From 578112393462b20514fd000d034f83262af9783f Mon Sep 17 00:00:00 2001 From: xzy Date: Sun, 12 Jan 2025 17:36:48 +0800 Subject: [PATCH] update ans --- examples/atlas/sweep_results/Blood_ans.csv | 1107 ++++++++++-- examples/atlas/sweep_results/Brain_ans.csv | 1059 +++++++++++- examples/atlas/sweep_results/Heart_ans.csv | 1538 +++++++++++++++-- .../atlas/sweep_results/Intestine_ans.csv | 167 +- examples/atlas/sweep_results/Kidney_ans.csv | 564 +++++- examples/atlas/sweep_results/Lung_ans.csv | 1094 ++++++++++++ examples/atlas/sweep_results/Pancreas_ans.csv | 425 ++++- 7 files changed, 5562 insertions(+), 392 deletions(-) create mode 100644 examples/atlas/sweep_results/Lung_ans.csv diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index 206b7a70..4b43c72f 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check 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+",0.2874999940395355,all_total_runs:196|all_finished_runs:151|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:77.04%,False,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/965m42b6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2yalgnau,https://wandb.ai/xzy11632/dance-dev/sweeps/8t32838i,https://wandb.ai/xzy11632/dance-dev/sweeps/vudu58gr","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.289000004529953,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.83%,False fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lx05p3vr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iuazawqt,https://wandb.ai/xzy11632/dance-dev/sweeps/s9ckkiye,https://wandb.ai/xzy11632/dance-dev/sweeps/kval7p9y","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -110,7 +141,38 @@ fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9215070605278016,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/igxg3cvm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0fxcrj2d,https://wandb.ai/xzy11632/dance-dev/sweeps/ldrt5co9,https://wandb.ai/xzy11632/dance-dev/sweeps/f375yojf","- type: filter.gene target: FilterGenesPercentile params: @@ -173,7 +235,28 @@ 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target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2879999876022339,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mz273ff5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gm5ga5mm,https://wandb.ai/xzy11632/dance-dev/sweeps/gh2p49n8,https://wandb.ai/xzy11632/dance-dev/sweeps/2w6dihtz","- type: filter.gene target: FilterGenesPercentile params: @@ -228,7 +311,37 @@ 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mode: rv +- type: normalize + target: NormalizeTotal + params: + target_sum: 100000 + max_fraction: 0.01 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 230 + top: true + mode: rv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 842 + feat_norm_mode: minmax +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1675000041723251,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgjtmzk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4lc9v41j,https://wandb.ai/xzy11632/dance-dev/sweeps/qgpqm3rx,https://wandb.ai/xzy11632/dance-dev/sweeps/l6uoduzp","- type: filter.gene target: FilterGenesPercentile params: {} @@ -284,7 +397,38 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.18799999356269836,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,,,,, 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SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1655000001192093,all_total_runs:601|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:21|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:84.53%,False 84230ea4-998d-4aa8-8456-81dd54ce23af,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4lhkspy4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v3i9xvkp,https://wandb.ai/xzy11632/dance-dev/sweeps/4kznqqwz,https://wandb.ai/xzy11632/dance-dev/sweeps/ntv3k0kl","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -369,7 +513,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type 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SCNFeature label_channel: cell_type -",0.3631910426871938,all_total_runs:150|all_finished_runs:130|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:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:86.67%,False +",0.3631910426871938,all_total_runs:150|all_finished_runs:130|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:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:86.67%,False,,,,, 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: {} @@ -478,8 +622,7 @@ 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+",0.4636363685131073,all_total_runs:510|all_finished_runs:417|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:20|finished_rate:81.76%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ofw1llkf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uge2k7vi,https://wandb.ai/xzy11632/dance-dev/sweeps/qn85rgjd,https://wandb.ai/xzy11632/dance-dev/sweeps/kcp8pt1y","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -494,46 +637,50 @@ a5d95a42-0137-496f-8a60-101e17f263c8,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: 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HighlyVariableGenesRawCount params: - n_top_genes: 9665 - n_bins: 29 - flavor: cell_ranger + n_top_genes: 9344 + span: 0.16241092053064884 - type: feature.cell - target: WeightedFeatureSVD + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 106 + n_components: 593 feat_norm_mode: minmax - type: graph.cell target: CellFeatureGraph @@ -694,23 +806,72 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,,,,, 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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 +",0.2010000050067901,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.29%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51cpr0d9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/95hn1egh,https://wandb.ai/xzy11632/dance-dev/sweeps/peld3u5u,https://wandb.ai/xzy11632/dance-dev/sweeps/on2ik08p","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 95 + mode: sum +- type: normalize + target: Log1P + params: + base: 9.417934904058548 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9808 + span: 0.19479949862140847 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 505 + feat_norm_mode: l2 - type: graph.cell target: CellFeatureGraph params: @@ -720,8 +881,64 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:10|finished_rate:78.57%,False,,,,, -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 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+ target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3030000030994415,all_total_runs:510|all_finished_runs:378|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.12%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xo0nl62w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8mbj6ni4,https://wandb.ai/xzy11632/dance-dev/sweeps/z5plqd2c,https://wandb.ai/xzy11632/dance-dev/sweeps/8yrbdg1z","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -754,17 +971,48 @@ ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,"step2:https://wandb.ai/xzy11632/dance params: config_dict: label_channel: cell_type 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target: SetConfig + params: + 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 +01209dce-3575-4bed-b1df-129f57fbc031,,,,,,"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: 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 @@ -780,25 +1028,55 @@ 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feature_channel: feature.cell + label_channel: cell_type +",0.3709999918937683,all_total_runs:600|all_finished_runs:477|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:79.50%,False +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 target: FilterGenesPlaceHolder - type: normalize - target: ScaleFeature + target: Log1P params: - mode: minmax - eps: 0.3 + base: 2.12228660428801 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 2457 - span: 0.4560040203055745 + n_top_genes: 4984 + n_bins: 29 + flavor: cell_ranger - type: feature.cell target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 963 + n_components: 872 feat_norm_mode: minmax - type: graph.cell target: CellFeatureGraph @@ -809,9 +1087,8 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,"step2:https://wandb.ai/xzy11632/dance 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,,,,, -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 - target: FilterGenesPlaceHolder 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- min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.19499999284744263,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 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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 +",0.3179999887943268,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,,,,,,,,,, +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: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- 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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,,,,,,,,,, +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 + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4535000026226044,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.62%,False,,,,,,,,,, +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: + min_val: 4 + max_val: 96 + mode: cv +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 6 + gmean_eps: 1 + n_genes: 2483 + n_cells: null + bin_size: 600 + bw_adjust: 2.93757162686828 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 5146 + span: 0.3488075399257312 +- 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 +",0.4626086950302124,all_total_runs:510|all_finished_runs:328|step2_total_runs:450|step2_finished_runs:323|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.31%,False,"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 + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4626086950302124,all_total_runs:210|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:62.86%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xsnur0f9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2r2wyqzg,https://wandb.ai/xzy11632/dance-dev/sweeps/fmc6g0fd,https://wandb.ai/xzy11632/dance-dev/sweeps/03yxho1k","- 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 +",0.44608695652173913,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,"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: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4365217387676239,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 +8a554710-08bc-4005-87cd-da9675bdc2e7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uukbxis0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pyigoma7,https://wandb.ai/xzy11632/dance-dev/sweeps/6d5lmjn3,https://wandb.ai/xzy11632/dance-dev/sweeps/hpbmdmp5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8536009192466736,all_total_runs:511|all_finished_runs:361|step2_total_runs:451|step2_finished_runs:339|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:3|finished_rate:70.65%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nqd73gpc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0vkv2rcm,https://wandb.ai/xzy11632/dance-dev/sweeps/guwhe3e7,https://wandb.ai/xzy11632/dance-dev/sweeps/p9citqd9","- 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: 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 +",0.8547815680503845,all_total_runs:210|all_finished_runs:174|step2_total_runs:150|step2_finished_runs:114|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:82.86%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ehzrgrvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fun57502,https://wandb.ai/xzy11632/dance-dev/sweeps/vt0nrjd6,https://wandb.ai/xzy11632/dance-dev/sweeps/iagsk9eg","- 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 +",0.8429752066115702,all_total_runs:150|all_finished_runs:90|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:14|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:60.00%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/olvgy5r3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hq27jio9,https://wandb.ai/xzy11632/dance-dev/sweeps/pcdnersx,https://wandb.ai/xzy11632/dance-dev/sweeps/jdcr8j28","- 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 + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8453364968299866,all_total_runs:586|all_finished_runs:467|step2_total_runs:540|step2_finished_runs:427|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.69%,False +eeacb0c1-2217-4cf6-b8ce-1f0fedf1b569,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8ixv1rhg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r9jacav6,https://wandb.ai/xzy11632/dance-dev/sweeps/q6cmvwu6,https://wandb.ai/xzy11632/dance-dev/sweeps/t5aju4tb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4641327559947967,all_total_runs:510|all_finished_runs:337|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:66.08%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7bo3ceh1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dtijfdv0,https://wandb.ai/xzy11632/dance-dev/sweeps/hdzrhugh,https://wandb.ai/xzy11632/dance-dev/sweeps/41dsr5zv","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 2.104951608085805 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3803 + top: true + mode: cv +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 127 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5342612266540527,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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c3yy5fd3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dr1ls28c,https://wandb.ai/xzy11632/dance-dev/sweeps/7rl62qzb,https://wandb.ai/xzy11632/dance-dev/sweeps/33lvyrau","- 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 +",0.5187366167023555,all_total_runs:150|all_finished_runs:79|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:2|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:52.67%,True,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rf2i7twp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/85j5c24x,https://wandb.ai/xzy11632/dance-dev/sweeps/kwna8mqg,https://wandb.ai/xzy11632/dance-dev/sweeps/8tvxcuym","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5251606106758118,all_total_runs:600|all_finished_runs:492|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.00%,False diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index 65011f78..9e23d1ef 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check 0bc7235a-ae5a-479d-a487-510435377e55,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q8thzcku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/67icoeh5,https://wandb.ai/xzy11632/dance-dev/sweeps/2yzyyprb,https://wandb.ai/xzy11632/dance-dev/sweeps/l4guxas3","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -49,7 +49,65 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5544999837875366,all_total_runs:182|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:68.13%,False +",0.5544999837875366,all_total_runs:182|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:68.13%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/oxjgrsrd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w5pscp3d,https://wandb.ai/xzy11632/dance-dev/sweeps/s6b7bfmw,https://wandb.ai/xzy11632/dance-dev/sweeps/x51l7r3s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5509999990463257,all_total_runs:600|all_finished_runs:504|step2_total_runs:540|step2_finished_runs:445|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xuu3n6fc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fin2t33m,https://wandb.ai/xzy11632/dance-dev/sweeps/77fw5o6f,https://wandb.ai/xzy11632/dance-dev/sweeps/aqsvve2s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5315,all_total_runs:150|all_finished_runs:61|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:40.67%,True 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Brain),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0fw2so56|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmr1g5de,https://wandb.ai/xzy11632/dance-dev/sweeps/7izot7qs,https://wandb.ai/xzy11632/dance-dev/sweeps/jlmorjb4","- type: filter.gene target: FilterGenesPercentile params: {} @@ -101,7 +159,48 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3714999854564667,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:83.33%,False +",0.3714999854564667,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:83.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q84d43mh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7kx3k7oq,https://wandb.ai/xzy11632/dance-dev/sweeps/euoz4xtn,https://wandb.ai/xzy11632/dance-dev/sweeps/2mr5ac2i","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.382999986410141,all_total_runs:600|all_finished_runs:506|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o748tsyg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/py2yh3r8,https://wandb.ai/xzy11632/dance-dev/sweeps/cdz2iob0,https://wandb.ai/xzy11632/dance-dev/sweeps/ax6j7ylt","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3795,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:64.67%,False 9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tjo2gadd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0h9izpy1,https://wandb.ai/xzy11632/dance-dev/sweeps/i8ghsgev,https://wandb.ai/xzy11632/dance-dev/sweeps/h1l9teot","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -134,22 +233,26 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5149999856948853,all_total_runs:510|all_finished_runs:353|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:69.22%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lm5mwxkq,https://wandb.ai/xzy11632/dance-dev/sweeps/ortq51x9,https://wandb.ai/xzy11632/dance-dev/sweeps/lakwxgnu","- type: filter.gene +",0.5149999856948853,all_total_runs:510|all_finished_runs:353|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:69.22%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ml42ca0j,https://wandb.ai/xzy11632/dance-dev/sweeps/nsx84eyz,https://wandb.ai/xzy11632/dance-dev/sweeps/3k71zgrp","- type: filter.gene target: FilterGenesPlaceHolder - params: {} - type: normalize target: ScaleFeature - params: {} + params: + mode: normalize + eps: 0.7 - type: filter.gene target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 3000 + n_top_genes: 2467 + n_bins: 23 + flavor: cell_ranger - type: feature.cell + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + n_components: 490 + feat_norm_mode: null - type: graph.cell target: CellFeatureGraph params: @@ -159,7 +262,65 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5440000295639038,all_total_runs:182|all_finished_runs:114|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.64%,False +",0.5460000038146973,all_total_runs:215|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:26|step3_1_finished_runs:20|step3_2_total_runs:19|step3_2_finished_runs:15|finished_rate:76.74%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/updcwamn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ohu0gf1,https://wandb.ai/xzy11632/dance-dev/sweeps/90jvnxg4,https://wandb.ai/xzy11632/dance-dev/sweeps/wuc8ylei","- type: filter.gene + target: FilterGenesScanpyOrder + params: + 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 +",0.5335000157356262,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:444|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.83%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w0h5fqbq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pw550ttt,https://wandb.ai/xzy11632/dance-dev/sweeps/0zjzlktf,https://wandb.ai/xzy11632/dance-dev/sweeps/mzcibev2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5295,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.67%,False 52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5awnfxur|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3bspph5d,https://wandb.ai/xzy11632/dance-dev/sweeps/4wkwaao0,https://wandb.ai/xzy11632/dance-dev/sweeps/gosfxkg9","- type: filter.gene target: FilterGenesPercentile params: {} @@ -221,7 +382,57 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.5895000100135803,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False +",0.5895000100135803,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h5sox1qq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tkk37137,https://wandb.ai/xzy11632/dance-dev/sweeps/8kuofdmo,https://wandb.ai/xzy11632/dance-dev/sweeps/v8plc2lh","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5895000100135803,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/obu7ohqs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuwhe23l,https://wandb.ai/xzy11632/dance-dev/sweeps/mje7v676,https://wandb.ai/xzy11632/dance-dev/sweeps/30rb0den","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 9.81581694983002 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 8533 + span: 0.5476309362757072 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5825,all_total_runs:150|all_finished_runs:121|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:80.67%,False 56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/om1u72x5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bfpl63bz,https://wandb.ai/xzy11632/dance-dev/sweeps/h86ptqve,https://wandb.ai/xzy11632/dance-dev/sweeps/hoc145hn","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -272,7 +483,47 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False +",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0xq25wc4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vmop7pif,https://wandb.ai/xzy11632/dance-dev/sweeps/8tn7yvjs,https://wandb.ai/xzy11632/dance-dev/sweeps/1dpu33ih","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3544999957084656,all_total_runs:600|all_finished_runs:502|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.67%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpa8itbf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yxhw6hrg,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwvhde7,https://wandb.ai/xzy11632/dance-dev/sweeps/1mzn11g0","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.373,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:71|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:61.33%,False 43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njrfx2sd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d0qeq1ft,https://wandb.ai/xzy11632/dance-dev/sweeps/ao28i16e,https://wandb.ai/xzy11632/dance-dev/sweeps/1tkopoue","- type: filter.gene target: FilterGenesPercentile params: @@ -381,31 +632,71 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type 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+",0.873,all_total_runs:150|all_finished_runs:125|step2_total_runs:90|step2_finished_runs:68|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.33%,False +22658f4f-9268-41ad-8828-cc53f4baa9fa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/aio76f5y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4igc6uwy,https://wandb.ai/xzy11632/dance-dev/sweeps/c21dzyzr,https://wandb.ai/xzy11632/dance-dev/sweeps/tesqknws","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7515000104904175,all_total_runs:510|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:63.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene + target: FilterGenesScanpyOrder params: order: - min_counts @@ -438,7 +729,38 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.7710000276565552,all_total_runs:182|all_finished_runs:122|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:67.03%,False 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params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7609999775886536,all_total_runs:600|all_finished_runs:509|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.83%,False,,,,, 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: @@ -503,7 +825,28 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.92849999666214,all_total_runs:208|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:7|step3_2_total_runs:19|step3_2_finished_runs:8|finished_rate:57.69%,True +",0.92849999666214,all_total_runs:208|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:7|step3_2_total_runs:19|step3_2_finished_runs:8|finished_rate:57.69%,True,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mtgx8qhv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wllx4ks3,https://wandb.ai/xzy11632/dance-dev/sweeps/u1ypef2p,https://wandb.ai/xzy11632/dance-dev/sweeps/hsa4s4fk","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9419999718666076,all_total_runs:600|all_finished_runs:498|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.00%,False,,,,, 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: @@ -573,7 +916,38 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.7954999804496765,all_total_runs:179|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:17|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.27%,False +",0.7954999804496765,all_total_runs:179|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:17|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.27%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/crxrjodt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s31c4wq8,https://wandb.ai/xzy11632/dance-dev/sweeps/ard4f4u9,https://wandb.ai/xzy11632/dance-dev/sweeps/6mriem5a","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7795000076293945,all_total_runs:600|all_finished_runs:488|step2_total_runs:540|step2_finished_runs:437|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.33%,False,,,,, 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: @@ -686,7 +1060,29 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.49549999833106995,all_total_runs:182|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.33%,False +",0.4954999983310699,all_total_runs:182|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/grhvlnli|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pr5mnq0v,https://wandb.ai/xzy11632/dance-dev/sweeps/160tm6oy,https://wandb.ai/xzy11632/dance-dev/sweeps/o05jmzta","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4884999990463257,all_total_runs:600|all_finished_runs:502|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.67%,False,,,,, 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: @@ -753,7 +1149,42 @@ 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min_cells + - min_counts + min_counts: 40 + min_cells: 0.08125217299144956 + max_counts: 0.9080661177583162 + max_cells: 0.9518281878428064 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 1510 + n_bins: 15 + flavor: cell_ranger +- type: feature.cell + target: CellPCA + params: + out: feature.cell + log_level: INFO + n_components: 110 +- type: misc + target: SetConfig + params: + 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,,,,, 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+",0.4934999942779541,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:78.10%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ixh7uwhg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9ichlmte,https://wandb.ai/xzy11632/dance-dev/sweeps/akgvfhvf,https://wandb.ai/xzy11632/dance-dev/sweeps/0yr2q39w","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - max_cells + - min_counts + min_counts: 490 + min_cells: 0.0799339187017819 + max_counts: 0.9194196815998212 + max_cells: 0.9645400767614664 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9664 + span: 0.1714636071756561 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 279 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5130000114440918,all_total_runs:600|all_finished_runs:486|step2_total_runs:540|step2_finished_runs:434|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:81.00%,False,,,,, 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: {} @@ -860,7 +1326,29 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type 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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 +",0.5214999914169312,all_total_runs:600|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.67%,False,,,,, 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: @@ -918,7 +1406,29 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.640999972820282,all_total_runs:580|all_finished_runs:460|step2_total_runs:540|step2_finished_runs:420|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|finished_rate:79.31%,False,,,,, 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: {} @@ -975,7 +1485,38 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7954999804496765,all_total_runs:600|all_finished_runs:505|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.17%,False,,,,, 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: {} @@ -1023,7 +1564,33 @@ 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type: normalize + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 532 + feat_norm_mode: minmax +- type: misc + target: SetConfig + params: + 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,,,,, 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 @@ -1087,7 +1654,39 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5115000009536743,all_total_runs:168|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False +",0.5115000009536743,all_total_runs:168|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6mib6vb3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rrbcza8h,https://wandb.ai/xzy11632/dance-dev/sweeps/84l9elo3,https://wandb.ai/xzy11632/dance-dev/sweeps/j16ha10r","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5139999985694885,all_total_runs:587|all_finished_runs:458|step2_total_runs:540|step2_finished_runs:424|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:21|step3_2_finished_runs:14|finished_rate:78.02%,False,,,,, 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+",0.5866336822509766,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.83%,False,,,,, 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: @@ -1212,7 +1832,28 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5299860239028931,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:389|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.83%,False,,,,, 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: {} @@ -1261,7 +1902,38 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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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,all_total_runs:600|all_finished_runs:482|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.33%,False,,,,, 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: {} @@ -1283,7 +1955,48 @@ 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+",0.5130813717842102,all_total_runs:510|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:342|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:78.43%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9sheweny,https://wandb.ai/xzy11632/dance-dev/sweeps/b0rongi3,https://wandb.ai/xzy11632/dance-dev/sweeps/ekmf487e","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - min_counts + - max_cells + min_counts: 263 + min_cells: 0.09338611959221152 + max_counts: 0.9103664063089278 + max_cells: 0.9776450063364456 +- type: normalize + target: Log1P + params: + base: 9.78567214435452 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: 0.42152838507294543 + max_disp: 90.25784555274645 + min_mean: 0.003754725333592855 + max_mean: 13.674551723139253 + n_bins: 13 + flavor: seurat +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 484 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5167151093482971,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c6dubcot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6h51vv85,https://wandb.ai/xzy11632/dance-dev/sweeps/3wbf935e,https://wandb.ai/xzy11632/dance-dev/sweeps/eaxe9v47","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1296,10 +2009,10 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: NormalizePlaceHolder params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -1307,17 +2020,14 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.5130813717842102,all_total_runs:182|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.27%,False +",0.5254360437393188,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,,,,, 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 @@ -1366,7 +2076,28 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6637080907821655,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:117|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:75.00%,False +",0.6637080907821655,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:117|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:75.00%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/983ind0g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jcaz6527,https://wandb.ai/xzy11632/dance-dev/sweeps/wfvyft6a,https://wandb.ai/xzy11632/dance-dev/sweeps/c947lcfl","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6814595460891724,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:423|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.83%,False,,,,, 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: {} @@ -1414,7 +2145,29 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5260545611381531,all_total_runs:210|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.52%,False +",0.5260545611381531,all_total_runs:210|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.52%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hczkf4io|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6hi8qvm1,https://wandb.ai/xzy11632/dance-dev/sweeps/lgckqg0v,https://wandb.ai/xzy11632/dance-dev/sweeps/t06qe0t3","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5136476159095764,all_total_runs:600|all_finished_runs:493|step2_total_runs:540|step2_finished_runs:433|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.17%,False,,,,, 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: {} @@ -1437,7 +2190,7 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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+",0.468804657459259,all_total_runs:493|all_finished_runs:368|step2_total_runs:450|step2_finished_runs:345|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.65%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wsvx4b09,https://wandb.ai/xzy11632/dance-dev/sweeps/onnj2wg3,https://wandb.ai/xzy11632/dance-dev/sweeps/lgf5xaby","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1462,7 +2215,29 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.48571428656578064,all_total_runs:210|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.67%,False 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+",0.5026239156723022,all_total_runs:600|all_finished_runs:485|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:20|finished_rate:80.83%,False,,,,, 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: @@ -1496,7 +2271,65 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True +",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d0dp8leo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/clti5xmd,https://wandb.ai/xzy11632/dance-dev/sweeps/gwwbfyoy,https://wandb.ai/xzy11632/dance-dev/sweeps/bji8pgf5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:81.17%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kygmspb8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lgj6yg3p,https://wandb.ai/xzy11632/dance-dev/sweeps/2kgqnf6r,https://wandb.ai/xzy11632/dance-dev/sweeps/j7yqtdud","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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:15|step2_total_runs:90|step2_finished_runs:7|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:10.00%,True 146216e1-ec30-4fee-a1fb-25defe801e2d,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1531,7 +2364,65 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False +",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/94jlkvhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pwo0mfuv,https://wandb.ai/xzy11632/dance-dev/sweeps/d1zcq1f3,https://wandb.ai/xzy11632/dance-dev/sweeps/45ment3z","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:487|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:15|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:81.17%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pwpb4rfm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/smon44r5,https://wandb.ai/xzy11632/dance-dev/sweeps/rzc9i7hm,https://wandb.ai/xzy11632/dance-dev/sweeps/hdlybnl7","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - 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 +",1.0,all_total_runs:150|all_finished_runs:18|step2_total_runs:90|step2_finished_runs:14|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:12.00%,True 700aed19-c16e-4ba8-9191-07da098a8626,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9vvinymt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0f6156l,https://wandb.ai/xzy11632/dance-dev/sweeps/fmt50h6n,https://wandb.ai/xzy11632/dance-dev/sweeps/pbhkpdsh","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1566,7 +2457,38 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:194|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:18|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:74.74%,False +",1.0,all_total_runs:194|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:18|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:74.74%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/15mt3eq3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3pcc3teq,https://wandb.ai/xzy11632/dance-dev/sweeps/vsssu6xu,https://wandb.ai/xzy11632/dance-dev/sweeps/k69a11h0","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.17%,False,,,,, 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: {} @@ -1592,4 +2514,35 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:168|all_finished_runs:21|step2_total_runs:150|step2_finished_runs:21|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:12.50%,True +",1.0,all_total_runs:168|all_finished_runs:21|step2_total_runs:150|step2_finished_runs:21|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:12.50%,True,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lqheset7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxs7x3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/zlciejor,https://wandb.ai/xzy11632/dance-dev/sweeps/x840lvth","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:478|step2_total_runs:540|step2_finished_runs:430|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:79.67%,False,,,,, diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index 7e0faff6..60925f7d 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check 5a11f879-d1ef-458a-910c-9b0bdfca5ebf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzv8jp6b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hcdwfsqe,https://wandb.ai/xzy11632/dance-dev/sweeps/hr9dvt9y,https://wandb.ai/xzy11632/dance-dev/sweeps/vw8htm3n","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -54,7 +54,56 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.9506173133850098,all_total_runs:210|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:103|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:17|finished_rate:57.14%,True +",0.9506173133850098,all_total_runs:210|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:103|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:17|finished_rate:57.14%,True,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vzuxzpj3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d7f23zg1,https://wandb.ai/xzy11632/dance-dev/sweeps/uzh7wc9b,https://wandb.ai/xzy11632/dance-dev/sweeps/675mh1vq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9365079402923584,all_total_runs:586|all_finished_runs:391|step2_total_runs:540|step2_finished_runs:353|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:66.72%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wl63ncu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tyhv65th,https://wandb.ai/xzy11632/dance-dev/sweeps/0d2njqgp,https://wandb.ai/xzy11632/dance-dev/sweeps/nmhbwu4c","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9435626102292768,all_total_runs:150|all_finished_runs:102|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:68.00%,False 572f3f3e-d3e4-4d13-8e2b-88215e508481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/usfsqcao|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fn99c0s6,https://wandb.ai/xzy11632/dance-dev/sweeps/uff7y5g5,https://wandb.ai/xzy11632/dance-dev/sweeps/vgjmwbae","- type: filter.gene target: FilterGenesPercentile params: @@ -114,7 +163,55 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.4004999995231629,all_total_runs:210|all_finished_runs:178|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:20|finished_rate:84.76%,False +",0.4004999995231629,all_total_runs:210|all_finished_runs:178|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:20|finished_rate:84.76%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dllmfk0t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pdu1htvk,https://wandb.ai/xzy11632/dance-dev/sweeps/9mfsvnog,https://wandb.ai/xzy11632/dance-dev/sweeps/fohrpha2","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3944999873638153,all_total_runs:558|all_finished_runs:349|step2_total_runs:540|step2_finished_runs:349|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.54%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uwriv450|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9hfqgivj,https://wandb.ai/xzy11632/dance-dev/sweeps/hp8z8z34,https://wandb.ai/xzy11632/dance-dev/sweeps/ejfw0jpu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_counts + - max_counts + - min_cells + min_counts: 346 + min_cells: 0.0694734963763344 + max_counts: 0.9289519358097762 + max_cells: 0.9793397916743596 +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.5 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.386,all_total_runs:150|all_finished_runs:102|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:68.00%,False 9434b020-de42-43eb-bcc4-542b2be69015,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/scbko4h4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/aym16539,https://wandb.ai/xzy11632/dance-dev/sweeps/4cex2w1l,https://wandb.ai/xzy11632/dance-dev/sweeps/al84eum0","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -179,7 +276,60 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.9725000262260436,all_total_runs:196|all_finished_runs:156|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:20|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.59%,False +",0.9725000262260436,all_total_runs:196|all_finished_runs:156|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:20|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.59%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ljcbdxpa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cd3jmhod,https://wandb.ai/xzy11632/dance-dev/sweeps/iuk576pz,https://wandb.ai/xzy11632/dance-dev/sweeps/xgyejfld","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - max_cells + - min_cells + - min_counts + min_counts: 464 + min_cells: 0.03355997076275901 + max_counts: 0.9675911149628488 + max_cells: 0.956159811249128 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4104 + span: 0.5225329617640444 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 662 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9670000076293944,all_total_runs:600|all_finished_runs:419|step2_total_runs:540|step2_finished_runs:371|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:69.83%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cyx8x2ef|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cm2y2e85,https://wandb.ai/xzy11632/dance-dev/sweeps/znjdtv6p,https://wandb.ai/xzy11632/dance-dev/sweeps/46gbjbvk","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9405,all_total_runs:150|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:59.33%,True a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1128huxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/98s1vpgx,https://wandb.ai/xzy11632/dance-dev/sweeps/dkxsnzmu,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6fvur7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -246,7 +396,56 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6399999856948853,all_total_runs:210|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:108|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:60.48%,False +",0.6399999856948853,all_total_runs:210|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:108|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:60.48%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xkh6yuxk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spekwsdz,https://wandb.ai/xzy11632/dance-dev/sweeps/6dh4dpk0,https://wandb.ai/xzy11632/dance-dev/sweeps/i3do9zdc","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + 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 +",0.6345000267028809,all_total_runs:586|all_finished_runs:411|step2_total_runs:540|step2_finished_runs:371|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:70.14%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/evq18crq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hlqtxu6d,https://wandb.ai/xzy11632/dance-dev/sweeps/ijgh3h21,https://wandb.ai/xzy11632/dance-dev/sweeps/pwgh6hr9","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6355,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i94przah|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7ruaq9f1,https://wandb.ai/xzy11632/dance-dev/sweeps/o1o45k7l,https://wandb.ai/xzy11632/dance-dev/sweeps/lnl0snl5","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -304,7 +503,47 @@ 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NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.822429895401001,all_total_runs:586|all_finished_runs:433|step2_total_runs:540|step2_finished_runs:393|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.89%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x92janfg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cs9lr34q,https://wandb.ai/xzy11632/dance-dev/sweeps/b6e4q5lc,https://wandb.ai/xzy11632/dance-dev/sweeps/nbea554w","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8271028037383178,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.33%,False d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0kyb9nc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/px7yqntj,https://wandb.ai/xzy11632/dance-dev/sweeps/a1ye7fv1,https://wandb.ai/xzy11632/dance-dev/sweeps/vx4ibf72","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -369,7 +608,46 @@ d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2540000081062317,all_total_runs:600|all_finished_runs:500|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:83.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6wmjqpgy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n2e1k541,https://wandb.ai/xzy11632/dance-dev/sweeps/sa9ksi62,https://wandb.ai/xzy11632/dance-dev/sweeps/6j62a8fd","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2405,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4raopmgl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tj8oqma7,https://wandb.ai/xzy11632/dance-dev/sweeps/j7f8tlxr,https://wandb.ai/xzy11632/dance-dev/sweeps/vo4w0lty","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -420,21 +698,63 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29249998927116394,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False -e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - max_cells - - min_cells - - max_counts - min_counts: 324 - min_cells: 0.0994897883945216 - max_counts: 0.9671792921176364 - max_cells: 0.952327145046576 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+",0.3075000047683716,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:82.83%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gyyf7mvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uhzoul7q,https://wandb.ai/xzy11632/dance-dev/sweeps/gvcfxbmn,https://wandb.ai/xzy11632/dance-dev/sweeps/aenj1m4d","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 1941 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.276,all_total_runs:150|all_finished_runs:90|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:60.00%,False +e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 324 + min_cells: 0.0994897883945216 + max_counts: 0.9671792921176364 + max_cells: 0.952327145046576 +- type: normalize + target: NormalizePlaceHolder - type: filter.gene target: FilterGenesRegression params: @@ -486,7 +806,58 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: 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type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6230000257492065,all_total_runs:600|all_finished_runs:478|step2_total_runs:540|step2_finished_runs:418|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.67%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w5rpqy3q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ntx4v8m0,https://wandb.ai/xzy11632/dance-dev/sweeps/qcc4kp5w,https://wandb.ai/xzy11632/dance-dev/sweeps/wzg4qmk6","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 5497 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6275,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:70|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:84.00%,False f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/datmwta4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ri7gpq3f,https://wandb.ai/xzy11632/dance-dev/sweeps/6apaq3my,https://wandb.ai/xzy11632/dance-dev/sweeps/crgctmfi","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -535,7 +906,65 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3880000114440918,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:83.17%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lhd5hw1j|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/a006m2c5,https://wandb.ai/xzy11632/dance-dev/sweeps/0qg9p4iv,https://wandb.ai/xzy11632/dance-dev/sweeps/uf4gs6jq","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - 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 +",0.3880000114440918,all_total_runs:600|all_finished_runs:442|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:73.67%,False fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -601,7 +1030,55 @@ 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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 +",0.687,all_total_runs:150|all_finished_runs:125|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:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.33%,False 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Heart),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3qs9s7s9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m84q60x9,https://wandb.ai/xzy11632/dance-dev/sweeps/wu90yl9e,https://wandb.ai/xzy11632/dance-dev/sweeps/t9t6we7t","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -668,7 +1145,56 @@ 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FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.353035738226729 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3613 + span: 0.5980502565579662 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3535,all_total_runs:150|all_finished_runs:135|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:90.00%,False 65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n9pv9var|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uox7hj7b,https://wandb.ai/xzy11632/dance-dev/sweeps/lghef4b7,https://wandb.ai/xzy11632/dance-dev/sweeps/16q0x97m","- type: filter.gene target: FilterGenesPercentile params: @@ -708,16 +1234,675 @@ 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2223 + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 167 - feat_norm_mode: null + split_name: train + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -781,47 +1996,47 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6460000276565552,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:80.95%,False -ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fadl6x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f6na6k1n,https://wandb.ai/xzy11632/dance-dev/sweeps/1hwk0ec1,https://wandb.ai/xzy11632/dance-dev/sweeps/g73ajpao","- type: filter.gene - target: FilterGenesScanpyOrder 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FilterGenesTopK params: - num_genes: 9618 - top: true - mode: var + num_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3149999976158142,all_total_runs:510|all_finished_runs:340|step2_total_runs:450|step2_finished_runs:337|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:66.67%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b47t3rbw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xf8y2bet,https://wandb.ai/xzy11632/dance-dev/sweeps/60mja5m8,https://wandb.ai/xzy11632/dance-dev/sweeps/y27ceukr","- type: filter.gene 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CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3375000059604645,all_total_runs:210|all_finished_runs:155|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:73.81%,False -4ed927e9-c099-49af-b8ce-a2652d069333,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gl8a9d5v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nrpkd1s1,https://wandb.ai/xzy11632/dance-dev/sweeps/i4ot3t4a,https://wandb.ai/xzy11632/dance-dev/sweeps/1off7yhe","- type: filter.gene - target: FilterGenesPercentile 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type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:81.90%,False -1252c5fb-945f-42d6-b1a8-8a3bd864384b,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:81.67%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/azji707t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wkrd46cp,https://wandb.ai/xzy11632/dance-dev/sweeps/snjn7ct3,https://wandb.ai/xzy11632/dance-dev/sweeps/m3aqfp6h","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1071,29 +2282,22 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False -bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/frisdu4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fywjox,https://wandb.ai/xzy11632/dance-dev/sweeps/dz23lu62,https://wandb.ai/xzy11632/dance-dev/sweeps/g0d29txd","- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:27|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:18.00%,True +f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1127,8 +2331,7 @@ bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,"step2:https://wandb.ai/xzy11632/dance params: config_dict: label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False -f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/as6ivetf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/icsk75i5,https://wandb.ai/xzy11632/dance-dev/sweeps/vtlcraw8,https://wandb.ai/xzy11632/dance-dev/sweeps/qjov7ai7","- type: filter.gene +",1.0,all_total_runs:210|all_finished_runs:149|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.95%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jv6l7zfb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1sctem2k,https://wandb.ai/xzy11632/dance-dev/sweeps/p40vryym,https://wandb.ai/xzy11632/dance-dev/sweeps/g0mqq7jx","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1153,17 +2356,13 @@ f75f2ff4-2884-4c2d-b375-70de37a34507,,,,,,"step2:https://wandb.ai/xzy11632/dance log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.88%,False -f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:489|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:81.50%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/syusb3sn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rkq3icqq,https://wandb.ai/xzy11632/dance-dev/sweeps/x0txps05,https://wandb.ai/xzy11632/dance-dev/sweeps/3avow7ff","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1176,25 +2375,18 @@ f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,"step2:https://wandb.ai/xzy11632/dance min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:149|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.95%,False +",1.0,all_total_runs:150|all_finished_runs:17|step2_total_runs:90|step2_finished_runs:7|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:11.33%,True diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index 2fe1b8a7..447485b4 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_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check 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: @@ -58,7 +58,28 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c params: config_dict: label_channel: cell_type -",0.4494999945163727,all_total_runs:210|all_finished_runs:148|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:70.48%,False +",0.4494999945163727,all_total_runs:210|all_finished_runs:148|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:70.48%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w85f0jr1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yvez2as1,https://wandb.ai/xzy11632/dance-dev/sweeps/3r5lt9pe,https://wandb.ai/xzy11632/dance-dev/sweeps/78288m6z","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4645000100135803,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False 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: @@ -123,7 +144,28 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.4900000095367432,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.05%,False +",0.4900000095367432,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.05%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1h4jwpys|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iz2i7d43,https://wandb.ai/xzy11632/dance-dev/sweeps/zcebhj28,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bod1sy","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.48100000619888306,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False 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: {} @@ -184,7 +226,29 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3653995394706726,all_total_runs:196|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:86|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.78%,False +",0.3653995394706726,all_total_runs:196|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:86|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.78%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8izf00fq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/60jnxyqe,https://wandb.ai/xzy11632/dance-dev/sweeps/oi5dwmnr,https://wandb.ai/xzy11632/dance-dev/sweeps/omvup8nd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3941039443016052,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.83%,False 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: {} @@ -246,7 +310,42 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.450367659330368,all_total_runs:196|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.10%,False +",0.450367659330368,all_total_runs:196|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.10%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h9h46fsq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fh35mitj,https://wandb.ai/xzy11632/dance-dev/sweeps/lzx18s0e,https://wandb.ai/xzy11632/dance-dev/sweeps/tvi3f3a1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_cells + - max_counts + min_counts: 431 + min_cells: 0.09906132245998966 + max_counts: 0.923950882549364 + max_cells: 0.981253017438922 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 2113 + n_bins: 15 + flavor: seurat +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 885 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4375,all_total_runs:600|all_finished_runs:509|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.83%,False 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: @@ -309,7 +408,38 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.512499988079071,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.00%,False +",0.512499988079071,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.00%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vg93532i|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/42fh6nzf,https://wandb.ai/xzy11632/dance-dev/sweeps/659h8tiv,https://wandb.ai/xzy11632/dance-dev/sweeps/asrfudv3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5304999947547913,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False 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: @@ -368,4 +498,27 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5648086071014404,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False +",0.5648086071014404,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w4ju135u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8plcumyk,https://wandb.ai/xzy11632/dance-dev/sweeps/67bwy8sx,https://wandb.ai/xzy11632/dance-dev/sweeps/ltrjfmqu","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.580926775932312,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.83%,False diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index ed01dbcc..a134fc34 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_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check 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: {} @@ -46,7 +46,29 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False +",0.2730000019073486,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/80xdc1ba|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sny3930k,https://wandb.ai/xzy11632/dance-dev/sweeps/volqelag,https://wandb.ai/xzy11632/dance-dev/sweeps/5jxnqx6h","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2770000100135803,all_total_runs:600|all_finished_runs:447|step2_total_runs:540|step2_finished_runs:401|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:74.50%,False 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: {} @@ -95,7 +117,29 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5799999833106995,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:80.95%,False +",0.5799999833106995,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:80.95%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9toa84vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t5uul8vm,https://wandb.ai/xzy11632/dance-dev/sweeps/1mgc0dge,https://wandb.ai/xzy11632/dance-dev/sweeps/azn53fsv","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.578499972820282,all_total_runs:600|all_finished_runs:439|step2_total_runs:540|step2_finished_runs:387|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:73.17%,False 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: @@ -160,7 +204,37 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5964999794960022,all_total_runs:196|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.94%,False +",0.5964999794960022,all_total_runs:196|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.94%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/e43anxgn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3stmar8u,https://wandb.ai/xzy11632/dance-dev/sweeps/s2cpm80t,https://wandb.ai/xzy11632/dance-dev/sweeps/u3ugwnhn","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5914999842643738,all_total_runs:600|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:391|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:73.00%,False 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: @@ -234,7 +308,38 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.7020000219345093,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:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.95%,False +",0.7020000219345093,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:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.95%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/avkuxvpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jdctlnyj,https://wandb.ai/xzy11632/dance-dev/sweeps/2i0dhz25,https://wandb.ai/xzy11632/dance-dev/sweeps/esaiggjt","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7124999761581421,all_total_runs:600|all_finished_runs:440|step2_total_runs:540|step2_finished_runs:392|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:73.33%,False 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 @@ -298,7 +403,29 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.2815000116825104,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.14%,False +",0.2815000116825104,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.14%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x43ntzx4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/irntnkow,https://wandb.ai/xzy11632/dance-dev/sweeps/9tdspve1,https://wandb.ai/xzy11632/dance-dev/sweeps/5yvw6kpr","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2994999885559082,all_total_runs:586|all_finished_runs:420|step2_total_runs:540|step2_finished_runs:386|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.67%,False 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: {} @@ -349,7 +476,36 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.25,all_total_runs:196|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.96%,False +",0.25,all_total_runs:196|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.96%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51phjfg4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rb2c4x3n,https://wandb.ai/xzy11632/dance-dev/sweeps/4m4fq5j5,https://wandb.ai/xzy11632/dance-dev/sweeps/pqqd7mez","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 99 + mode: rv +- type: normalize + target: Log1P + params: + base: 7.449177659482961 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 5312 + top: true + mode: var +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 375 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2224999964237213,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.17%,False 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: @@ -411,7 +567,32 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 108 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27649998664855957,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:403|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:73.83%,False 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: @@ -451,7 +632,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: 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feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2370000034570694,all_total_runs:600|all_finished_runs:501|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.50%,False 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: @@ -592,7 +816,29 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2485000044107437,all_total_runs:600|all_finished_runs:470|step2_total_runs:540|step2_finished_runs:416|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:78.33%,False 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: @@ -658,7 +904,38 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:74.83%,False 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: @@ -728,7 +1005,29 @@ 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ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5,all_total_runs:572|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:77.45%,False 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: {} @@ -779,7 +1078,39 @@ 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min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3672456443309784,all_total_runs:558|all_finished_runs:429|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.88%,False 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+",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 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 @@ -887,7 +1240,38 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3620437979698181,all_total_runs:600|all_finished_runs:469|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:78.17%,False 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: @@ -949,7 +1333,28 @@ 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params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28049999475479126,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 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: @@ -1014,7 +1419,29 @@ 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filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4284999966621399,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:430|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.67%,False 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: @@ -1072,7 +1499,38 @@ 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max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.244499996304512,all_total_runs:600|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:406|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.67%,False 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config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.488034188747406,all_total_runs:599|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:408|step3_0_total_runs:19|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.80%,False 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: @@ -1199,4 +1688,35 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8755832314491272,all_total_runs:210|all_finished_runs:154|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:8|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:73.33%,False +",0.8755832314491272,all_total_runs:210|all_finished_runs:154|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:8|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:73.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yvdvm8br|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuecazpp,https://wandb.ai/xzy11632/dance-dev/sweeps/1axejlbz,https://wandb.ai/xzy11632/dance-dev/sweeps/zpq9n7oj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708,all_total_runs:586|all_finished_runs:488|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.28%,False diff --git a/examples/atlas/sweep_results/Lung_ans.csv b/examples/atlas/sweep_results/Lung_ans.csv new file mode 100644 index 00000000..81fc3447 --- /dev/null +++ b/examples/atlas/sweep_results/Lung_ans.csv @@ -0,0 +1,1094 @@ +Dataset_id,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check +fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/88sp4mxc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uz23y4v1,https://wandb.ai/xzy11632/dance-dev/sweeps/4mlv8rqb,https://wandb.ai/xzy11632/dance-dev/sweeps/vc7o5nsc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4790000021457672,all_total_runs:600|all_finished_runs:479|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:10|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:79.83%,False,,,,, +f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fbs68rd7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xcit9qy8,https://wandb.ai/xzy11632/dance-dev/sweeps/4ftre5j8,https://wandb.ai/xzy11632/dance-dev/sweeps/f5uutcyi","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 96 + mode: cv +- type: normalize + target: Log1P + params: + base: 9.29338977585692 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 4645 + top: false + mode: sum +- type: feature.cell + target: CellPCA + params: + out: feature.cell + log_level: INFO + n_components: 671 +- type: 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HighlyVariableGenesRawCount + params: + n_top_genes: 1528 + span: 0.25048936376968134 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 757 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + 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,,,,, +1e5bd3b8-6a0e-4959-8d69-cafed30fe814,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q46hxsfq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6dkzww83,https://wandb.ai/xzy11632/dance-dev/sweeps/ctnmrdn1,https://wandb.ai/xzy11632/dance-dev/sweeps/6og1pgzb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - 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+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sddbq9kk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i32fl00z,https://wandb.ai/xzy11632/dance-dev/sweeps/3ux4j65s,https://wandb.ai/xzy11632/dance-dev/sweeps/wevylzje","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4050359725952149,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:76.19%,False +a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xn9x8pbm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g2cw98af,https://wandb.ai/xzy11632/dance-dev/sweeps/cuif1dsz,https://wandb.ai/xzy11632/dance-dev/sweeps/twq492am","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3876652121543884,all_total_runs:600|all_finished_runs:461|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:76.83%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8vygl5n6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/il88es7n,https://wandb.ai/xzy11632/dance-dev/sweeps/kyv0eh67,https://wandb.ai/xzy11632/dance-dev/sweeps/qx4x5rqz","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3348017632961273,all_total_runs:210|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:105|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:60.48%,False +8c42cfd0-0b0a-46d5-910c-fc833d83c45e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6pmayeh5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qllm738w,https://wandb.ai/xzy11632/dance-dev/sweeps/9bevhqje,https://wandb.ai/xzy11632/dance-dev/sweeps/axo7zz7i","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 7.282700138506678 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 355 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.24250000715255737,all_total_runs:600|all_finished_runs:489|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.50%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/77gxykh3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vql4ta4g,https://wandb.ai/xzy11632/dance-dev/sweeps/bwiyitpi,https://wandb.ai/xzy11632/dance-dev/sweeps/wvnzhocs","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2515000104904175,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.90%,False +2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qb638tpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qnbj3gg0,https://wandb.ai/xzy11632/dance-dev/sweeps/kfih2j62,https://wandb.ai/xzy11632/dance-dev/sweeps/fe79qk1l","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.83%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x7ca9zjk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g69bgevs,https://wandb.ai/xzy11632/dance-dev/sweeps/lqjvl3t9,https://wandb.ai/xzy11632/dance-dev/sweeps/lcb0w1tc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_cells + - max_counts + - min_counts + min_counts: 452 + min_cells: 0.03353995237571974 + max_counts: 0.9121476758403412 + max_cells: 0.99348026292544 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.3 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 6962 + top: true + mode: cv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 755 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.22349999845027924,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:116|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:82.38%,False 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+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7n25es77|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vslww26r,https://wandb.ai/xzy11632/dance-dev/sweeps/dnhruay0,https://wandb.ai/xzy11632/dance-dev/sweeps/213rny4x","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.1815000027418137,all_total_runs:210|all_finished_runs:169|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:80.48%,False +4023a2bc-6325-47db-bfdf-9639e91042c2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w6h9lrkf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/828yc8fb,https://wandb.ai/xzy11632/dance-dev/sweeps/xetdwps8,https://wandb.ai/xzy11632/dance-dev/sweeps/6mtvx8u2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6615384817123413,all_total_runs:586|all_finished_runs:480|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.91%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hv9b5aer|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/clfj1oh7,https://wandb.ai/xzy11632/dance-dev/sweeps/myvaevvn,https://wandb.ai/xzy11632/dance-dev/sweeps/xkcoq40e","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 95 + mode: cv +- type: normalize + target: Log1P + params: + base: 1.8942568918726996 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 1319 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 515 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.648901104927063,all_total_runs:196|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.61%,False +71be997d-ff75-41b9-8a9f-1288c865f921(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4zpkroz8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ya78zvj,https://wandb.ai/xzy11632/dance-dev/sweeps/etsb2867,https://wandb.ai/xzy11632/dance-dev/sweeps/ul16ui5e","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4848484992980957,all_total_runs:572|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.57%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/v5hbb1ob|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/la5t6f69,https://wandb.ai/xzy11632/dance-dev/sweeps/6f1i7xhi,https://wandb.ai/xzy11632/dance-dev/sweeps/q7mkmn1w","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5454545617103577,all_total_runs:168|all_finished_runs:119|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.83%,False diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv index c694b27e..63f5d2af 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 +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check 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 +37,38 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",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 +",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/22ozz7li|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7af40uoa,https://wandb.ai/xzy11632/dance-dev/sweeps/go7b10ao,https://wandb.ai/xzy11632/dance-dev/sweeps/fogjho7h","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4149999916553498,all_total_runs:586|all_finished_runs:442|step2_total_runs:540|step2_finished_runs:402|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.43%,False 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: @@ -72,7 +103,37 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:77.62%,False +",1.0,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:77.62%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t544qsq4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mdst6ozg,https://wandb.ai/xzy11632/dance-dev/sweeps/5wuust9u,https://wandb.ai/xzy11632/dance-dev/sweeps/0jz8lzw5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:75.83%,False f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ki0b8xal,https://wandb.ai/xzy11632/dance-dev/sweeps/hzv5a32f,https://wandb.ai/xzy11632/dance-dev/sweeps/vvy7c4q9","- type: filter.gene target: FilterGenesPercentile params: {} @@ -98,7 +159,28 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.25999999046325684,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 +",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mb7tyn1a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tbsp1xsw,https://wandb.ai/xzy11632/dance-dev/sweeps/cx1inrux,https://wandb.ai/xzy11632/dance-dev/sweeps/ffjmt120","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:410|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:76.17%,False 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: @@ -131,7 +213,28 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.3165000081062317,all_total_runs:210|all_finished_runs:139|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:66.19%,False +",0.3165000081062317,all_total_runs:210|all_finished_runs:139|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:66.19%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nflips6b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k7q8z2pc,https://wandb.ai/xzy11632/dance-dev/sweeps/qcv9a0iw,https://wandb.ai/xzy11632/dance-dev/sweeps/252d5f2x","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.328000009059906,all_total_runs:600|all_finished_runs:436|step2_total_runs:540|step2_finished_runs:376|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:72.67%,False 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: @@ -166,7 +269,38 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:116|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:63.33%,False +",1.0,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:116|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:63.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wolfmyb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9mvl5sx5,https://wandb.ai/xzy11632/dance-dev/sweeps/9fpnmpj0,https://wandb.ai/xzy11632/dance-dev/sweeps/ryu2aorc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:586|all_finished_runs:451|step2_total_runs:540|step2_finished_runs:424|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.96%,False fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g8eo9qp4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/scpo55vu,https://wandb.ai/xzy11632/dance-dev/sweeps/jem8ckkq,https://wandb.ai/xzy11632/dance-dev/sweeps/qozeoh02","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -205,7 +339,38 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.24699999392032623,all_total_runs:178|all_finished_runs:172|step2_total_runs:118|step2_finished_runs:118|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:96.63%,False +",0.2469999939203262,all_total_runs:178|all_finished_runs:172|step2_total_runs:118|step2_finished_runs:118|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:96.63%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l86ls3ov|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lnfv32gq,https://wandb.ai/xzy11632/dance-dev/sweeps/2q0nk04q,https://wandb.ai/xzy11632/dance-dev/sweeps/16gfa1y6","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:448|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.83%,False 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: {} @@ -231,7 +396,27 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",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 +",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n58tiwn8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uhkwcf89,https://wandb.ai/xzy11632/dance-dev/sweeps/ucmsvu93,https://wandb.ai/xzy11632/dance-dev/sweeps/ws9k52zd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.39201876521110535,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False 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: @@ -270,7 +455,38 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.6612021923065186,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:108|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:18|finished_rate:78.10%,False +",0.6612021923065186,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:108|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:18|finished_rate:78.10%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0vghv5c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v0trjp3v,https://wandb.ai/xzy11632/dance-dev/sweeps/ghm1g52e,https://wandb.ai/xzy11632/dance-dev/sweeps/w5ig97h5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6502732038497925,all_total_runs:600|all_finished_runs:496|step2_total_runs:540|step2_finished_runs:437|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:82.67%,False 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: {} @@ -296,7 +512,29 @@ 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NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.931818187236786,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:383|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.83%,False 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: @@ -332,7 +570,38 @@ 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+ min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:432|step2_total_runs:540|step2_finished_runs:382|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.00%,False 3294d050-6eeb-4a00-b24c-71aacc9b777f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rq1aqcks|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w7fykvmx,https://wandb.ai/xzy11632/dance-dev/sweeps/7zg7srym,https://wandb.ai/xzy11632/dance-dev/sweeps/qgcvp9vy","- type: filter.gene target: FilterGenesPercentile params: {} @@ -358,7 +627,34 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.47699999809265137,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 +",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0e382wf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hemo1t7y,https://wandb.ai/xzy11632/dance-dev/sweeps/x2gofgl5,https://wandb.ai/xzy11632/dance-dev/sweeps/9cwz7pvl","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 8 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 6.12335875625052 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 8561 +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 909 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4634999930858612,all_total_runs:599|all_finished_runs:425|step2_total_runs:539|step2_finished_runs:367|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:70.95%,False 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+",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 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: @@ -419,7 +736,38 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.41350001096725464,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False 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: @@ -454,7 +802,27 @@ 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ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4420432150363922,all_total_runs:600|all_finished_runs:494|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.33%,False 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: {} @@ -480,4 +848,29 @@ 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type: normalize + target: Log1P + params: + base: 9.215313360927013 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 323 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6792452931404114,all_total_runs:600|all_finished_runs:486|step2_total_runs:540|step2_finished_runs:426|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.00%,False