From 25bf8328c5841e763e69d1e7993dd1d20ad8273f Mon Sep 17 00:00:00 2001 From: xzy Date: Mon, 13 Jan 2025 11:33:09 +0800 Subject: [PATCH] update ans --- examples/atlas/sweep_results/Blood_ans.csv | 2299 +++++++++++++++-- examples/atlas/sweep_results/Brain_ans.csv | 1009 +++++++- examples/atlas/sweep_results/Heart_ans.csv | 116 +- .../atlas/sweep_results/Intestine_ans.csv | 247 +- examples/atlas/sweep_results/Kidney_ans.csv | 964 ++++++- examples/atlas/sweep_results/Lung_ans.csv | 1811 +++++++++++-- examples/atlas/sweep_results/Pancreas_ans.csv | 824 +++++- 7 files changed, 6626 insertions(+), 644 deletions(-) diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index cbbb8812..5c0a1293 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -1,5 +1,5 @@ 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 +2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bym68vxb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ecznwhs3,https://wandb.ai/xzy11632/dance-dev/sweeps/kqtogj5m,https://wandb.ai/xzy11632/dance-dev/sweeps/w9mcnr87","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -20,7 +20,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2469999939203262,all_total_runs:493|all_finished_runs:376|step2_total_runs:450|step2_finished_runs:336|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:20|finished_rate:76.27%,False,"- type: filter.gene 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filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.900654074287924 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 1878 + span: 0.5494886821562931 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2645,all_total_runs:150|all_finished_runs:120|step2_total_runs:90|step2_finished_runs:60|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:80.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + 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 +",0.2635,"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: @@ -282,7 +318,59 @@ fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.9113029837608336,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kdroab03|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/03u2wz8j,https://wandb.ai/xzy11632/dance-dev/sweeps/axsgwcx0,https://wandb.ai/xzy11632/dance-dev/sweeps/j8ds8gtj","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.923861852433281,all_total_runs:150|all_finished_runs:107|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.33%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.923861852433281,"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: @@ -471,7 +559,61 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 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+",0.284,"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 @@ -624,7 +766,43 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.1724999994039535,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/06p1lum5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dh1b7ovm,https://wandb.ai/xzy11632/dance-dev/sweeps/bjql1aor","- 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 +",0.169,all_total_runs:130|all_finished_runs:71|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:13|finished_rate:54.62%,True,"- 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 +",0.169,"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 @@ -779,7 +957,41 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.176499992609024,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/r5o2z89s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zdzqqtvz,https://wandb.ai/xzy11632/dance-dev/sweeps/xp9872vg,https://wandb.ai/xzy11632/dance-dev/sweeps/74ynsvg4","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.1715,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.1715,"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: @@ -1011,8 +1223,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",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 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-",0.372288316488266,all_total_runs:510|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:357|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:78.24%,False,"- type: filter.gene +",0.7584670186042786,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: @@ -1055,53 +1267,115 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: NormalizeTotal 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: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.372288316488266,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/osyfv0bk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sni6qvye,https://wandb.ai/xzy11632/dance-dev/sweeps/zqf37ih0,https://wandb.ai/xzy11632/dance-dev/sweeps/9vy9sc81","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: ScaleFeature +",0.7584670186042786 +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: - mode: standardize - eps: 0.1 + 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 + target: FilterGenesRegression params: - num_genes: 7305 - top: true - mode: sum + num_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 188 - feat_norm_mode: l2 -- 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 -",0.3771868348121643,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:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:80.48%,False,"- type: filter.gene 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normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- 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 +",0.3596920967102051,all_total_runs:600|all_finished_runs:453|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:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:75.50%,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: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- 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 +",0.3596920967102051 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: {} @@ -1284,7 +1618,45 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4272727370262146,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/owszihkr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f49c7zeb,https://wandb.ai/xzy11632/dance-dev/sweeps/3l7yyix3,https://wandb.ai/xzy11632/dance-dev/sweeps/3hwiq1ug","- type: filter.gene 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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 +",0.4545454545454546,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/owszihkr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f49c7zeb,https://wandb.ai/xzy11632/dance-dev/sweeps/3l7yyix3,https://wandb.ai/xzy11632/dance-dev/sweeps/3hwiq1ug","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1405,7 +1777,7 @@ a5d95a42-0137-496f-8a60-101e17f263c8,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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-1560,7 +1972,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.1944999992847442,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: @@ -1594,7 +2006,61 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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label_channel: cell_type +",0.206,all_total_runs:150|all_finished_runs:106|step2_total_runs:90|step2_finished_runs:52|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:20|finished_rate:70.67%,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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.206,"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 @@ -1616,7 +2082,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.2060000002384185,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 @@ -1638,7 +2104,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20600000023841855 +",0.2060000002384185 456e8b9b-f872-488b-871d-94534090a865,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wri3w9ug|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9c166tcq,https://wandb.ai/xzy11632/dance-dev/sweeps/0j1n56kx,https://wandb.ai/xzy11632/dance-dev/sweeps/3761sh9x","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1712,7 +2178,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.2339999973773956,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 @@ -1737,14 +2203,62 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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: {} +",0.2335000038146973,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lv0fx66b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ddug6xp,https://wandb.ai/xzy11632/dance-dev/sweeps/idxr1y9z,https://wandb.ai/xzy11632/dance-dev/sweeps/0iz6wobo","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 466 + min_cells: 0.0660564715580836 + max_counts: 0.9574165855780944 + max_cells: 0.956786246060403 - type: normalize - target: Log1P - params: {} + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.05 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2925 + span: 0.4795559241062898 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2295,all_total_runs:150|all_finished_runs:109|step2_total_runs:90|step2_finished_runs:69|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|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: 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 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filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.338,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tsfqsce4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qlbcth45,https://wandb.ai/xzy11632/dance-dev/sweeps/qsdgy6a1,https://wandb.ai/xzy11632/dance-dev/sweeps/uzqb64rs","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1935,7 +2483,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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: 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FilterGenesRegression + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: CellSVD + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3709999918937683 -055ca631-6ffb-40de-815e-b931e10718c0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51smdbay|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mhvqib1h,https://wandb.ai/xzy11632/dance-dev/sweeps/qpmixdis,https://wandb.ai/xzy11632/dance-dev/sweeps/j2p0o87d","- type: filter.gene +",0.3400000035762787,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cjdtc2ag|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fzjbv8p0,https://wandb.ai/xzy11632/dance-dev/sweeps/gtz5viph,https://wandb.ai/xzy11632/dance-dev/sweeps/4l2hy0fx","- type: filter.gene target: FilterGenesPlaceHolder + params: {} - type: normalize - target: Log1P - params: - base: 2.12228660428801 + target: NormalizeTotal + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 4984 - n_bins: 29 - flavor: cell_ranger + num_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 872 - feat_norm_mode: minmax + split_name: train + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -2106,11 +2602,11 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2179999947547913,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:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.33%,False,"- type: filter.gene 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-",0.22349999845027924,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:428|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:81.17%,False,"- type: filter.gene +",0.3635,all_total_runs:150|all_finished_runs:106|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:70.67%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: Log1P + target: NormalizeTotal 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 + target: SCNFeature - type: misc target: SetConfig params: 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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: CellSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2105000019073486,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:80.95%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} 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-",0.2105000019073486,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b9mqelgd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3v1qtxjw,https://wandb.ai/xzy11632/dance-dev/sweeps/ww8lnegz,https://wandb.ai/xzy11632/dance-dev/sweeps/4o928ijc","- type: filter.gene +",0.3709999918937683 +055ca631-6ffb-40de-815e-b931e10718c0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dooszu50|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ot9m5uei,https://wandb.ai/xzy11632/dance-dev/sweeps/latzm9d1,https://wandb.ai/xzy11632/dance-dev/sweeps/tqrr3dft","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2239,25 +2743,24 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + 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 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 -",0.19499999284744263,all_total_runs:600|all_finished_runs:477|step2_total_runs:540|step2_finished_runs:427|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:13|finished_rate:79.50%,False,"- type: filter.gene +",0.19699999690055847,all_total_runs:510|all_finished_runs:401|step2_total_runs:450|step2_finished_runs:351|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.63%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2270,47 +2773,41 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + 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 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 -",0.19499999284744263 -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 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FilterGenesPlaceHolder +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 1587 + top: true + mode: cv +- type: feature.cell target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 291 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.23849999904632568,all_total_runs:600|all_finished_runs:496|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:20|finished_rate:82.67%,False,"- type: filter.gene 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CellFeatureGraph params: @@ -2448,8 +3040,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2730000019073486,,,,,,,,,,,,,, -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 +",0.2105000019073486,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mmgjtqss|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tqhl4chp,https://wandb.ai/xzy11632/dance-dev/sweeps/y6bpyb1x,https://wandb.ai/xzy11632/dance-dev/sweeps/q2ypjc9v","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2462,27 +3053,21 @@ ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan 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: WeightedFeaturePCA -- 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 -",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 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SCNFeature 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: {} +",0.188,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b9mqelgd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3v1qtxjw,https://wandb.ai/xzy11632/dance-dev/sweeps/ww8lnegz,https://wandb.ai/xzy11632/dance-dev/sweeps/4o928ijc","- 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: {} @@ -2531,19 +3118,25 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan 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 -",0.3285000026226043,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 - target: FilterGenesPlaceHolder - params: {} +",0.1949999928474426,all_total_runs:600|all_finished_runs:477|step2_total_runs:540|step2_finished_runs:427|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:13|finished_rate:79.50%,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: ScaleFeature params: {} @@ -2556,53 +3149,929 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dan 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 -",0.3285000026226043,,,,,,,,,,,,,, -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 - target: FilterGenesPlaceHolder -- type: normalize - target: ScaleFeature +",0.1949999928474426 +3faad104-2ab8-4434-816d-474d8d2641db,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fizus47n|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/opykbimx,https://wandb.ai/xzy11632/dance-dev/sweeps/i46fxdho,https://wandb.ai/xzy11632/dance-dev/sweeps/0rpl7b1w","- type: filter.gene + target: FilterGenesScanpyOrder params: - mode: minmax - eps: 0.3 + 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 + target: FilterGenesTopK params: - n_top_genes: 2457 - span: 0.4560040203055745 + num_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 + target: GaussRandProjFeature - 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 - target: FilterGenesPlaceHolder - params: {} +",0.22200000286102295,all_total_runs:510|all_finished_runs:408|step2_total_runs:450|step2_finished_runs:350|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:80.00%,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 + target: NormalizeTotal params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + 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 +",0.22200000286102295,"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 + params: + min_val: 4 + max_val: 95 + mode: cv +- type: normalize + target: Log1P + params: + base: 3.32067047306569 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 9665 + n_bins: 29 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + 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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: + 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 +",0.34299999475479126,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:13|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: 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: 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 +",0.34299999475479126 +bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8b6rksvv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/79j345m5,https://wandb.ai/xzy11632/dance-dev/sweeps/b7oac1ul,https://wandb.ai/xzy11632/dance-dev/sweeps/zjfaokju","- 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 + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22100000083446503,all_total_runs:510|all_finished_runs:371|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:72.75%,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 + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22100000083446503,"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 + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.3 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2457 + span: 0.4560040203055745 +- 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 +- type: misc + target: SetConfig + params: + config_dict: + 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 + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -2620,8 +4089,168 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.2384999990463256,,,,,,,,,,,,,, -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 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type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.242,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jhrb659k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4414dhzk,https://wandb.ai/xzy11632/dance-dev/sweeps/annv74ih,https://wandb.ai/xzy11632/dance-dev/sweeps/sebccxo2","- 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: 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 +",0.22849999368190765,all_total_runs:600|all_finished_runs:464|step2_total_runs:540|step2_finished_runs:433|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:77.33%,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: 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 +",0.22849999368190765 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+",0.3714999854564667,all_total_runs:510|all_finished_runs:278|step2_total_runs:450|step2_finished_runs:278|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:54.51%,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: 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 +",0.3714999854564667,"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 target: FilterGenesPlaceHolder params: {} - type: normalize @@ -2671,7 +4300,107 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.4535000026226044,,,,,,,,,,,,,, +",0.4535000026226044,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jr5laoce|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f26y92js,https://wandb.ai/xzy11632/dance-dev/sweeps/6ll9tzpu,https://wandb.ai/xzy11632/dance-dev/sweeps/0k3mtj5w","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3714999854564667,all_total_runs:510|all_finished_runs:278|step2_total_runs:450|step2_finished_runs:278|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:54.51%,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: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3714999854564667,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m6m2bupx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/l1zrtkhn,https://wandb.ai/xzy11632/dance-dev/sweeps/ht752ldv,https://wandb.ai/xzy11632/dance-dev/sweeps/bdlp03ds","- type: filter.gene + target: FilterGenesPercentile + 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: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4325000047683716,all_total_runs:600|all_finished_runs:464|step2_total_runs:540|step2_finished_runs:425|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:18|finished_rate:77.33%,False,"- type: filter.gene + target: FilterGenesPercentile + 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: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4325000047683716 471647b3-04fe-4c76-8372-3264feb950e8,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/294cixrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/82nqs7xy,https://wandb.ai/xzy11632/dance-dev/sweeps/sr152dog,https://wandb.ai/xzy11632/dance-dev/sweeps/9db3oova","- type: filter.gene target: FilterGenesPercentile params: @@ -2726,7 +4455,7 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: feature.cell label_channel: cell_type -",0.45391303300857544,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b2sjyq38|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmw9arqn,https://wandb.ai/xzy11632/dance-dev/sweeps/j3manvbb,https://wandb.ai/xzy11632/dance-dev/sweeps/p3ar3r8e","- type: filter.gene +",0.4539130330085754,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b2sjyq38|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmw9arqn,https://wandb.ai/xzy11632/dance-dev/sweeps/j3manvbb,https://wandb.ai/xzy11632/dance-dev/sweeps/p3ar3r8e","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -2802,7 +4531,7 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.44608695652173913,all_total_runs:150|all_finished_runs:95|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:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False,"- type: filter.gene +",0.4460869565217391,all_total_runs:150|all_finished_runs:95|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:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2828,7 +4557,7 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.44608695652173913,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8o3jnu7v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jlyqtiff,https://wandb.ai/xzy11632/dance-dev/sweeps/vax5rga7,https://wandb.ai/xzy11632/dance-dev/sweeps/14jfmmg9","- type: filter.gene +",0.4460869565217391,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8o3jnu7v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jlyqtiff,https://wandb.ai/xzy11632/dance-dev/sweeps/vax5rga7,https://wandb.ai/xzy11632/dance-dev/sweeps/14jfmmg9","- type: filter.gene target: FilterGenesScanpyOrder params: order: diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index f9a8e694..a4b4fd9f 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -1459,7 +1459,61 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7609999775886536,,,,,,, +",0.7609999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vo5e6hw9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5w7eenvp,https://wandb.ai/xzy11632/dance-dev/sweeps/jz7dz1rv,https://wandb.ai/xzy11632/dance-dev/sweeps/zaq3sba8","- 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 +",0.7735,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:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|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: 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 +",0.7735 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 target: FilterGenesScanpyOrder params: @@ -1630,7 +1684,61 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.9419999718666076,,,,,,, +",0.9419999718666076,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fdskrg67|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v4hxj53u,https://wandb.ai/xzy11632/dance-dev/sweeps/59sb97va,https://wandb.ai/xzy11632/dance-dev/sweeps/69x4485s","- 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 +",0.9265,all_total_runs:150|all_finished_runs:101|step2_total_runs:90|step2_finished_runs:61|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:2|finished_rate:67.33%,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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9265 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 target: FilterGenesPercentile params: @@ -1828,7 +1936,61 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7795000076293945,,,,,,, +",0.7795000076293945,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nxmpirmv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uav0gqma,https://wandb.ai/xzy11632/dance-dev/sweeps/0c6gmy6y,https://wandb.ai/xzy11632/dance-dev/sweeps/gm2eowtj","- 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 +",0.7595,all_total_runs:150|all_finished_runs:68|step2_total_runs:90|step2_finished_runs:68|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:45.33%,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 +",0.7595 70e4f35b-c98c-45a1-9aa9-2053b07315dd,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y71ibr35|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8m159qsq,https://wandb.ai/xzy11632/dance-dev/sweeps/dl6qvpyt,https://wandb.ai/xzy11632/dance-dev/sweeps/2xcjlwtg","- type: filter.gene target: FilterGenesPercentile params: @@ -2041,7 +2203,63 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4884999990463257,,,,,,, +",0.4884999990463257,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1dxe2l0w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ab7lhlo3,https://wandb.ai/xzy11632/dance-dev/sweeps/7yjr744v,https://wandb.ai/xzy11632/dance-dev/sweeps/4u07d9ec","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - max_cells + - min_counts + min_counts: 64 + min_cells: 0.09731136945676208 + max_counts: 0.9966478293559916 + max_cells: 0.9887500429224624 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 8255 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4845,all_total_runs:150|all_finished_runs:116|step2_total_runs:90|step2_finished_runs:61|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:16|finished_rate:77.33%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.484 72822932-10f6-466f-baf3-a2c1d89364bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fqlyzkgn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xii6bzr5,https://wandb.ai/xzy11632/dance-dev/sweeps/vi11qjbr,https://wandb.ai/xzy11632/dance-dev/sweeps/bkatxi6c","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2190,7 +2408,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.34150001406669617,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 +",0.3415000140666961,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: FilterGenesScanpyOrder params: order: @@ -2221,7 +2439,55 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3409999907016754,,,,,,, +",0.3409999907016754,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/66gvcj96|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dfkmrl1i,https://wandb.ai/xzy11632/dance-dev/sweeps/ciietvtw,https://wandb.ai/xzy11632/dance-dev/sweeps/f1mqyetb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 309 + min_cells: 0.03282765645433316 + max_counts: 0.9979696820991064 + max_cells: 0.9842200110060252 +- type: normalize + target: NormalizeTotal + params: + target_sum: null + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 858 + span: 0.1494170169182795 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3445,all_total_runs:150|all_finished_runs:104|step2_total_runs:90|step2_finished_runs:69|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:69.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- 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 +",0.3435 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 target: FilterGenesScanpyOrder params: @@ -2402,18 +2668,56 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5120000243186951,,,,,,, -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 - target: FilterGenesPlaceHolder - params: {} +",0.5120000243186951,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vugxebv6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iqwj2j8c,https://wandb.ai/xzy11632/dance-dev/sweeps/tta7mfwk,https://wandb.ai/xzy11632/dance-dev/sweeps/zmiplrsx","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 96 + mode: rv - type: normalize - target: ScTransform + target: ScaleFeature params: - processes_num: 8 + mode: normalize + eps: 0.3 - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5035,all_total_runs:150|all_finished_runs:83|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:55.33%,True,"- type: filter.gene + target: FilterGenesPercentile + 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 +",0.5 +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 + 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 @@ -2543,7 +2847,55 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5214999914169312,,,,,,, +",0.5214999914169312,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ol3ztzsp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4y8mkdbc,https://wandb.ai/xzy11632/dance-dev/sweeps/227yfu9d,https://wandb.ai/xzy11632/dance-dev/sweeps/p7ic9i6t","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - min_counts + - max_cells + min_counts: 464 + min_cells: 0.08771271564181772 + max_counts: 0.9772928029677204 + max_cells: 0.9973074494435608 +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 4103 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.521,all_total_runs:150|all_finished_runs:91|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:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:60.67%,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 +",0.52 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: @@ -2702,7 +3054,43 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.640999972820282,,,,,,, +",0.640999972820282,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m9ewkyjd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yvjbuz2i,https://wandb.ai/xzy11632/dance-dev/sweeps/83qmid0p,https://wandb.ai/xzy11632/dance-dev/sweeps/wncozogi","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.6525,all_total_runs:150|all_finished_runs:109|step2_total_runs:90|step2_finished_runs:53|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:20|finished_rate:72.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.6525 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 target: FilterGenesPlaceHolder params: {} @@ -2877,7 +3265,43 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7954999804496765,,,,,,, +",0.7954999804496765,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/k94ikq6w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2sifydjq,https://wandb.ai/xzy11632/dance-dev/sweeps/muqarbip,https://wandb.ai/xzy11632/dance-dev/sweeps/p255tp2y","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + 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 +",0.8025,all_total_runs:150|all_finished_runs:96|step2_total_runs:90|step2_finished_runs:59|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:0|finished_rate:64.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + 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 +",0.8025 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: {} @@ -2998,7 +3422,7 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.47200000286102295,all_total_runs:600|all_finished_runs:484|step2_total_runs:540|step2_finished_runs:425|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:80.67%,False,"- type: filter.gene +",0.4720000028610229,all_total_runs:600|all_finished_runs:484|step2_total_runs:540|step2_finished_runs:425|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:80.67%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -3020,7 +3444,61 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4715000092983246,,,,,,, +",0.4715000092983246,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9ulcm4zs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lc65vlu9,https://wandb.ai/xzy11632/dance-dev/sweeps/102sw7wh,https://wandb.ai/xzy11632/dance-dev/sweeps/xg2gclj5","- 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 +",0.4675,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.33%,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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4675 93cb76aa-a84b-4a92-8e6c-66a914e26d4c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7d180py8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yskxemo0,https://wandb.ai/xzy11632/dance-dev/sweeps/0t8yh7s0,https://wandb.ai/xzy11632/dance-dev/sweeps/7s7n24pt","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -3213,7 +3691,61 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5139999985694885,,,,,,, +",0.5139999985694885,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ipf0tqke|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3gh8isu6,https://wandb.ai/xzy11632/dance-dev/sweeps/j5574zjm,https://wandb.ai/xzy11632/dance-dev/sweeps/70m1w1tx","- 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 +",0.5005,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:67|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:65.33%,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: 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 +",0.5005 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: @@ -3366,7 +3898,63 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5866336822509766,,,,,,, +",0.5866336822509766,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qegua12o|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/na4v8g99,https://wandb.ai/xzy11632/dance-dev/sweeps/f9oyzlth,https://wandb.ai/xzy11632/dance-dev/sweeps/2sb4k5ve","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5983910891089109,all_total_runs:150|all_finished_runs:111|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:74.00%,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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5983910891089109 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: @@ -3534,7 +4122,59 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5299860239028931,,,,,,, +",0.5299860239028931,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ayv8er0u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iz7l716f,https://wandb.ai/xzy11632/dance-dev/sweeps/au13vzvx,https://wandb.ai/xzy11632/dance-dev/sweeps/89kft6qm","- 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 +",0.4825662482566248,all_total_runs:150|all_finished_runs:103|step2_total_runs:90|step2_finished_runs:48|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:18|finished_rate:68.67%,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 +",0.4825662482566248 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: {} @@ -3675,25 +4315,61 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + 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 +",0.3901515007019043,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/miscnge3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/23lpopcy,https://wandb.ai/xzy11632/dance-dev/sweeps/b41qby5x,https://wandb.ai/xzy11632/dance-dev/sweeps/tyxa0naz","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 9.242037197483024 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 107 + span: 0.4291184002623445 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4090909090909091,all_total_runs:150|all_finished_runs:112|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + 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: WeightedFeatureSVD + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature label_channel: cell_type -",0.3901515007019043,,,,,,, +",0.4053030303030303 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: {} @@ -3873,7 +4549,64 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5254360437393188,,,,,,, +",0.5254360437393188,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6dd8f769|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rzk9xa5x,https://wandb.ai/xzy11632/dance-dev/sweeps/onruvxox","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 500 + min_cells: 0.06393007765980539 + max_counts: 0.976667396355037 + max_cells: 0.9642353149258592 +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 7772 + span: 0.4864283691327307 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5188953488372093,all_total_runs:130|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:54|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|finished_rate:68.46%,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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5159883720930233 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 @@ -4011,7 +4744,43 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6814595460891724,,,,,,, +",0.6814595460891724,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bti6u79m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nr43xqu5,https://wandb.ai/xzy11632/dance-dev/sweeps/ol7bbm2a,https://wandb.ai/xzy11632/dance-dev/sweeps/hvb1fsf0","- 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 +",0.6617357001972387,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:74|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:20|finished_rate:64.67%,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 +",0.6617357001972387 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: {} @@ -4150,7 +4919,43 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5136476159095764,,,,,,, +",0.5136476159095764,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zzzd70pb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jykr43e9,https://wandb.ai/xzy11632/dance-dev/sweeps/gyjktfxe,https://wandb.ai/xzy11632/dance-dev/sweeps/s06xv871","- 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 +",0.5268817204301075,all_total_runs:150|all_finished_runs:74|step2_total_runs:90|step2_finished_runs:73|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:1|finished_rate:49.33%,True,"- 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 +",0.5268817204301075 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: {} @@ -4289,7 +5094,41 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5026239156723022,,,,,,, +",0.5026239156723022,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d2u4p3ti|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mbb5jpgc,https://wandb.ai/xzy11632/dance-dev/sweeps/1anx19g8,https://wandb.ai/xzy11632/dance-dev/sweeps/igfltnzc","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- 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 +",0.4921282798833819,all_total_runs:150|all_finished_runs:133|step2_total_runs:90|step2_finished_runs:74|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:88.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- 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 +",0.4921282798833819 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: @@ -4788,7 +5627,43 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,, +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/veqwly0p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m5no45rs,https://wandb.ai/xzy11632/dance-dev/sweeps/s3krb2sa,https://wandb.ai/xzy11632/dance-dev/sweeps/3js0dhw4","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",1.0,all_total_runs:150|all_finished_runs:13|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:8.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",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: {} @@ -4901,4 +5776,58 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,, +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uot5zwd7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ic3r42l1,https://wandb.ai/xzy11632/dance-dev/sweeps/6uyjhppn,https://wandb.ai/xzy11632/dance-dev/sweeps/vsm4o34t","- 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 + 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:12|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:8.00%,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: NormalizeTotal + 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 +",1.0 diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index eb3c6ef5..5350b856 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -2991,7 +2991,65 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ feature_channel: SCNFeature label_channel: cell_type ",0.329 -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 +1c739a3e-c3f5-49d5-98e0-73975e751201,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z2v6lwrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zebalczl,https://wandb.ai/xzy11632/dance-dev/sweeps/av6xm0h7,https://wandb.ai/xzy11632/dance-dev/sweeps/lx1ky4rl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - max_counts + - min_cells + min_counts: 226 + min_cells: 0.047663500071270286 + max_counts: 0.9287568186013924 + max_cells: 0.991629947014312 +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 10 + gmean_eps: 1 + n_genes: 1261 + n_cells: 100 + bin_size: 528 + bw_adjust: 1.8575579429886373 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 7844 +- 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 +",0.304500013589859,all_total_runs:510|all_finished_runs:397|step2_total_runs:450|step2_finished_runs:356|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:77.84%,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 + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28450000286102295,"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 target: FilterGenesPlaceHolder - type: normalize target: ScaleFeature @@ -3095,7 +3153,7 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.32850000262260437,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cz5nv4k7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7y02zy49,https://wandb.ai/xzy11632/dance-dev/sweeps/2osv7399,https://wandb.ai/xzy11632/dance-dev/sweeps/zo9ku2lg","- type: filter.gene +",0.3285000026226043,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cz5nv4k7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7y02zy49,https://wandb.ai/xzy11632/dance-dev/sweeps/2osv7399,https://wandb.ai/xzy11632/dance-dev/sweeps/zo9ku2lg","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -3130,7 +3188,59 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ feature_channel: SCNFeature label_channel: cell_type ",0.353 -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 +4ed927e9-c099-49af-b8ce-a2652d069333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lxi0z80g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spk2mp9z,https://wandb.ai/xzy11632/dance-dev/sweeps/xwvu3aat,https://wandb.ai/xzy11632/dance-dev/sweeps/ssfi4ars","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 6.02274143830023 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 8532 +- 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 +",0.24899999797344208,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:329|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:72.35%,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 + 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 +",0.24699999392032623,"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 params: min_val: 4 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index eef41b0d..051e7ff9 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,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 +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 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: @@ -155,7 +155,45 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4645000100135803 +",0.4645000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yjg75eb2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6n6m09lu,https://wandb.ai/xzy11632/dance-dev/sweeps/5o2qlh8l,https://wandb.ai/xzy11632/dance-dev/sweeps/is374gfu","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4595,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|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:20|finished_rate:58.00%,True,"- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4595 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: @@ -306,7 +344,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 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 +",0.481000006198883,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 @@ -327,7 +365,43 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.48100000619888306 +",0.481000006198883,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kxkmzv41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rwswn0ja,https://wandb.ai/xzy11632/dance-dev/sweeps/cayifo99,https://wandb.ai/xzy11632/dance-dev/sweeps/y40of4uy","- 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 +",0.496,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:58.00%,True,"- 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 +",0.496 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: {} @@ -488,7 +562,46 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3941039443016052 +",0.3941039443016052,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lydev3fk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q4cn3mtb,https://wandb.ai/xzy11632/dance-dev/sweeps/3rx39oxw,https://wandb.ai/xzy11632/dance-dev/sweeps/xhgs2c15","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 99 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3840186190845617,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:11|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 +",0.3770364623739333 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: {} @@ -673,7 +786,51 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4319852888584137 +",0.4319852888584137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2w7qh6m9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/orery7et,https://wandb.ai/xzy11632/dance-dev/sweeps/w60mlkdg,https://wandb.ai/xzy11632/dance-dev/sweeps/gmdyzho8","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 3 + gmean_eps: 1 + n_genes: 2584 + n_cells: null + bin_size: 380 + bw_adjust: 4.122403001571971 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 9393 + n_bins: 15 + flavor: cell_ranger +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4522058823529412,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:75|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:65.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- 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 +",0.44485294117647056 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: @@ -863,7 +1020,43 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5304999947547913 +",0.5304999947547913,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jocmyjw4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zo3i9mg9,https://wandb.ai/xzy11632/dance-dev/sweeps/cx6569af,https://wandb.ai/xzy11632/dance-dev/sweeps/o8jyq6rr","- 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 +",0.506,all_total_runs:150|all_finished_runs:95|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.33%,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 +",0.506 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: @@ -1024,4 +1217,42 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.580926775932312 +",0.580926775932312,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/f0izdcdt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cp84ljtg,https://wandb.ai/xzy11632/dance-dev/sweeps/6tb70g8g,https://wandb.ai/xzy11632/dance-dev/sweeps/oa5ayktp","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5601074546675622,all_total_runs:150|all_finished_runs:76|step2_total_runs:90|step2_finished_runs:75|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:0|finished_rate:50.67%,True,"- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5601074546675622 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index 8343c080..74bb77a6 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,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 +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 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: {} @@ -137,7 +137,45 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2770000100135803 +",0.2770000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l0ayhmzb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tus9enye,https://wandb.ai/xzy11632/dance-dev/sweeps/72p9xtzb,https://wandb.ai/xzy11632/dance-dev/sweeps/6djo4d5d","- 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 +",0.2725,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.67%,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 +",0.2725 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: {} @@ -278,7 +316,43 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.578499972820282 +",0.578499972820282,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q6fawkyp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ygkup2y2,https://wandb.ai/xzy11632/dance-dev/sweeps/2fu1tsj8,https://wandb.ai/xzy11632/dance-dev/sweeps/fu62rjas","- 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 +",0.5945,all_total_runs:150|all_finished_runs:66|step2_total_runs:90|step2_finished_runs:64|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:44.00%,True,"- 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 +",0.5945 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: @@ -467,7 +541,43 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5914999842643738 +",0.5914999842643738,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wm8pq6ig|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/csv3mlbn,https://wandb.ai/xzy11632/dance-dev/sweeps/885assxx,https://wandb.ai/xzy11632/dance-dev/sweeps/fgeio7m9","- 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 +",0.5705,all_total_runs:150|all_finished_runs:68|step2_total_runs:90|step2_finished_runs:65|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:0|finished_rate:45.33%,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 +",0.5705 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: @@ -668,7 +778,59 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7124999761581421 +",0.7124999761581421,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bwld9xlk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6sopj3bj,https://wandb.ai/xzy11632/dance-dev/sweeps/6xqavd24,https://wandb.ai/xzy11632/dance-dev/sweeps/528j1po3","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6975,all_total_runs:150|all_finished_runs:93|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:62.00%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6975 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 @@ -831,7 +993,45 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2994999885559082 +",0.2994999885559082,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jnktyajr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5eigq4mq,https://wandb.ai/xzy11632/dance-dev/sweeps/b5lw76u0,https://wandb.ai/xzy11632/dance-dev/sweeps/bfchr0lr","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2625,all_total_runs:151|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:67|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:21|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:58.94%,True,"- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2625 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: {} @@ -979,7 +1179,61 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22100000083446503 +",0.221000000834465,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ubj3byxy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vj3djhsu,https://wandb.ai/xzy11632/dance-dev/sweeps/sfz5a11n,https://wandb.ai/xzy11632/dance-dev/sweeps/7k9birau","- 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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.229,all_total_runs:150|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:61|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:0|finished_rate:66.00%,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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.229 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: @@ -1113,7 +1367,7 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.2764999866485595,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 @@ -1135,7 +1389,43 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.27549999952316284 +",0.2754999995231628,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mb2cyn4c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uha7jepq,https://wandb.ai/xzy11632/dance-dev/sweeps/nq1sd8jx,https://wandb.ai/xzy11632/dance-dev/sweeps/fhvkz6ju","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.2735,all_total_runs:150|all_finished_runs:122|step2_total_runs:90|step2_finished_runs:64|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:81.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.2735 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: @@ -1230,7 +1520,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.43849998712539673,all_total_runs: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 +",0.4384999871253967,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: @@ -1264,7 +1554,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",0.4384999871253967,"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 @@ -1308,8 +1598,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.4440000057220459,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xl2nwacs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qhr4km04,https://wandb.ai/xzy11632/dance-dev/sweeps/7vqnpicq,https://wandb.ai/xzy11632/dance-dev/sweeps/t8ovlamf","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1317,9 +1606,46 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.451,all_total_runs:150|all_finished_runs:76|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:3|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:50.67%,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 +",0.451 +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: {} +- 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 @@ -1445,7 +1771,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2370000034570694 +",0.2370000034570694,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/abphixpv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/46zj4ous,https://wandb.ai/xzy11632/dance-dev/sweeps/ql3ox0ee,https://wandb.ai/xzy11632/dance-dev/sweeps/oaiwrhfs","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - max_cells + - min_counts + min_counts: 132 + min_cells: 0.045921635815448794 + max_counts: 0.9851254486346562 + max_cells: 0.9786632198872888 +- type: normalize + target: Log1P + params: + base: 4.927714595143703 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.249,all_total_runs:150|all_finished_runs:116|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.247 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: @@ -1603,7 +1973,55 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2485000044107437 +",0.2485000044107437,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s6rn5ps8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mg255re6,https://wandb.ai/xzy11632/dance-dev/sweeps/45j03ilz,https://wandb.ai/xzy11632/dance-dev/sweeps/701eayg8","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 263 + min_cells: 0.023032742875690015 + max_counts: 0.9761189040538616 + max_cells: 0.9659085418084716 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 4654 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2395,all_total_runs:150|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:66.00%,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 +",0.2355 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: @@ -1795,7 +2213,63 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8750647902488708 +",0.8750647902488708,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/onc0rdcc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fle277i2,https://wandb.ai/xzy11632/dance-dev/sweeps/v1vpz6gs,https://wandb.ai/xzy11632/dance-dev/sweeps/jo5s8o6z","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8657335406946605,all_total_runs:150|all_finished_runs:105|step2_total_runs:90|step2_finished_runs:65|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:2|finished_rate:70.00%,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: 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 +",0.8657335406946605 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: @@ -1973,7 +2447,43 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5 +",0.5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ulj3xxmi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/22ifljz1,https://wandb.ai/xzy11632/dance-dev/sweeps/jqzc266f","- type: filter.gene + target: FilterGenesPlaceHolder + 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 +",0.16666666666666666,all_total_runs:130|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|finished_rate:76.15%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + 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 +",0.16666666666666666 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: {} @@ -2144,7 +2654,43 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3672456443309784 +",0.3672456443309784,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qoaxxv3r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/scykgn20,https://wandb.ai/xzy11632/dance-dev/sweeps/n8btsi9f,https://wandb.ai/xzy11632/dance-dev/sweeps/z5tkx4n0","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.34491315136476425,all_total_runs:150|all_finished_runs:97|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:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.34491315136476425 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 @@ -2281,7 +2827,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.332479178905487,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 @@ -2303,7 +2849,59 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.33247917890548706 +",0.332479178905487,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xx97kth1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2ij5ijlv,https://wandb.ai/xzy11632/dance-dev/sweeps/euzr7ujg,https://wandb.ai/xzy11632/dance-dev/sweeps/dlrnxq72","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3042921204356182,all_total_runs:150|all_finished_runs:131|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:16|finished_rate:87.33%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3042921204356182 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 @@ -2460,7 +3058,62 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3620437979698181 +",0.3620437979698181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x7o546sk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xoxj0wu3,https://wandb.ai/xzy11632/dance-dev/sweeps/fp7afgvx,https://wandb.ai/xzy11632/dance-dev/sweeps/oo1am6pb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_counts + - min_cells + - max_cells + min_counts: 22 + min_cells: 0.05741156858919219 + max_counts: 0.91367665193381 + max_cells: 0.9829848013655572 +- type: normalize + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.01 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.37664233576642336,all_total_runs:150|all_finished_runs:96|step2_total_runs:90|step2_finished_runs:74|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:64.00%,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: 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 +",0.3759124087591241 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: @@ -2599,7 +3252,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.2804999947547912,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 @@ -2620,7 +3273,41 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.28049999475479126 +",0.2804999947547912,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rfy7muvr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0pdtdvge,https://wandb.ai/xzy11632/dance-dev/sweeps/7qoqqm29,https://wandb.ai/xzy11632/dance-dev/sweeps/z3tsakmq","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- 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 +",0.2915,all_total_runs:150|all_finished_runs:115|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:0|finished_rate:76.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- 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 +",0.2915 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: @@ -2795,7 +3482,61 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4284999966621399 +",0.4284999966621399,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2xlnu6s7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ged3jw2n,https://wandb.ai/xzy11632/dance-dev/sweeps/au2t88g0,https://wandb.ai/xzy11632/dance-dev/sweeps/z6zqb0ij","- 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 +",0.4125,all_total_runs:150|all_finished_runs:121|step2_total_runs:90|step2_finished_runs:68|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: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: 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 +",0.4125 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: @@ -2972,7 +3713,43 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.244499996304512 +",0.244499996304512,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wcb9vpq4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4bgd5dkd,https://wandb.ai/xzy11632/dance-dev/sweeps/ap5p1ejx,https://wandb.ai/xzy11632/dance-dev/sweeps/8vpkidbc","- type: filter.gene + target: FilterGenesPlaceHolder + 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 +",0.2465,all_total_runs:150|all_finished_runs:85|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:56.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + 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 +",0.2465 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 @@ -3026,31 +3803,32 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4589743614196777,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1het6p1z,https://wandb.ai/xzy11632/dance-dev/sweeps/7z429hba,https://wandb.ai/xzy11632/dance-dev/sweeps/81ikkh2i","- type: filter.gene - target: FilterGenesScanpyOrder +",0.4589743614196777,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r6m7zdo1,https://wandb.ai/xzy11632/dance-dev/sweeps/rvpunccy,https://wandb.ai/xzy11632/dance-dev/sweeps/50vokx7l","- 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 + min_val: 4 + max_val: 98 + mode: cv - type: normalize target: Log1P - params: {} + params: + base: 1.0842803516615516 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: - n_top_genes: 3000 + min_disp: 0.06377687896770325 + max_disp: 41.939375689351905 + min_mean: 0.0025444527190867693 + max_mean: 17.950279292657427 + n_bins: 21 + flavor: seurat - type: feature.cell + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + n_components: 664 + feat_norm_mode: standardize - type: graph.cell target: CellFeatureGraph params: @@ -3060,7 +3838,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5,all_total_runs:182|all_finished_runs:134|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:73.63%,False,"- type: filter.gene +",0.5051282048225403,all_total_runs:210|all_finished_runs:161|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:1|finished_rate:76.67%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -3156,7 +3934,43 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.488034188747406 +",0.488034188747406,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ebnsel1o|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hzm9cmea,https://wandb.ai/xzy11632/dance-dev/sweeps/im8zzzed,https://wandb.ai/xzy11632/dance-dev/sweeps/0v22gcsp","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.488034188034188,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.488034188034188 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: @@ -3351,4 +4165,60 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8750647902488708 +",0.8750647902488708,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n2s4t1f7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h78trrkg,https://wandb.ai/xzy11632/dance-dev/sweeps/5i7grztx,https://wandb.ai/xzy11632/dance-dev/sweeps/k7zpw3jk","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8657335406946605,all_total_runs:150|all_finished_runs:130|step2_total_runs:90|step2_finished_runs:70|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:86.67%,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: 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 +",0.8657335406946605 diff --git a/examples/atlas/sweep_results/Lung_ans.csv b/examples/atlas/sweep_results/Lung_ans.csv index bc991b72..62397df1 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,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 +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,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 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: {} @@ -103,7 +103,93 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4790000021457672,,,,,,, +",0.4790000021457672,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/31p1jl13|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jv0qygxw,https://wandb.ai/xzy11632/dance-dev/sweeps/3k1x4ael,https://wandb.ai/xzy11632/dance-dev/sweeps/0drfyazl","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.4790000021457672,all_total_runs:210|all_finished_runs:173|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:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:82.38%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.4790000021457672,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/umip8col|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8rbu9tz5,https://wandb.ai/xzy11632/dance-dev/sweeps/s2x3klie,https://wandb.ai/xzy11632/dance-dev/sweeps/xq1tygx9","- 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 +",0.486,all_total_runs:150|all_finished_runs:111|step2_total_runs:90|step2_finished_runs:56|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:20|finished_rate:74.00%,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 +",0.486 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: {} @@ -195,7 +281,91 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.29350000619888306,,,,,,, +",0.293500006198883,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/u66vt0zy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0e4fl2ig,https://wandb.ai/xzy11632/dance-dev/sweeps/26t9dcb3,https://wandb.ai/xzy11632/dance-dev/sweeps/6er1nf7y","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.30799999833106995,all_total_runs:225|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:35|step3_0_finished_runs:26|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:80.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.30799999833106995,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sa0zrzyh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ddp05p3y,https://wandb.ai/xzy11632/dance-dev/sweeps/4n5kvy4f,https://wandb.ai/xzy11632/dance-dev/sweeps/4nw3qvss","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.306,all_total_runs:150|all_finished_runs:106|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:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:70.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.3055 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: @@ -290,7 +460,7 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.1739999949932098,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: @@ -321,7 +491,113 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.17299999296665192,,,,,,, +",0.1729999929666519,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cztlwh8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xnekcm5a,https://wandb.ai/xzy11632/dance-dev/sweeps/92k8gjvn,https://wandb.ai/xzy11632/dance-dev/sweeps/ebwccpe0","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.1770000010728836,all_total_runs:211|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:21|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.41%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.1770000010728836,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ya45i0hj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/txt2fqri,https://wandb.ai/xzy11632/dance-dev/sweeps/eartlz9g,https://wandb.ai/xzy11632/dance-dev/sweeps/4q91ab4x","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_cells + - max_counts + min_counts: 154 + min_cells: 0.007759793169660634 + max_counts: 0.9471824565588984 + max_cells: 0.977680030415662 +- type: normalize + target: Log1P + params: + base: 5.73752690176084 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 7401 + span: 0.5600576148418653 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.168,all_total_runs:150|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:66.00%,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: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.167 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 @@ -412,26 +688,640 @@ 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: 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 +",0.3650000095367432,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gvzf9hvu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xn6gkyue,https://wandb.ai/xzy11632/dance-dev/sweeps/wohspkph,https://wandb.ai/xzy11632/dance-dev/sweeps/0es2sjqj","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 99 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3133 + n_bins: 25 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 327 + 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 +",0.35850000381469727,all_total_runs:210|all_finished_runs:168|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:80.00%,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: 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 +",0.3569999933242798,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fk9bgw6i|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/u9bvksor,https://wandb.ai/xzy11632/dance-dev/sweeps/y6np5hym,https://wandb.ai/xzy11632/dance-dev/sweeps/a2uwktag","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3405 + span: 0.1243084522697208 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.343,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:56|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.34 +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 + 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: 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 + 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",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: + - 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: 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 +",0.6570000052452087,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: + - 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: 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 +",0.6570000052452087,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/up1qmjf2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xlh552ry,https://wandb.ai/xzy11632/dance-dev/sweeps/w64bnq3j,https://wandb.ai/xzy11632/dance-dev/sweeps/t7nbjgz0","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 95 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: -1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9736 + span: 0.25241821131495124 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 891 + 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 +",0.6175000071525574,all_total_runs:220|all_finished_runs:184|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:40|step3_1_finished_runs:35|step3_2_total_runs:10|step3_2_finished_runs:10|finished_rate:83.64%,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 +",0.6169999837875366,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3d1v8h2t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/c1w0za8n,https://wandb.ai/xzy11632/dance-dev/sweeps/6bzf7x2w,https://wandb.ai/xzy11632/dance-dev/sweeps/28wpkbwl","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6425,all_total_runs:150|all_finished_runs:109|step2_total_runs:90|step2_finished_runs:54|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:72.67%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6425 +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 + params: + min_val: 6 + max_val: 99 + mode: var +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 1122 +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 476 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",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: NormalizePlaceHolder + 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 +",0.2834999859333038,"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: 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 +",0.3019999861717224,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: 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 +",0.3019999861717224,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bhc72mqi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgh7gu1,https://wandb.ai/xzy11632/dance-dev/sweeps/oyrg3g50,https://wandb.ai/xzy11632/dance-dev/sweeps/yazhk2wh","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 8 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 2.3999362085689735 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2774 + span: 0.14012171784395563 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 143 + 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 +",0.30799999833106995,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: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.304500013589859,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wyv759w9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/shkhipgt,https://wandb.ai/xzy11632/dance-dev/sweeps/fkgincu3,https://wandb.ai/xzy11632/dance-dev/sweeps/2ai1maaq","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_cells + - max_counts + min_counts: 268 + min_cells: 0.09282122792071212 + max_counts: 0.9111506923231292 + max_cells: 0.9791784429304778 +- type: normalize + target: NormalizeTotal + params: + target_sum: null + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2846 + span: 0.4736431293720086 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.289,all_total_runs:150|all_finished_runs:112|step2_total_runs:90|step2_finished_runs:53|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: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: NormalizeTotal + 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 +",0.2835 +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: 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,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: 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 + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3650000095367432,,,,,,, -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 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-",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 +",0.703000009059906,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: @@ -480,22 +1370,22 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ params: processes_num: 8 - 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: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.703000009059906,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0nyymfuu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2pkvz50m,https://wandb.ai/xzy11632/dance-dev/sweeps/f08kfu41,https://wandb.ai/xzy11632/dance-dev/sweeps/hqrfqchi","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -508,25 +1398,28 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"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: 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 -",0.6570000052452087,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 +",0.6800000071525574,all_total_runs:210|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:70.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -539,72 +1432,67 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"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: 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 -",0.6570000052452087,,,,,,, -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 - params: - min_val: 6 - max_val: 99 - mode: var +",0.6800000071525574,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9p8xgwaa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mhdq21lf,https://wandb.ai/xzy11632/dance-dev/sweeps/n17pymb1,https://wandb.ai/xzy11632/dance-dev/sweeps/kpo3scgj","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: NormalizePlaceHolder + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: FilterGenesRegression params: - method: seurat3 - num_genes: 1122 + num_genes: 3000 - type: feature.cell - target: GaussRandProjFeature - params: - out: feature.cell - log_level: INFO - n_components: 476 + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature label_channel: cell_type -",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 +",0.6965,all_total_runs:151|all_finished_runs:75|step2_total_runs:91|step2_finished_runs:74|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:1|finished_rate:49.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizePlaceHolder - params: {} + 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: GaussRandProjFeature + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature 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 +",0.6965 +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: @@ -617,12 +1505,13 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P - params: {} + target: ScTransform + 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 @@ -635,7 +1524,7 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",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: @@ -648,68 +1537,26 @@ 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feature.cell - params: - out: feature.cell - log_level: INFO - target: GaussRandProjFeature -- type: misc - target: SetConfig + target: ScTransform 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 - params: {} -- type: normalize - target: NormalizePlaceHolder - 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 - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - 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 +",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: @@ -722,11 +1569,10 @@ 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: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -741,7 +1587,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",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: @@ -754,11 +1600,10 @@ 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: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -773,8 +1618,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.6759999990463257,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/be4nwgbf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s51pse9z,https://wandb.ai/xzy11632/dance-dev/sweeps/x2q55wwy,https://wandb.ai/xzy11632/dance-dev/sweeps/1358q46s","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -787,11 +1631,10 @@ 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: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -800,13 +1643,16 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc 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 -",0.6570000052452087,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 +",0.6744999885559082,all_total_runs:210|all_finished_runs:177|step2_total_runs:150|step2_finished_runs:120|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:84.29%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -819,11 +1665,10 @@ 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: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell @@ -832,13 +1677,16 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc 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 -",0.6570000052452087,"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 +",0.6744999885559082,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i6274vfx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7dcfwbih,https://wandb.ai/xzy11632/dance-dev/sweeps/teou6ic8,https://wandb.ai/xzy11632/dance-dev/sweeps/b0q7l3ro","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -854,22 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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: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.147499993443489,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9c0qxaop|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cu25ez82,https://wandb.ai/xzy11632/dance-dev/sweeps/0gnr41ck,https://wandb.ai/xzy11632/dance-dev/sweeps/91zgl42j","- 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 -",0.14900000393390656,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:120|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:16|finished_rate:82.38%,False,"- type: filter.gene +",0.1545,all_total_runs:150|all_finished_runs:92|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:19|finished_rate:61.33%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: FilterGenesRegression + target: ScTransform params: - num_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 -",0.14749999344348907 +",0.1545 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 target: FilterGenesScanpyOrder params: @@ -1215,7 +2091,61 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc params: config_dict: label_channel: cell_type -",0.5394999980926514 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filter.gene target: FilterGenesScanpyOrder params: order: @@ -1501,7 +2431,59 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc params: config_dict: label_channel: cell_type -",0.16908212006092072 +",0.1690821200609207,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/llbot2wd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7rwgizyg,https://wandb.ai/xzy11632/dance-dev/sweeps/f72tj8le,https://wandb.ai/xzy11632/dance-dev/sweeps/teurxxdt","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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+",0.1299076229333877,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: @@ -1664,7 +2646,54 @@ e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.12990762293338776 +",0.1299076229333877,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0p7su6u6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wglkhxfr,https://wandb.ai/xzy11632/dance-dev/sweeps/7wvua5jk,https://wandb.ai/xzy11632/dance-dev/sweeps/idsyyyng","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 99 + mode: sum +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: -1 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.12009237875288684,all_total_runs:149|all_finished_runs:122|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:19|step3_2_finished_runs:19|finished_rate:81.88%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.11431870669745958 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: {} @@ -1841,7 +2870,61 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8185998797416687 +",0.8185998797416687,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4hf1e1zt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/17uqbg1j,https://wandb.ai/xzy11632/dance-dev/sweeps/w8z7bp2m,https://wandb.ai/xzy11632/dance-dev/sweeps/609y6mnf","- 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 +",0.8252427184466019,all_total_runs:150|all_finished_runs:75|step2_total_runs:90|step2_finished_runs:73|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:1|finished_rate:50.00%,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: 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 +",0.8252427184466019 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 - type: normalize @@ -1927,7 +3010,7 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.4345323741436004,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: @@ -1958,7 +3041,41 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 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+",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: @@ -1992,41 +3109,45 @@ e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.4050359725952149,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nzqxkwr2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dxp2byqu,https://wandb.ai/xzy11632/dance-dev/sweeps/lkiksixl,https://wandb.ai/xzy11632/dance-dev/sweeps/txxkqm04","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4014388489208633,all_total_runs:150|all_finished_runs:117|step2_total_runs:90|step2_finished_runs:75|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:78.00%,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: 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 -",0.4050359725952149 +",0.4014388489208633 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: @@ -2201,7 +3322,42 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc params: config_dict: label_channel: cell_type -",0.3348017632961273 +",0.3348017632961273,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ugznmank|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zv9lzme,https://wandb.ai/xzy11632/dance-dev/sweeps/8ptyl7c3","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 2 + max_val: 98 + mode: rv +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.36123348017621143,all_total_runs:130|all_finished_runs:105|step2_total_runs:90|step2_finished_runs:67|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|finished_rate:80.77%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + 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 +",0.3303964757709251 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: @@ -2286,7 +3442,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc 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 +",0.2425000071525573,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: @@ -2367,7 +3523,63 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc params: config_dict: label_channel: cell_type -",0.2515000104904175 +",0.2515000104904175,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvhvfd0e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r8kvjad3,https://wandb.ai/xzy11632/dance-dev/sweeps/2gztfme0,https://wandb.ai/xzy11632/dance-dev/sweeps/moka4ir1","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.265,all_total_runs:149|all_finished_runs:113|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.84%,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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.265 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: {} @@ -2513,7 +3725,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc 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 +",0.2234999984502792,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: @@ -2547,7 +3759,41 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/danc params: config_dict: label_channel: cell_type -",0.2214999943971634 +",0.2214999943971634,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8wu00rrs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emkgdv7m,https://wandb.ai/xzy11632/dance-dev/sweeps/yz3ptmyb,https://wandb.ai/xzy11632/dance-dev/sweeps/8zpy4daf","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + 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 +",0.2355,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:64|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:20|finished_rate:78.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + 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 +",0.2355 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: {} @@ -2621,7 +3867,7 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.1724999994039535,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: @@ -2652,7 +3898,7 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.1724999994039535,"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: @@ -2720,7 +3966,43 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.1815000027418137 +",0.1815000027418137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qpyso58s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n9xhwciz,https://wandb.ai/xzy11632/dance-dev/sweeps/zb5fdqlj,https://wandb.ai/xzy11632/dance-dev/sweeps/gdl97dnb","- 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 +",0.1705,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: 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 +",0.1705 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: {} @@ -2885,7 +4167,63 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6483516693115234 +",0.6483516693115234,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s1tkaoyx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/48ud2zju,https://wandb.ai/xzy11632/dance-dev/sweeps/hvco0aoq,https://wandb.ai/xzy11632/dance-dev/sweeps/hab6rxge","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.65,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|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:64.67%,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: 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 +",0.65 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: @@ -3044,4 +4382,55 @@ d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5454545617103577 +",0.5454545617103577,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tmb6nbhs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xwzuin,https://wandb.ai/xzy11632/dance-dev/sweeps/3xl8m5ai,https://wandb.ai/xzy11632/dance-dev/sweeps/a6q7uf5a","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 7 + max_val: 99 + mode: var +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000000 + max_fraction: 0.05 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9586 + span: 0.4808965576925112 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4393939393939394,all_total_runs:150|all_finished_runs:129|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:86.00%,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: 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 +",0.42424242424242425 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv index ebcfe263..88c41cf2 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,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 +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,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 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: @@ -37,7 +37,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.402999997138977,all_total_runs:210|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:99|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:20|step3_1_finished_runs:10|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.00%,False,"- type: filter.gene +",0.40299999713897705,all_total_runs:210|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:99|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:20|step3_1_finished_runs:10|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -177,7 +177,49 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4149999916553498 +",0.4149999916553498,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gpj4i6jb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pqpwvbcl,https://wandb.ai/xzy11632/dance-dev/sweeps/hc0zyrsm,https://wandb.ai/xzy11632/dance-dev/sweeps/oqeg7gt6","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 95 + mode: cv +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3006 + span: 0.3081446146760134 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4035,all_total_runs:150|all_finished_runs:91|step2_total_runs:90|step2_finished_runs:57|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + 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 +",0.402 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: @@ -306,8 +348,60 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mjxq9wbz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mb64lqt6,https://wandb.ai/xzy11632/dance-dev/sweeps/gaeji3wq,https://wandb.ai/xzy11632/dance-dev/sweeps/jdxyftrd","- 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: 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:33|step2_total_runs:90|step2_finished_runs:16|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:22.00%,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: 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 -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 +f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pncdq2k1,https://wandb.ai/xzy11632/dance-dev/sweeps/z1tnppgo,https://wandb.ai/xzy11632/dance-dev/sweeps/s4ka2u4s","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -332,7 +426,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.2599999904632568,all_total_runs:210|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:57.62%,True,"- type: filter.gene +",0.25999999046325684,all_total_runs:210|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:62.86%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -357,7 +451,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.2599999904632568,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q7pjlbgz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hn65sj20,https://wandb.ai/xzy11632/dance-dev/sweeps/0aloe2j4,https://wandb.ai/xzy11632/dance-dev/sweeps/2fp77b7l","- type: filter.gene +",0.25999999046325684,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q7pjlbgz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hn65sj20,https://wandb.ai/xzy11632/dance-dev/sweeps/0aloe2j4,https://wandb.ai/xzy11632/dance-dev/sweeps/2fp77b7l","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -422,7 +516,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ 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 +",0.2585000097751617,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 @@ -443,7 +537,54 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.25850000977516174 +",0.2585000097751617,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/szccibek|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ncv8d9cl,https://wandb.ai/xzy11632/dance-dev/sweeps/9c2q16tc,https://wandb.ai/xzy11632/dance-dev/sweeps/t3jzvjsd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 290 + min_cells: 0.09769546522542771 + max_counts: 0.9875755318917276 + max_cells: 0.9902514987938889 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.3 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 7878 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2475,all_total_runs:150|all_finished_runs:90|step2_total_runs:90|step2_finished_runs:56|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:60.00%,False,"- 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 +",0.2375 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: @@ -604,7 +745,61 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.328000009059906 +",0.328000009059906,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ertfvv8w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lo5r447c,https://wandb.ai/xzy11632/dance-dev/sweeps/1hcwus9e,https://wandb.ai/xzy11632/dance-dev/sweeps/8tzyznbb","- 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: 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 +",0.3160000145435333,all_total_runs:210|all_finished_runs:104|step2_total_runs:150|step2_finished_runs:104|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:49.52%,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: ScaleFeature + 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 +",0.3160000145435333 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: @@ -735,6 +930,62 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7oluz6cx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0fcdpmmt,https://wandb.ai/xzy11632/dance-dev/sweeps/ov9j4tv9,https://wandb.ai/xzy11632/dance-dev/sweeps/uj2tgfav","- 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 + 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:25|step2_total_runs:90|step2_finished_runs:11|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:16.67%,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: 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 ",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 @@ -874,7 +1125,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ 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 +",0.2585000097751617,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: @@ -905,7 +1156,42 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.25850000977516174 +",0.2585000097751617,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b7bg7l7f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i15ygwm0,https://wandb.ai/xzy11632/dance-dev/sweeps/sk1wej2m,https://wandb.ai/xzy11632/dance-dev/sweeps/kyoy45e1","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.7 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.26,all_total_runs:150|all_finished_runs:79|step2_total_runs:90|step2_finished_runs:57|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:20|finished_rate:52.67%,True,"- 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 +",0.252 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: {} @@ -931,7 +1217,7 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3896713554859161,all_total_runs:210|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:61.43%,False,"- type: filter.gene +",0.38967135548591614,all_total_runs:210|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:61.43%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -956,7 +1242,7 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3896713554859161,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4y7bjr73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2bftkn2f,https://wandb.ai/xzy11632/dance-dev/sweeps/6wksp40t,https://wandb.ai/xzy11632/dance-dev/sweeps/b0igv55h","- type: filter.gene +",0.38967135548591614,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4y7bjr73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2bftkn2f,https://wandb.ai/xzy11632/dance-dev/sweeps/6wksp40t,https://wandb.ai/xzy11632/dance-dev/sweeps/b0igv55h","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1018,7 +1304,7 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.3920187652111053,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 @@ -1038,7 +1324,61 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.39201876521110535 +",0.3920187652111053,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y7k7yxnm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eokqtgdx,https://wandb.ai/xzy11632/dance-dev/sweeps/a6sdhtgr,https://wandb.ai/xzy11632/dance-dev/sweeps/1qwufafk","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.392018779342723,all_total_runs:150|all_finished_runs:119|step2_total_runs:90|step2_finished_runs:64|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:20|finished_rate:79.33%,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: NormalizeTotal + 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 +",0.392018779342723 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: @@ -1217,7 +1557,59 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6502732038497925 +",0.6502732038497925,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x1qjt8yx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ke45liig,https://wandb.ai/xzy11632/dance-dev/sweeps/2vx40yev,https://wandb.ai/xzy11632/dance-dev/sweeps/jficu6da","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7231329690346083,all_total_runs:150|all_finished_runs:115|step2_total_runs:90|step2_finished_runs:57|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:76.67%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7231329690346083 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: {} @@ -1339,42 +1731,98 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ - type: filter.gene target: FilterGenesRegression params: - num_genes: 3000 + 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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c6qilb4p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2j09x0xu,https://wandb.ai/xzy11632/dance-dev/sweeps/ing4i47q,https://wandb.ai/xzy11632/dance-dev/sweeps/wkox37xs","- 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 + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature 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: {} +",0.9204545454545454,all_total_runs:150|all_finished_runs:77|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:7|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:51.33%,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: 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 - log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature label_channel: cell_type -",0.931818187236786 +",0.9204545454545454 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: @@ -1507,8 +1955,62 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p1kvq9l5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mj8qxe4y,https://wandb.ai/xzy11632/dance-dev/sweeps/o382i5n0,https://wandb.ai/xzy11632/dance-dev/sweeps/tl4iv383","- 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 + 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:27|step2_total_runs:90|step2_finished_runs:15|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:18.00%,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 + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type ",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 +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/00hfamxx,https://wandb.ai/xzy11632/dance-dev/sweeps/2l74ctr7","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1533,7 +2035,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.4769999980926513,all_total_runs:193|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:66.32%,False,"- type: filter.gene +",0.47699999809265137,all_total_runs:210|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:59.52%,True,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1558,7 +2060,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.4769999980926513,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g85syyzg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cdggwljw,https://wandb.ai/xzy11632/dance-dev/sweeps/natn1hgy,https://wandb.ai/xzy11632/dance-dev/sweeps/b0eefc5r","- type: filter.gene +",0.47699999809265137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g85syyzg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cdggwljw,https://wandb.ai/xzy11632/dance-dev/sweeps/natn1hgy,https://wandb.ai/xzy11632/dance-dev/sweeps/b0eefc5r","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1652,8 +2154,45 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ 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 +",0.4589999914169311,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3ch2l5s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pgj5t8lc,https://wandb.ai/xzy11632/dance-dev/sweeps/tmjfipc9,https://wandb.ai/xzy11632/dance-dev/sweeps/zudbm7ur","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 8585 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4775,all_total_runs:150|all_finished_runs:100|step2_total_runs:90|step2_finished_runs:54|step3_0_total_runs:20|step3_0_finished_runs:10|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:66.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- 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 +",0.4745 +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/1g4wscpu","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1678,7 +2217,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.2739999890327453,all_total_runs:210|all_finished_runs:147|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:2|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:70.00%,False,"- type: filter.gene +",0.27399998903274536,all_total_runs:210|all_finished_runs:152|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:2|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:72.38%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1703,7 +2242,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.2739999890327453,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tnlms8f7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/37b6ag4h,https://wandb.ai/xzy11632/dance-dev/sweeps/drrj9j62,https://wandb.ai/xzy11632/dance-dev/sweeps/yrm085kp","- type: filter.gene +",0.27399998903274536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tnlms8f7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/37b6ag4h,https://wandb.ai/xzy11632/dance-dev/sweeps/drrj9j62,https://wandb.ai/xzy11632/dance-dev/sweeps/yrm085kp","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: ScaleFeature @@ -1772,7 +2311,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ 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 +",0.2585000097751617,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 @@ -1793,7 +2332,60 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.25850000977516174 +",0.2585000097751617,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d1q0greq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxfkabxr,https://wandb.ai/xzy11632/dance-dev/sweeps/br7tiz9e,https://wandb.ai/xzy11632/dance-dev/sweeps/rarxceli","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_cells + - max_counts + min_counts: 29 + min_cells: 0.055457586675047424 + max_counts: 0.9981740240410047 + max_cells: 0.960870897330556 +- 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 +",0.261,all_total_runs:150|all_finished_runs:91|step2_total_runs:90|step2_finished_runs:56|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:0|finished_rate:60.67%,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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2605 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: @@ -1937,7 +2529,7 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",0.4135000109672546,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: @@ -1968,7 +2560,55 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.41350001096725464 +",0.4135000109672546,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qmyvmdq1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/repllvxm,https://wandb.ai/xzy11632/dance-dev/sweeps/1u1hsnc6,https://wandb.ai/xzy11632/dance-dev/sweeps/0romoagi","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - min_counts + - max_cells + min_counts: 142 + min_cells: 0.09808550094261272 + max_counts: 0.9702330969318216 + max_cells: 0.9570367158864392 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 5791 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4135,all_total_runs:150|all_finished_runs:112|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- 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 +",0.4095 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: @@ -2132,7 +2772,43 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4420432150363922 +",0.4420432150363922,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0tpkjxr3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dxjir4oa,https://wandb.ai/xzy11632/dance-dev/sweeps/ozctmfyc,https://wandb.ai/xzy11632/dance-dev/sweeps/ie0fgnbo","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.35952848722986247,all_total_runs:150|all_finished_runs:115|step2_total_runs:90|step2_finished_runs:60|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:20|finished_rate:76.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.35952848722986247 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: {} @@ -2283,4 +2959,52 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6786366105079651 +",0.6786366105079651,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/09vtppjh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/l5fovbpb,https://wandb.ai/xzy11632/dance-dev/sweeps/utu1c0zt,https://wandb.ai/xzy11632/dance-dev/sweeps/689d3b91","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_counts + - max_cells + min_counts: 327 + min_cells: 0.08986191604520012 + max_counts: 0.9467699188647029 + max_cells: 0.9545870083635444 +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 571 + top: true + mode: sum +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6518563603164942,all_total_runs:150|all_finished_runs:116|step2_total_runs:90|step2_finished_runs:56|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:77.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.6378575776019476