-dev/sweeps/omvup8nd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3941039443016052,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3941039443016052 6a270451-b4d9-43e0-aa89-e33aac1ac74b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y7qskew9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w5f3puka,https://wandb.ai/xzy11632/dance-dev/sweeps/ys90com4,https://wandb.ai/xzy11632/dance-dev/sweeps/xpfyrv5k","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -479,7 +607,73 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4485294222831726 +",0.4485294222831726,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h9h46fsq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fh35mitj,https://wandb.ai/xzy11632/dance-dev/sweeps/lzx18s0e,https://wandb.ai/xzy11632/dance-dev/sweeps/tvi3f3a1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_cells + - max_counts + min_counts: 431 + min_cells: 0.09906132245998966 + max_counts: 0.923950882549364 + max_cells: 0.981253017438922 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 2113 + n_bins: 15 + flavor: seurat +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 885 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4375,all_total_runs:600|all_finished_runs:509|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4319852888584137 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1gc9d2ad|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yq6minkn,https://wandb.ai/xzy11632/dance-dev/sweeps/tjw6o4v5,https://wandb.ai/xzy11632/dance-dev/sweeps/0bads4k9","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -607,7 +801,69 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.5109999775886536 +",0.5109999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vg93532i|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/42fh6nzf,https://wandb.ai/xzy11632/dance-dev/sweeps/659h8tiv,https://wandb.ai/xzy11632/dance-dev/sweeps/asrfudv3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5304999947547913,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5304999947547913 d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2efkko22|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5tshgz51,https://wandb.ai/xzy11632/dance-dev/sweeps/xj7266k8,https://wandb.ai/xzy11632/dance-dev/sweeps/hyob32ut","- type: filter.gene target: FilterGenesPercentile params: @@ -722,4 +978,50 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5648086071014404 +",0.5648086071014404,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w4ju135u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8plcumyk,https://wandb.ai/xzy11632/dance-dev/sweeps/67bwy8sx,https://wandb.ai/xzy11632/dance-dev/sweeps/ltrjfmqu","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.580926775932312,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.580926775932312 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index 50ef0b0a..8343c080 100644 --- a/examples/atlas/sweep_results/Kidney_ans.csv +++ b/examples/atlas/sweep_results/Kidney_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rl1d9a6f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ml9ih0o4,https://wandb.ai/xzy11632/dance-dev/sweeps/ze74pmm9,https://wandb.ai/xzy11632/dance-dev/sweeps/8mgnvsae","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -68,7 +68,7 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"- type: filter.gene +",0.2730000019073486,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -93,7 +93,51 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863 +",0.2730000019073486,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/80xdc1ba|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sny3930k,https://wandb.ai/xzy11632/dance-dev/sweeps/volqelag,https://wandb.ai/xzy11632/dance-dev/sweeps/5jxnqx6h","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2770000100135803,all_total_runs:600|all_finished_runs:447|step2_total_runs:540|step2_finished_runs:401|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:74.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2770000100135803 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cycuwjwr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/oi569cof,https://wandb.ai/xzy11632/dance-dev/sweeps/xbw7b98v,https://wandb.ai/xzy11632/dance-dev/sweeps/agfkdw1i","- type: filter.gene target: FilterGenesPercentile params: {} @@ -190,7 +234,51 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5799999833106995 +",0.5799999833106995,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9toa84vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t5uul8vm,https://wandb.ai/xzy11632/dance-dev/sweeps/1mgc0dge,https://wandb.ai/xzy11632/dance-dev/sweeps/azn53fsv","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.578499972820282,all_total_runs:600|all_finished_runs:439|step2_total_runs:540|step2_finished_runs:387|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:73.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.578499972820282 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8kh86ent|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s95wr9an,https://wandb.ai/xzy11632/dance-dev/sweeps/vc4fkvqd,https://wandb.ai/xzy11632/dance-dev/sweeps/9cswqwn1","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -319,7 +407,67 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5964999794960022 +",0.5964999794960022,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/e43anxgn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3stmar8u,https://wandb.ai/xzy11632/dance-dev/sweeps/s2cpm80t,https://wandb.ai/xzy11632/dance-dev/sweeps/u3ugwnhn","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5914999842643738,all_total_runs:600|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:391|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:73.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5914999842643738 105c7dad-0468-4628-a5be-2bb42c6a8ae4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ifoggvrj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ux35adas,https://wandb.ai/xzy11632/dance-dev/sweeps/3eqw1s6m,https://wandb.ai/xzy11632/dance-dev/sweeps/g8eti0ga","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -458,7 +606,69 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.7020000219345093 +",0.7020000219345093,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/avkuxvpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jdctlnyj,https://wandb.ai/xzy11632/dance-dev/sweeps/2i0dhz25,https://wandb.ai/xzy11632/dance-dev/sweeps/esaiggjt","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7124999761581421,all_total_runs:600|all_finished_runs:440|step2_total_runs:540|step2_finished_runs:392|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:73.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7124999761581421 5af90777-6760-4003-9dba-8f945fec6fdf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t28984so|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zp5tc3mj,https://wandb.ai/xzy11632/dance-dev/sweeps/j4r41ulh,https://wandb.ai/xzy11632/dance-dev/sweeps/bgn8k0bo","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -577,7 +787,51 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.2809999883174896 +",0.2809999883174896,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x43ntzx4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/irntnkow,https://wandb.ai/xzy11632/dance-dev/sweeps/9tdspve1,https://wandb.ai/xzy11632/dance-dev/sweeps/5yvw6kpr","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2994999885559082,all_total_runs:586|all_finished_runs:420|step2_total_runs:540|step2_finished_runs:386|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2994999885559082 dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kp7sqzxs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jpbtevry,https://wandb.ai/xzy11632/dance-dev/sweeps/rsajt836,https://wandb.ai/xzy11632/dance-dev/sweeps/u5gqonzj","- type: filter.gene target: FilterGenesPercentile params: {} @@ -674,21 +928,72 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24950000643730164 -9df60c57-fdf3-4e93-828e-fe9303f20438,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c0t2tf8r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nychgnxo,https://wandb.ai/xzy11632/dance-dev/sweeps/393j00a1","- type: filter.gene - target: FilterGenesScanpyOrder +",0.2495000064373016,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51phjfg4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rb2c4x3n,https://wandb.ai/xzy11632/dance-dev/sweeps/4m4fq5j5,https://wandb.ai/xzy11632/dance-dev/sweeps/pqqd7mez","- type: filter.gene + target: FilterGenesPercentile params: - order: - - max_counts - - min_counts - - min_cells - - max_cells - min_counts: 219 - min_cells: 0.008850691529276644 - max_counts: 0.9795338990303774 - max_cells: 0.9567690816372924 + min_val: 6 + max_val: 99 + mode: rv - type: normalize - target: NormalizeTotal + target: Log1P + params: + base: 7.449177659482961 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 5312 + top: true + mode: var +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 375 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2224999964237213,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22100000083446503 +9df60c57-fdf3-4e93-828e-fe9303f20438,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c0t2tf8r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nychgnxo,https://wandb.ai/xzy11632/dance-dev/sweeps/393j00a1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_counts + - min_cells + - max_cells + min_counts: 219 + min_cells: 0.008850691529276644 + max_counts: 0.9795338990303774 + max_cells: 0.9567690816372924 +- type: normalize + target: NormalizeTotal params: target_sum: 1000000 max_fraction: 1 @@ -783,7 +1088,54 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2615000009536743 +",0.2615000009536743,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ku1n6b7v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ng92wwrv,https://wandb.ai/xzy11632/dance-dev/sweeps/67oq9j9d,https://wandb.ai/xzy11632/dance-dev/sweeps/4holfqbm","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.085645037530894 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8932 + top: false + mode: rv +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 108 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27649998664855957,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:403|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:73.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27549999952316284 be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/byfq8l0c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yipzivr0,https://wandb.ai/xzy11632/dance-dev/sweeps/ct2q8ugk,https://wandb.ai/xzy11632/dance-dev/sweeps/kgcii9t1","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -844,7 +1196,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.382999986410141,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1a0xicia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wunz1pqq,https://wandb.ai/xzy11632/dance-dev/sweeps/0n5dswxy,https://wandb.ai/xzy11632/dance-dev/sweeps/13if0wtd","- type: filter.gene +",0.382999986410141,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1a0xicia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h2asuybg,https://wandb.ai/xzy11632/dance-dev/sweeps/8uxvnhwl,https://wandb.ai/xzy11632/dance-dev/sweeps/ph5yhz9y","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -878,7 +1230,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.43849998712539673,all_total_runs:183|all_finished_runs:139|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:75.96%,False,"- type: filter.gene +",0.43849998712539673,all_total_runs:212|all_finished_runs:167|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:21|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:78.77%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -912,7 +1264,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.43849998712539673 +",0.43849998712539673,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bueblvgh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qxcu5gfb,https://wandb.ai/xzy11632/dance-dev/sweeps/dl2izc9t,https://wandb.ai/xzy11632/dance-dev/sweeps/11iznmvf","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4440000057220459,all_total_runs:600|all_finished_runs:445|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:8|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:74.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4440000057220459 32b9bdce-2481-4c85-ba1b-6ad5fcea844c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wimg2shl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4y52ea9r,https://wandb.ai/xzy11632/dance-dev/sweeps/i3uqbr79,https://wandb.ai/xzy11632/dance-dev/sweeps/rfefu9nm","- type: filter.gene target: FilterGenesPercentile params: {} @@ -982,7 +1378,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.23549999296665192,all_total_runs:210|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:75.71%,False,"- type: filter.gene +",0.2354999929666519,all_total_runs:210|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:75.71%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1007,7 +1403,49 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.23549999296665192 +",0.2354999929666519,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ch3i3tkk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3ra9d12m,https://wandb.ai/xzy11632/dance-dev/sweeps/0yy5nksn,https://wandb.ai/xzy11632/dance-dev/sweeps/0dpb06b7","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2370000034570694,all_total_runs:600|all_finished_runs:501|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2370000034570694 0b4a15a7-4e9e-4555-9733-2423e5c66469,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nyj1bpi3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m9go9yqe,https://wandb.ai/xzy11632/dance-dev/sweeps/z7jtisk2,https://wandb.ai/xzy11632/dance-dev/sweeps/t16m4wm2","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1121,7 +1559,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2294999957084656 +",0.2294999957084656,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b17chya1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2knyp5e6,https://wandb.ai/xzy11632/dance-dev/sweeps/fpvymfqu,https://wandb.ai/xzy11632/dance-dev/sweeps/7yvf6lid","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2485000044107437,all_total_runs:600|all_finished_runs:470|step2_total_runs:540|step2_finished_runs:416|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:78.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2485000044107437 53d208b0-2cfd-4366-9866-c3c6114081bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/23fzd0cr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ltc7pxdm,https://wandb.ai/xzy11632/dance-dev/sweeps/lnn8aqay,https://wandb.ai/xzy11632/dance-dev/sweeps/vhcg91li","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1251,43 +1733,38 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8755832314491272 -6a30bf44-c490-41ac-965b-0bb58432b10a,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hn06vbc0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f0pf2vll,https://wandb.ai/xzy11632/dance-dev/sweeps/yd0s5ou6,https://wandb.ai/xzy11632/dance-dev/sweeps/8spua97g","- type: filter.gene +",0.8755832314491272,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p6h1i8ws|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fhzengv5,https://wandb.ai/xzy11632/dance-dev/sweeps/23unbp67,https://wandb.ai/xzy11632/dance-dev/sweeps/9j9n7dtn","- type: filter.gene target: FilterGenesScanpyOrder params: order: + - min_counts - min_cells - - max_cells - max_counts - - min_counts - min_counts: 255 - min_cells: 0.01511082364107167 - max_counts: 0.9497483701603496 - max_cells: 0.9750075182668252 + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P - params: - base: 8.039331292267493 + target: ScaleFeature + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 9640 - top: true - mode: var + n_top_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 768 - feat_norm_mode: l2 + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2777777910232544,all_total_runs:510|all_finished_runs:438|step2_total_runs:450|step2_finished_runs:378|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.88%,False,"- type: filter.gene +",0.8750647902488708,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:74.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1300,7 +1777,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: ScaleFeature params: {} - type: filter.gene target: HighlyVariableGenesRawCount @@ -1310,18 +1787,85 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2222222238779068,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nbuoq984|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v8k3ecyi,https://wandb.ai/xzy11632/dance-dev/sweeps/i30iteaa,https://wandb.ai/xzy11632/dance-dev/sweeps/wc6rut0d","- type: filter.gene +",0.8750647902488708 +6a30bf44-c490-41ac-965b-0bb58432b10a,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hn06vbc0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f0pf2vll,https://wandb.ai/xzy11632/dance-dev/sweeps/yd0s5ou6,https://wandb.ai/xzy11632/dance-dev/sweeps/8spua97g","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - min_counts + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 255 + min_cells: 0.01511082364107167 + max_counts: 0.9497483701603496 + max_cells: 0.9750075182668252 +- type: normalize + target: Log1P + params: + base: 8.039331292267493 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9640 + top: true + mode: var +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 768 + feat_norm_mode: l2 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2777777910232544,all_total_runs:510|all_finished_runs:438|step2_total_runs:450|step2_finished_runs:378|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.88%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2222222238779068,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nbuoq984|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v8k3ecyi,https://wandb.ai/xzy11632/dance-dev/sweeps/i30iteaa,https://wandb.ai/xzy11632/dance-dev/sweeps/wc6rut0d","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts - min_cells - max_counts - max_cells @@ -1385,7 +1929,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2222222238779068 +",0.2222222238779068,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0vjmseqv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tjum1tpz,https://wandb.ai/xzy11632/dance-dev/sweeps/buc7ui45,https://wandb.ai/xzy11632/dance-dev/sweeps/dsbpgsg6","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5,all_total_runs:572|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:77.45%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5 f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hrylvzb1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/km714tee,https://wandb.ai/xzy11632/dance-dev/sweeps/5yr6v6hl,https://wandb.ai/xzy11632/dance-dev/sweeps/44mxsz2v","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1492,7 +2080,71 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3647642731666565 +",0.3647642731666565,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0my62r0x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2j2fewq5,https://wandb.ai/xzy11632/dance-dev/sweeps/cepp4w5d,https://wandb.ai/xzy11632/dance-dev/sweeps/6xvxfv4t","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3672456443309784,all_total_runs:558|all_finished_runs:429|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.88%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3672456443309784 20d87640-4be8-487f-93d4-dce38378d00f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ajwsfjty|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m73ege01,https://wandb.ai/xzy11632/dance-dev/sweeps/tnm2ji4l,https://wandb.ai/xzy11632/dance-dev/sweeps/acrse11l","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1573,7 +2225,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29468289017677307,all_total_runs:209|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:19|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:75.12%,False,"- type: filter.gene +",0.294682890176773,all_total_runs:209|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:19|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:75.12%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1607,7 +2259,51 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29468289017677307 +",0.294682890176773,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zn9j6dg5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/06i2q2p7,https://wandb.ai/xzy11632/dance-dev/sweeps/1te143pv,https://wandb.ai/xzy11632/dance-dev/sweeps/i2bo7l98","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33247917890548706,all_total_runs:600|all_finished_runs:483|step2_total_runs:540|step2_finished_runs:423|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33247917890548706 2d31c0ca-0233-41ce-bd1a-05aa8404b073,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pvarw0pp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/x4irukl6,https://wandb.ai/xzy11632/dance-dev/sweeps/5lzcuql4,https://wandb.ai/xzy11632/dance-dev/sweeps/h1ibvdke","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1677,7 +2373,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36496350169181824,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:79.05%,False,"- type: filter.gene +",0.3649635016918182,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:79.05%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1702,7 +2398,69 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36496350169181824 +",0.3649635016918182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0vcqva6z|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t219mhhy,https://wandb.ai/xzy11632/dance-dev/sweeps/o8k3c6lv,https://wandb.ai/xzy11632/dance-dev/sweeps/n54ib73r","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3620437979698181,all_total_runs:600|all_finished_runs:469|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:78.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3620437979698181 fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58296xo1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ckbfs7l7,https://wandb.ai/xzy11632/dance-dev/sweeps/ri8pts3d,https://wandb.ai/xzy11632/dance-dev/sweeps/8i66984j","- type: filter.gene target: FilterGenesPercentile params: @@ -1768,59 +2526,101 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ target: Log1P params: {} - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2759999930858612,all_total_runs:196|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:74.49%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2759999930858612,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l6gb8igg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/avpo32k2,https://wandb.ai/xzy11632/dance-dev/sweeps/8ga8qet1,https://wandb.ai/xzy11632/dance-dev/sweeps/0lz70ruz","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2759999930858612,all_total_runs:196|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:74.49%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.28049999475479126,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:427|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2759999930858612 +",0.28049999475479126 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sf8u6xh6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/90x7mz4f,https://wandb.ai/xzy11632/dance-dev/sweeps/39aa3jfz,https://wandb.ai/xzy11632/dance-dev/sweeps/hl4ld5tp","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1951,7 +2751,51 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4375 +",0.4375,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/75eb8mu2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m6j8n05u,https://wandb.ai/xzy11632/dance-dev/sweeps/hvbyary3,https://wandb.ai/xzy11632/dance-dev/sweeps/536wy46e","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4284999966621399,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:430|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4284999966621399 0b75c598-0893-4216-afe8-5414cab7739d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5j0mk5dm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qj8fwcsn,https://wandb.ai/xzy11632/dance-dev/sweeps/s1ybint1,https://wandb.ai/xzy11632/dance-dev/sweeps/np4gc8ac","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2040,7 +2884,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24050000309944153,all_total_runs:182|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.23%,False,"- type: filter.gene +",0.2405000030994415,all_total_runs:182|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.23%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -2066,7 +2910,69 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24050000309944153 +",0.2405000030994415,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zw08f3vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zokwex9g,https://wandb.ai/xzy11632/dance-dev/sweeps/6w8eah70,https://wandb.ai/xzy11632/dance-dev/sweeps/rh47nlz0","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.244499996304512,all_total_runs:600|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:406|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.244499996304512 2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/098iecnp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0a785nvw,https://wandb.ai/xzy11632/dance-dev/sweeps/05d33k6p,https://wandb.ai/xzy11632/dance-dev/sweeps/a878cw3h","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -2188,7 +3094,69 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5 +",0.5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zw2x3j2g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yayfm8nk,https://wandb.ai/xzy11632/dance-dev/sweeps/shh6b1z9,https://wandb.ai/xzy11632/dance-dev/sweeps/oyem3gtm","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.488034188747406,all_total_runs:599|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:408|step3_0_total_runs:19|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.80%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.488034188747406 2423ce2c-3149-4cca-a2ff-cf682ea29b5f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3peh3ey|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pstn2il1,https://wandb.ai/xzy11632/dance-dev/sweeps/w0nlva0s,https://wandb.ai/xzy11632/dance-dev/sweeps/iw5hu22k","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2321,4 +3289,66 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8755832314491272 +",0.8755832314491272,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yvdvm8br|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuecazpp,https://wandb.ai/xzy11632/dance-dev/sweeps/1axejlbz,https://wandb.ai/xzy11632/dance-dev/sweeps/zpq9n7oj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708,all_total_runs:586|all_finished_runs:488|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.28%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708 diff --git a/examples/atlas/sweep_results/Lung_ans.csv b/examples/atlas/sweep_results/Lung_ans.csv index 53c10f71..bc991b72 100644 --- a/examples/atlas/sweep_results/Lung_ans.csv +++ b/examples/atlas/sweep_results/Lung_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p93dumjw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0garwmxd,https://wandb.ai/xzy11632/dance-dev/sweeps/s6vapi8h,https://wandb.ai/xzy11632/dance-dev/sweeps/vjyplvr1","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -41,51 +41,38 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4560000002384186 -f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cf7nubki|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0dqimbs,https://wandb.ai/xzy11632/dance-dev/sweeps/obby7pnt,https://wandb.ai/xzy11632/dance-dev/sweeps/mvohukm2","- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: NormalizePlaceHolder - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: GaussRandProjFeature -- type: misc - target: SetConfig +",0.4560000002384186,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/88sp4mxc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uz23y4v1,https://wandb.ai/xzy11632/dance-dev/sweeps/4mlv8rqb,https://wandb.ai/xzy11632/dance-dev/sweeps/vc7o5nsc","- type: filter.gene + target: FilterGenesScanpyOrder params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.27549999952316284,all_total_runs:510|all_finished_runs:324|step2_total_runs:450|step2_finished_runs:264|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.53%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.27549999952316284 -3de0ad6d-4378-4f62-b37b-ec0b75a50d94,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/82wyioi1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9stmezaf,https://wandb.ai/xzy11632/dance-dev/sweeps/w5sy9d7k,https://wandb.ai/xzy11632/dance-dev/sweeps/wpjgpvr7","- type: filter.gene +",0.4790000021457672,all_total_runs:600|all_finished_runs:479|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:10|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:79.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -98,84 +85,100 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.15850000083446503,all_total_runs:510|all_finished_runs:419|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.16%,False,"- type: filter.gene - target: FilterGenesScanpyOrder +",0.4790000021457672,,,,,,, +f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cf7nubki|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0dqimbs,https://wandb.ai/xzy11632/dance-dev/sweeps/obby7pnt,https://wandb.ai/xzy11632/dance-dev/sweeps/mvohukm2","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2754999995231628,all_total_runs:510|all_finished_runs:324|step2_total_runs:450|step2_finished_runs:264|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.53%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize - target: Log1P + target: NormalizePlaceHolder params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.15850000083446503 -1e5bd3b8-6a0e-4959-8d69-cafed30fe814,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6tj8p155|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/81avsh07,https://wandb.ai/xzy11632/dance-dev/sweeps/buygqdt4,https://wandb.ai/xzy11632/dance-dev/sweeps/4l19utts","- type: filter.gene - target: FilterGenesPlaceHolder +",0.2754999995231628,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fbs68rd7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xcit9qy8,https://wandb.ai/xzy11632/dance-dev/sweeps/4ftre5j8,https://wandb.ai/xzy11632/dance-dev/sweeps/f5uutcyi","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 96 + mode: cv - type: normalize - target: NormalizeTotal + target: Log1P params: - target_sum: 10000 - max_fraction: 0.5 + base: 9.29338977585692 - type: filter.gene target: FilterGenesTopK params: - num_genes: 2690 - top: true - mode: cv + num_genes: 4645 + top: false + mode: sum - type: feature.cell - target: GaussRandProjFeature + target: CellPCA params: out: feature.cell log_level: INFO - n_components: 461 + n_components: 671 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.33899998664855957,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.2939999997615814,all_total_runs:600|all_finished_runs:463|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:77.17%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -185,15 +188,15 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + target: CellPCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3334999978542328 -4ed927e9-c099-49af-b8ce-a2652d069333(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/go3pdoh7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v5kbmzlh,https://wandb.ai/xzy11632/dance-dev/sweeps/7jrk2f6s,https://wandb.ai/xzy11632/dance-dev/sweeps/mhxt4wt6","- type: filter.gene +",0.29350000619888306,,,,,,, +3de0ad6d-4378-4f62-b37b-ec0b75a50d94,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/82wyioi1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9stmezaf,https://wandb.ai/xzy11632/dance-dev/sweeps/w5sy9d7k,https://wandb.ai/xzy11632/dance-dev/sweeps/wpjgpvr7","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -206,26 +209,24 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5975000262260437,all_total_runs:459|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:78.43%,False,"- type: filter.gene +",0.158500000834465,all_total_runs:510|all_finished_runs:419|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.16%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -238,104 +239,124 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5975000262260437 -01209dce-3575-4bed-b1df-129f57fbc031(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kqfwox7t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/y0046ayn,https://wandb.ai/xzy11632/dance-dev/sweeps/ldnjitb7,https://wandb.ai/xzy11632/dance-dev/sweeps/lt59uias","- type: filter.gene - target: FilterGenesPercentile +",0.158500000834465,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gr6v110e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2af03zz4,https://wandb.ai/xzy11632/dance-dev/sweeps/q5e23azt,https://wandb.ai/xzy11632/dance-dev/sweeps/s3ytrjbv","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 6 - max_val: 99 - mode: var + order: + - min_counts + - max_counts + - max_cells + - min_cells + min_counts: 458 + min_cells: 0.011591892698839612 + max_counts: 0.9504786715733048 + max_cells: 0.968929807966842 - type: normalize - target: NormalizePlaceHolder + target: Log1P + params: + base: 2.5831898659365935 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - method: seurat3 - num_genes: 1122 + n_top_genes: 1528 + span: 0.25048936376968134 - type: feature.cell - target: GaussRandProjFeature + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 476 + n_components: 757 + feat_norm_mode: standardize - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.28450000286102295,all_total_runs:510|all_finished_runs:420|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.35%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.17399999499320984,all_total_runs:600|all_finished_runs:472|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: Log1P params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.28349998593330383 -c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uffahbta|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kce6ughj,https://wandb.ai/xzy11632/dance-dev/sweeps/a2x6wq1a,https://wandb.ai/xzy11632/dance-dev/sweeps/ahewlrh8","- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.17299999296665192,,,,,,, +1e5bd3b8-6a0e-4959-8d69-cafed30fe814,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6tj8p155|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/81avsh07,https://wandb.ai/xzy11632/dance-dev/sweeps/buygqdt4,https://wandb.ai/xzy11632/dance-dev/sweeps/4l19utts","- type: filter.gene + target: FilterGenesPlaceHolder - type: normalize - target: NormalizePlaceHolder - params: {} + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.5 - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 2690 + top: true + mode: cv - type: feature.cell + target: GaussRandProjFeature params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + n_components: 461 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6784999966621399,all_total_runs:510|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:315|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.53%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.3389999866485595,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizePlaceHolder + target: NormalizeTotal params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -347,8 +368,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6784999966621399 -9968be68-ab65-4a38-9e1a-c9b6abece194,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/idz72j8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zs9no5j,https://wandb.ai/xzy11632/dance-dev/sweeps/0a22jgfw,https://wandb.ai/xzy11632/dance-dev/sweeps/cqlbke6s","- type: filter.gene +",0.3334999978542328,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q46hxsfq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6dkzww83,https://wandb.ai/xzy11632/dance-dev/sweeps/ctnmrdn1,https://wandb.ai/xzy11632/dance-dev/sweeps/6og1pgzb","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -361,26 +381,25 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6570000052452087,all_total_runs:476|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.63%,False,"- type: filter.gene +",0.3650000095367432,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:392|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:74.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -393,27 +412,26 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6570000052452087 -1e6a6ef9-7ec9-4c90-bbfb-2ad3c3165fd1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b54i7xxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mgw2de3q,https://wandb.ai/xzy11632/dance-dev/sweeps/jfuj5vll,https://wandb.ai/xzy11632/dance-dev/sweeps/3r9o7kkx","- type: filter.gene +",0.3650000095367432,,,,,,, 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-",0.14749999344348907,all_total_runs:510|all_finished_runs:420|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.35%,False,"- type: filter.gene +",0.5975000262260437,all_total_runs:459|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:78.43%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -456,25 +476,26 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.14749999344348907 -486486d4-9462-43e5-9249-eb43fa5a49a6,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4sue5c56|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/o8vlmct0,https://wandb.ai/xzy11632/dance-dev/sweeps/xajb94o1,https://wandb.ai/xzy11632/dance-dev/sweeps/sgh0lqbn","- type: filter.gene +",0.5975000262260437,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o3xgoa6y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bqb8ige8,https://wandb.ai/xzy11632/dance-dev/sweeps/32xe959r,https://wandb.ai/xzy11632/dance-dev/sweeps/wajc9h8x","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -490,21 +511,22 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc target: NormalizeTotal params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4869999885559082,all_total_runs:476|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:79.83%,False,"- type: filter.gene +",0.6570000052452087,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:432|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.67%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -520,55 +542,87 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc target: NormalizeTotal params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4869999885559082 -7b3368a5-c1a0-4973-9e75-d95b4150c7da,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hlkac19s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ov3ryli8,https://wandb.ai/xzy11632/dance-dev/sweeps/6obgw9bs,https://wandb.ai/xzy11632/dance-dev/sweeps/izhbqz2a","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform +",0.6570000052452087,,,,,,, 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-",0.1557970941066742,all_total_runs:510|all_finished_runs:365|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:71.57%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.2845000028610229,all_total_runs:510|all_finished_runs:420|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.35%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize - target: ScTransform + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression params: - processes_num: 8 + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2834999859333038,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8072p0n9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eh05iegv,https://wandb.ai/xzy11632/dance-dev/sweeps/0hraadqb,https://wandb.ai/xzy11632/dance-dev/sweeps/pyj1uv1u","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -581,12 +635,20 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",0.1557970941066742 -e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fw95i0vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lzszad4s,https://wandb.ai/xzy11632/dance-dev/sweeps/2hg95kcf,https://wandb.ai/xzy11632/dance-dev/sweeps/ix89ykms","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.3019999861717224,all_total_runs:600|all_finished_runs:495|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -604,38 +666,67 @@ e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.11605080962181091,all_total_runs:510|all_finished_runs:335|step2_total_runs:450|step2_finished_runs:294|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.69%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.3019999861717224,,,,,,, +c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uffahbta|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kce6ughj,https://wandb.ai/xzy11632/dance-dev/sweeps/a2x6wq1a,https://wandb.ai/xzy11632/dance-dev/sweeps/ahewlrh8","- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize target: NormalizePlaceHolder params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.11605080962181091 -e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ihea1f9w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tra6ajgy,https://wandb.ai/xzy11632/dance-dev/sweeps/gpcxo6dy,https://wandb.ai/xzy11632/dance-dev/sweeps/5pbruy9a","- type: filter.gene +",0.6784999966621399,all_total_runs:510|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:315|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.53%,False,"- type: filter.gene target: FilterGenesPercentile params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6784999966621399,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g3u1qk0j|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nlje84qw,https://wandb.ai/xzy11632/dance-dev/sweeps/d8gpkrs5,https://wandb.ai/xzy11632/dance-dev/sweeps/anhsxtq2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -650,15 +741,24 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8007153868675232,all_total_runs:318|all_finished_runs:257|step2_total_runs:258|step2_finished_runs:255|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:80.82%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.703000009059906,all_total_runs:572|all_finished_runs:447|step2_total_runs:540|step2_finished_runs:427|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.15%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -673,31 +773,40 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8007153868675232 -0ba16f4b-cb87-4fa3-9363-19fc51eec6e7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/v0gc7aor|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t0gcfd2b,https://wandb.ai/xzy11632/dance-dev/sweeps/o4gnu5j7,https://wandb.ai/xzy11632/dance-dev/sweeps/w8we952e","- type: filter.gene - target: FilterGenesPlaceHolder +",0.703000009059906,,,,,,, +9968be68-ab65-4a38-9e1a-c9b6abece194,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/idz72j8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zs9no5j,https://wandb.ai/xzy11632/dance-dev/sweeps/0a22jgfw,https://wandb.ai/xzy11632/dance-dev/sweeps/cqlbke6s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: ScTransform params: - mode: normalize - eps: 0.3 + processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - method: seurat3 - num_genes: 9080 + n_top_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3712230324745178,all_total_runs:268|all_finished_runs:255|step2_total_runs:242|step2_finished_runs:239|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:95.15%,False,"- type: filter.gene +",0.6570000052452087,all_total_runs:476|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.63%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -714,22 +823,22 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.35827338695526123 -a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b76qr295|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dn8svl35,https://wandb.ai/xzy11632/dance-dev/sweeps/epc20utc,https://wandb.ai/xzy11632/dance-dev/sweeps/mg2pnd4n","- type: filter.gene +",0.6570000052452087,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zl582av4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zlh4j7ft,https://wandb.ai/xzy11632/dance-dev/sweeps/dxovufnv,https://wandb.ai/xzy11632/dance-dev/sweeps/ojvv4lhn","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -753,14 +862,14 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3480176329612732,all_total_runs:510|all_finished_runs:383|step2_total_runs:450|step2_finished_runs:326|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.10%,False,"- type: filter.gene +",0.6759999990463257,all_total_runs:600|all_finished_runs:489|step2_total_runs:540|step2_finished_runs:436|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:81.50%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -784,48 +893,45 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3480176329612732 -8c42cfd0-0b0a-46d5-910c-fc833d83c45e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mwjlq7a2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pt55s3l9,https://wandb.ai/xzy11632/dance-dev/sweeps/gk0raad1,https://wandb.ai/xzy11632/dance-dev/sweeps/sxex7w80","- type: filter.gene +",0.6759999990463257,,,,,,, +1e6a6ef9-7ec9-4c90-bbfb-2ad3c3165fd1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b54i7xxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mgw2de3q,https://wandb.ai/xzy11632/dance-dev/sweeps/jfuj5vll,https://wandb.ai/xzy11632/dance-dev/sweeps/3r9o7kkx","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - max_cells - - max_counts - min_counts - min_cells - min_counts: 455 - min_cells: 0.08766785970976693 - max_counts: 0.982343433796268 - max_cells: 0.9664774788562582 + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P - params: - base: 7.459782027773534 + target: NormalizePlaceHolder + params: {} - type: filter.gene target: FilterGenesTopK params: - num_genes: 9807 - top: true - mode: cv + num_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.226500004529953,all_total_runs:476|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:79.83%,False,"- type: filter.gene 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config_dict: feature_channel: feature.cell label_channel: cell_type -",0.21649999916553497,all_total_runs:493|all_finished_runs:388|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.70%,False,"- type: filter.gene +",0.13899999856948853,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.83%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: NormalizePlaceHolder + params: {} - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell @@ -900,50 +1005,1722 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",0.21649999916553497 -d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xbubo8oq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6vnfiblb,https://wandb.ai/xzy11632/dance-dev/sweeps/1rgmr3tb,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2wvt9c","- type: filter.gene +",0.13699999451637268,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yp0mgsmx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h8uoiu79,https://wandb.ai/xzy11632/dance-dev/sweeps/dkgaia78,https://wandb.ai/xzy11632/dance-dev/sweeps/byfhrep5","- type: filter.gene target: FilterGenesPercentile - params: {} + params: + min_val: 2 + max_val: 97 + mode: rv - type: normalize - target: NormalizePlaceHolder - params: {} + target: ScaleFeature + params: + mode: l2 + eps: 0.7 - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: - num_genes: 3000 + method: scmap + num_genes: 7341 - type: feature.cell + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + n_components: 791 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.15800000727176666,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene 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FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5285000205039978,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z3e3gntq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eal8ymn1,https://wandb.ai/xzy11632/dance-dev/sweeps/hdzb2brg,https://wandb.ai/xzy11632/dance-dev/sweeps/du2ryve3","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5394999980926514,all_total_runs:210|all_finished_runs:179|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.24%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5394999980926514 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type: filter.gene + target: FilterGenesPercentile + params: + min_val: 7 + max_val: 97 + mode: sum +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: -1 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 131 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.15942029654979706,all_total_runs:600|all_finished_runs:470|step2_total_runs:540|step2_finished_runs:423|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1582125574350357,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xtfsfufy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lu662hzj,https://wandb.ai/xzy11632/dance-dev/sweeps/zsy2u3xl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + values: + - - min_counts + - min_cells + - max_counts + - max_cells + - - min_counts + - min_cells + - max_cells + - max_counts + - - min_counts + - max_counts + - min_cells + - max_cells + - - min_counts + - max_counts + - max_cells + - min_cells + - - min_counts + - max_cells + - min_cells + - max_counts + - - min_counts + - max_cells + - max_counts + - min_cells + - - min_cells + - min_counts + - max_counts + - max_cells + - - min_cells + - min_counts + - max_cells + - max_counts + - - min_cells + - max_counts + - min_counts + 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min: 0.9 + max: 1.0 + max_cells: + min: 0.95 + max: 1.0 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: -1 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: + min: 100 + max: 10000 + top: + values: + - true + - false + mode: + values: + - sum + - var + - cv + - rv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: + min: 100 + max: 1000 + feat_norm_mode: + values: + - null + - normalize + - standardize + - minmax + - l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.17149758338928223,all_total_runs:190|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:116|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:14|finished_rate:74.74%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.16908212006092072 +e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fw95i0vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lzszad4s,https://wandb.ai/xzy11632/dance-dev/sweeps/2hg95kcf,https://wandb.ai/xzy11632/dance-dev/sweeps/ix89ykms","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1160508096218109,all_total_runs:510|all_finished_runs:335|step2_total_runs:450|step2_finished_runs:294|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.69%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1160508096218109,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wnsy4hn7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pwjmg1g4,https://wandb.ai/xzy11632/dance-dev/sweeps/cv0hjuqf,https://wandb.ai/xzy11632/dance-dev/sweeps/ts5o7hmt","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 99 + mode: sum +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.3 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2429 + span: 0.12907660564267995 +- type: feature.cell + target: CellSVD + params: + out: feature.cell + log_level: INFO + n_components: 624 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.12990762293338776,all_total_runs:210|all_finished_runs:156|step2_total_runs:150|step2_finished_runs:108|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:74.29%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.12990762293338776 +e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ihea1f9w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tra6ajgy,https://wandb.ai/xzy11632/dance-dev/sweeps/gpcxo6dy,https://wandb.ai/xzy11632/dance-dev/sweeps/5pbruy9a","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8007153868675232,all_total_runs:318|all_finished_runs:257|step2_total_runs:258|step2_finished_runs:255|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:80.82%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: 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filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3582733869552612,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d4ed7of2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4cqjlphf,https://wandb.ai/xzy11632/dance-dev/sweeps/wwtpqhff,https://wandb.ai/xzy11632/dance-dev/sweeps/2hsqujqo","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.43453237414360046,all_total_runs:600|all_finished_runs:468|step2_total_runs:540|step2_finished_runs:421|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:78.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.43453237414360046,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sddbq9kk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i32fl00z,https://wandb.ai/xzy11632/dance-dev/sweeps/3ux4j65s,https://wandb.ai/xzy11632/dance-dev/sweeps/wevylzje","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4050359725952149,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:76.19%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4050359725952149 +a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b76qr295|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dn8svl35,https://wandb.ai/xzy11632/dance-dev/sweeps/epc20utc,https://wandb.ai/xzy11632/dance-dev/sweeps/mg2pnd4n","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3480176329612732,all_total_runs:510|all_finished_runs:383|step2_total_runs:450|step2_finished_runs:326|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.10%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3480176329612732,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xn9x8pbm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g2cw98af,https://wandb.ai/xzy11632/dance-dev/sweeps/cuif1dsz,https://wandb.ai/xzy11632/dance-dev/sweeps/twq492am","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3876652121543884,all_total_runs:600|all_finished_runs:461|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:76.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3876652121543884,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8vygl5n6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/il88es7n,https://wandb.ai/xzy11632/dance-dev/sweeps/kyv0eh67,https://wandb.ai/xzy11632/dance-dev/sweeps/qx4x5rqz","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3348017632961273,all_total_runs:210|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:105|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:60.48%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3348017632961273 +8c42cfd0-0b0a-46d5-910c-fc833d83c45e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mwjlq7a2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pt55s3l9,https://wandb.ai/xzy11632/dance-dev/sweeps/gk0raad1,https://wandb.ai/xzy11632/dance-dev/sweeps/sxex7w80","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 455 + min_cells: 0.08766785970976693 + max_counts: 0.982343433796268 + max_cells: 0.9664774788562582 +- type: normalize + target: Log1P + params: + base: 7.459782027773534 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9807 + top: true + mode: cv +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,all_total_runs:476|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:79.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2230000048875808,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6pmayeh5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qllm738w,https://wandb.ai/xzy11632/dance-dev/sweeps/9bevhqje,https://wandb.ai/xzy11632/dance-dev/sweeps/axo7zz7i","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 7.282700138506678 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 355 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.24250000715255737,all_total_runs:600|all_finished_runs:489|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2419999986886978,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/77gxykh3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vql4ta4g,https://wandb.ai/xzy11632/dance-dev/sweeps/bwiyitpi,https://wandb.ai/xzy11632/dance-dev/sweeps/wvnzhocs","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2515000104904175,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.90%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2515000104904175 +2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ggmt3lbe|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gukxv9vr,https://wandb.ai/xzy11632/dance-dev/sweeps/a4gvm8jz,https://wandb.ai/xzy11632/dance-dev/sweeps/1yxm20rs","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2164999991655349,all_total_runs:493|all_finished_runs:388|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.70%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2164999991655349,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qb638tpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qnbj3gg0,https://wandb.ai/xzy11632/dance-dev/sweeps/kfih2j62,https://wandb.ai/xzy11632/dance-dev/sweeps/fe79qk1l","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x7ca9zjk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g69bgevs,https://wandb.ai/xzy11632/dance-dev/sweeps/lqjvl3t9,https://wandb.ai/xzy11632/dance-dev/sweeps/lcb0w1tc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_cells + - max_counts + - min_counts + min_counts: 452 + min_cells: 0.03353995237571974 + max_counts: 0.9121476758403412 + max_cells: 0.99348026292544 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.3 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 6962 + top: true + mode: cv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 755 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.22349999845027924,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:116|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:82.38%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2214999943971634 +d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xbubo8oq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6vnfiblb,https://wandb.ai/xzy11632/dance-dev/sweeps/1rgmr3tb,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2wvt9c","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1580000072717666,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1580000072717666,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1lf1dmfq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wmh2vp6l,https://wandb.ai/xzy11632/dance-dev/sweeps/9zkgyabm,https://wandb.ai/xzy11632/dance-dev/sweeps/eg7prnlf","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.17249999940395355,all_total_runs:600|all_finished_runs:493|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:82.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.15800000727176666 +",0.17249999940395355,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7n25es77|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vslww26r,https://wandb.ai/xzy11632/dance-dev/sweeps/dnhruay0,https://wandb.ai/xzy11632/dance-dev/sweeps/213rny4x","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.1815000027418137,all_total_runs:210|all_finished_runs:169|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:80.48%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.1815000027418137 4023a2bc-6325-47db-bfdf-9639e91042c2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7u7qawi2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n2403fvc,https://wandb.ai/xzy11632/dance-dev/sweeps/4jk06ql6,https://wandb.ai/xzy11632/dance-dev/sweeps/6t7sm8o0","- type: filter.gene target: FilterGenesPercentile params: {} @@ -988,7 +2765,127 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6186813116073608 +",0.6186813116073608,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w6h9lrkf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/828yc8fb,https://wandb.ai/xzy11632/dance-dev/sweeps/xetdwps8,https://wandb.ai/xzy11632/dance-dev/sweeps/6mtvx8u2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6615384817123413,all_total_runs:586|all_finished_runs:480|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.91%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6615384817123413,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hv9b5aer|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/clfj1oh7,https://wandb.ai/xzy11632/dance-dev/sweeps/myvaevvn,https://wandb.ai/xzy11632/dance-dev/sweeps/xkcoq40e","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 95 + mode: cv +- type: normalize + target: Log1P + params: + base: 1.8942568918726996 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 1319 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 515 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.648901104927063,all_total_runs:196|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.61%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6483516693115234 71be997d-ff75-41b9-8a9f-1288c865f921(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l2wuxpnd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t17ir30r,https://wandb.ai/xzy11632/dance-dev/sweeps/boxtoi63,https://wandb.ai/xzy11632/dance-dev/sweeps/wu62crhr","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1051,4 +2948,100 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5909090638160706 +",0.5909090638160706,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4zpkroz8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ya78zvj,https://wandb.ai/xzy11632/dance-dev/sweeps/etsb2867,https://wandb.ai/xzy11632/dance-dev/sweeps/ul16ui5e","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4848484992980957,all_total_runs:572|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.57%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4848484992980957,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/v5hbb1ob|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/la5t6f69,https://wandb.ai/xzy11632/dance-dev/sweeps/6f1i7xhi,https://wandb.ai/xzy11632/dance-dev/sweeps/q7mkmn1w","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5454545617103577,all_total_runs:168|all_finished_runs:119|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5454545617103577 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv index 2d8a197b..ebcfe263 100644 --- a/examples/atlas/sweep_results/Pancreas_ans.csv +++ b/examples/atlas/sweep_results/Pancreas_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 53d208b0-2cfd-4366-9866-c3c6114081bc(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g7t7xwhn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cf0x6364,https://wandb.ai/xzy11632/dance-dev/sweeps/ol212cn4,https://wandb.ai/xzy11632/dance-dev/sweeps/i688o13x","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -115,7 +115,69 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4020000100135803 +",0.4020000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/22ozz7li|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7af40uoa,https://wandb.ai/xzy11632/dance-dev/sweeps/go7b10ao,https://wandb.ai/xzy11632/dance-dev/sweeps/fogjho7h","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4149999916553498,all_total_runs:586|all_finished_runs:442|step2_total_runs:540|step2_finished_runs:402|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.43%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4149999916553498 78f10833-3e61-4fad-96c9-4bbd4f14bdfa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ile10jfv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8tfuwq6k,https://wandb.ai/xzy11632/dance-dev/sweeps/cwadf7td,https://wandb.ai/xzy11632/dance-dev/sweeps/6kx7b6kc","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -184,7 +246,67 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,,,,,,, +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t544qsq4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mdst6ozg,https://wandb.ai/xzy11632/dance-dev/sweeps/5wuust9u,https://wandb.ai/xzy11632/dance-dev/sweeps/0jz8lzw5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:75.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ki0b8xal,https://wandb.ai/xzy11632/dance-dev/sweeps/hzv5a32f,https://wandb.ai/xzy11632/dance-dev/sweeps/vvy7c4q9","- type: filter.gene target: FilterGenesPercentile params: {} @@ -279,7 +401,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.257999986410141 +",0.257999986410141,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mb7tyn1a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tbsp1xsw,https://wandb.ai/xzy11632/dance-dev/sweeps/cx1inrux,https://wandb.ai/xzy11632/dance-dev/sweeps/ffjmt120","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:410|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:76.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174 37b21763-7f0f-41ae-9001-60bad6e2841d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ertfvv8w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8r7518v2,https://wandb.ai/xzy11632/dance-dev/sweeps/hh8iu4b5,https://wandb.ai/xzy11632/dance-dev/sweeps/fd2zwr1f","- type: filter.gene target: FilterGenesPercentile params: @@ -398,7 +562,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3050000071525574 +",0.3050000071525574,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nflips6b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k7q8z2pc,https://wandb.ai/xzy11632/dance-dev/sweeps/qcv9a0iw,https://wandb.ai/xzy11632/dance-dev/sweeps/252d5f2x","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.328000009059906,all_total_runs:600|all_finished_runs:436|step2_total_runs:540|step2_finished_runs:376|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:72.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.328000009059906 9c4c8515-8f82-4c72-b0c6-f87647b00bbe,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m45z81gy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/40zgwwd2,https://wandb.ai/xzy11632/dance-dev/sweeps/mrhq79ks,https://wandb.ai/xzy11632/dance-dev/sweeps/3k6f32vq","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -467,7 +673,69 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",1.0,,,,,,, +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wolfmyb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9mvl5sx5,https://wandb.ai/xzy11632/dance-dev/sweeps/9fpnmpj0,https://wandb.ai/xzy11632/dance-dev/sweeps/ryu2aorc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:586|all_finished_runs:451|step2_total_runs:540|step2_finished_runs:424|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.96%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g8eo9qp4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/scpo55vu,https://wandb.ai/xzy11632/dance-dev/sweeps/jem8ckkq,https://wandb.ai/xzy11632/dance-dev/sweeps/qozeoh02","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -575,11 +843,73 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2450000047683716 -b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/acvxgobi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/367ly4lx,https://wandb.ai/xzy11632/dance-dev/sweeps/qyt8n1ye,https://wandb.ai/xzy11632/dance-dev/sweeps/yuvualyj","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize +",0.2450000047683716,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l86ls3ov|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lnfv32gq,https://wandb.ai/xzy11632/dance-dev/sweeps/2q0nk04q,https://wandb.ai/xzy11632/dance-dev/sweeps/16gfa1y6","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:448|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174 +b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/acvxgobi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/367ly4lx,https://wandb.ai/xzy11632/dance-dev/sweeps/qyt8n1ye,https://wandb.ai/xzy11632/dance-dev/sweeps/yuvualyj","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize target: ScaleFeature params: {} - type: filter.gene @@ -668,7 +998,47 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3849765360355377 +",0.3849765360355377,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n58tiwn8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uhkwcf89,https://wandb.ai/xzy11632/dance-dev/sweeps/ucmsvu93,https://wandb.ai/xzy11632/dance-dev/sweeps/ws9k52zd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.39201876521110535,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.39201876521110535 c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9nfe3jei|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6v7hplqp,https://wandb.ai/xzy11632/dance-dev/sweeps/mt4za374,https://wandb.ai/xzy11632/dance-dev/sweeps/zzx2pq9v","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -785,7 +1155,69 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6593806743621826 +",0.6593806743621826,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0vghv5c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v0trjp3v,https://wandb.ai/xzy11632/dance-dev/sweeps/ghm1g52e,https://wandb.ai/xzy11632/dance-dev/sweeps/w5ig97h5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6502732038497925,all_total_runs:600|all_finished_runs:496|step2_total_runs:540|step2_finished_runs:437|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:82.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6502732038497925 a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8n01i0az|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sckhppek,https://wandb.ai/xzy11632/dance-dev/sweeps/mnx13kpn,https://wandb.ai/xzy11632/dance-dev/sweeps/t0k7akxc","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -896,10 +1328,124 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: feature.cell + label_channel: cell_type +",0.9090909361839294,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/swbuefez|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4rfpc6i6,https://wandb.ai/xzy11632/dance-dev/sweeps/zh0y5b7w,https://wandb.ai/xzy11632/dance-dev/sweeps/es9x4wkl","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.931818187236786,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:383|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.931818187236786 +5a11f879-d1ef-458a-910c-9b0bdfca5ebf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zqtpjc1h|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3o7b2xs0,https://wandb.ai/xzy11632/dance-dev/sweeps/6glysub4,https://wandb.ai/xzy11632/dance-dev/sweeps/htrki617","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,all_total_runs:210|all_finished_runs:138|step2_total_runs:150|step2_finished_runs:87|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.71%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: label_channel: cell_type -",0.9090909361839294 -5a11f879-d1ef-458a-910c-9b0bdfca5ebf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zqtpjc1h|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3o7b2xs0,https://wandb.ai/xzy11632/dance-dev/sweeps/6glysub4,https://wandb.ai/xzy11632/dance-dev/sweeps/htrki617","- type: filter.gene +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ldwyub15|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wbohhp4w,https://wandb.ai/xzy11632/dance-dev/sweeps/4m9kquzw,https://wandb.ai/xzy11632/dance-dev/sweeps/dy3sel7f","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -912,29 +1458,25 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:138|step2_total_runs:150|step2_finished_runs:87|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.71%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:432|step2_total_runs:540|step2_finished_runs:382|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -947,29 +1489,25 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,, +",1.0 3294d050-6eeb-4a00-b24c-71aacc9b777f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rq1aqcks|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w7fykvmx,https://wandb.ai/xzy11632/dance-dev/sweeps/7zg7srym,https://wandb.ai/xzy11632/dance-dev/sweeps/qgcvp9vy","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1066,7 +1604,55 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4670000076293946 +",0.4670000076293946,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0e382wf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hemo1t7y,https://wandb.ai/xzy11632/dance-dev/sweeps/x2gofgl5,https://wandb.ai/xzy11632/dance-dev/sweeps/9cwz7pvl","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 8 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 6.12335875625052 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 8561 +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 909 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4634999930858612,all_total_runs:599|all_finished_runs:425|step2_total_runs:539|step2_finished_runs:367|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:70.95%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4589999914169311 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ghnlphpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qmwfsxt6,https://wandb.ai/xzy11632/dance-dev/sweeps/0bv97iz8,https://wandb.ai/xzy11632/dance-dev/sweeps/fhv7qkjx","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1143,7 +1729,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.27300000190734863,all_total_runs:510|all_finished_runs:395|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:77.45%,False,"- type: filter.gene +",0.2730000019073486,all_total_runs:510|all_finished_runs:395|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:77.45%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1165,7 +1751,49 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2644999921321869 +",0.2644999921321869,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vqaxcou0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3ade5ctl,https://wandb.ai/xzy11632/dance-dev/sweeps/wov6jky3,https://wandb.ai/xzy11632/dance-dev/sweeps/3bohi175","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:196|all_finished_runs:151|step2_total_runs:136|step2_finished_runs:91|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.04%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174 ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xrzp33gj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/erm7pgbk,https://wandb.ai/xzy11632/dance-dev/sweeps/z5w6mxqq,https://wandb.ai/xzy11632/dance-dev/sweeps/6gwdbnnf","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1278,7 +1906,69 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4115000069141388 +",0.4115000069141388,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lzckrtvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h108k8vo,https://wandb.ai/xzy11632/dance-dev/sweeps/yglgx70h,https://wandb.ai/xzy11632/dance-dev/sweeps/19oi9utb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.41350001096725464,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.41350001096725464 66d15835-5dc8-4e96-b0eb-f48971cb65e8,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vqiycw97|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mqxn1w2x,https://wandb.ai/xzy11632/dance-dev/sweeps/7xrgbuws,https://wandb.ai/xzy11632/dance-dev/sweeps/rfy7mvau","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1402,7 +2092,47 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3634577691555023 +",0.3634577691555023,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5i2bqatn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f3fnnke6,https://wandb.ai/xzy11632/dance-dev/sweeps/0nyyt1k7,https://wandb.ai/xzy11632/dance-dev/sweeps/oaa1e4hg","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4420432150363922,all_total_runs:600|all_finished_runs:494|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4420432150363922 97a17473-e2b1-4f31-a544-44a60773e2dd(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5sc3ymja|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tzb3gq58,https://wandb.ai/xzy11632/dance-dev/sweeps/epie6vgv,https://wandb.ai/xzy11632/dance-dev/sweeps/w6gc0mfl","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1497,4 +2227,60 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6755934357643127 +",0.6755934357643127,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q75qr9j4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sk8ji4mk,https://wandb.ai/xzy11632/dance-dev/sweeps/bjg9ihgt,https://wandb.ai/xzy11632/dance-dev/sweeps/w24yl7xi","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 98 + mode: rv +- type: normalize + target: Log1P + params: + base: 9.215313360927013 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 323 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6792452931404114,all_total_runs:600|all_finished_runs:486|step2_total_runs:540|step2_finished_runs:426|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6786366105079651