From 9ded6a28c4a65cab234f149bfc51d3aae7d3de8e Mon Sep 17 00:00:00 2001 From: xzy Date: Sun, 12 Jan 2025 21:16:46 -0500 Subject: [PATCH] update ans --- examples/atlas/sweep_results/Blood_ans.csv | 1386 ++++++++++- examples/atlas/sweep_results/Brain_ans.csv | 2204 ++++++++++++++--- examples/atlas/sweep_results/Heart_ans.csv | 1856 ++++++++++++-- .../atlas/sweep_results/Intestine_ans.csv | 400 ++- examples/atlas/sweep_results/Kidney_ans.csv | 1389 ++++++++++- 5 files changed, 6667 insertions(+), 568 deletions(-) diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index e510bee5..70470681 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0rvmzkia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e9ndxdji,https://wandb.ai/xzy11632/dance-dev/sweeps/6lndzud2,https://wandb.ai/xzy11632/dance-dev/sweeps/kboc5b0g","- type: filter.gene target: FilterGenesPercentile params: {} @@ -20,7 +20,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.24699999392032623,all_total_runs:493|all_finished_runs:376|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene +",0.2469999939203262,all_total_runs:493|all_finished_runs:376|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -41,7 +41,57 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.24699999392032623 +",0.2469999939203262,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ydgm0lth|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/26noy2pa,https://wandb.ai/xzy11632/dance-dev/sweeps/2f5d1v5q,https://wandb.ai/xzy11632/dance-dev/sweeps/tzq3n1vg","- 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 +",0.2874999940395355,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,"- 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 +",0.2874999940395355,,,,,,, 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: @@ -102,7 +152,75 @@ fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.9113029837608336 +",0.9113029837608336,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4oz0cf4p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2da7462h,https://wandb.ai/xzy11632/dance-dev/sweeps/heevau0y,https://wandb.ai/xzy11632/dance-dev/sweeps/x6elpm0s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.9113029837608336,all_total_runs:168|all_finished_runs:118|step2_total_runs:150|step2_finished_runs:118|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:70.24%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.9113029837608336,,,,,,, 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: @@ -161,7 +279,75 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2524999976158142 +",0.2524999976158142,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/com9229b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ix6500p3,https://wandb.ai/xzy11632/dance-dev/sweeps/ui6izi4v,https://wandb.ai/xzy11632/dance-dev/sweeps/ensewqbq","- 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 +",0.27149999141693115,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene + 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 +",0.27149999141693115,,,,,,, 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: @@ -222,7 +408,57 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.1515000015497207 +",0.1515000015497207,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7s03jiel|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8hpba3db,https://wandb.ai/xzy11632/dance-dev/sweeps/byxqu78j,https://wandb.ai/xzy11632/dance-dev/sweeps/njf028o0","- type: filter.gene + target: FilterGenesPercentile + 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 +",0.17249999940395355,all_total_runs:210|all_finished_runs:106|step2_total_runs:150|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:50.48%,True,"- type: filter.gene + target: FilterGenesPercentile + 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 +",0.17249999940395355,,,,,,, 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: {} @@ -245,7 +481,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.16099999845027924,all_total_runs:493|all_finished_runs:331|step2_total_runs:450|step2_finished_runs:327|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:67.14%,False,"- type: filter.gene +",0.1609999984502792,all_total_runs:493|all_finished_runs:331|step2_total_runs:450|step2_finished_runs:327|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:67.14%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -267,4 +503,1138 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.16099999845027924 +",0.1609999984502792,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/viqji691|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/djfq0kbd,https://wandb.ai/xzy11632/dance-dev/sweeps/07jhuvad,https://wandb.ai/xzy11632/dance-dev/sweeps/um5kl8ak","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 99 + mode: rv +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 2010 + n_bins: 28 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 719 + 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 +",0.18799999356269836,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.17649999260902405,,,,,,, +84230ea4-998d-4aa8-8456-81dd54ce23af,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4lhkspy4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v3i9xvkp,https://wandb.ai/xzy11632/dance-dev/sweeps/4kznqqwz,https://wandb.ai/xzy11632/dance-dev/sweeps/ntv3k0kl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_counts + - max_cells + min_counts: 28 + min_cells: 0.01009194186360022 + max_counts: 0.9387079584289736 + max_cells: 0.9674538063359476 +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 4 + gmean_eps: 1 + n_genes: 2153 + n_cells: 100 + bin_size: 778 + bw_adjust: 4.348275785008059 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 4617 + n_bins: 12 + flavor: seurat +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7798573970794678,all_total_runs:510|all_finished_runs:358|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.20%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7673797011375427,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sjqz38be|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9nzex39q,https://wandb.ai/xzy11632/dance-dev/sweeps/w8vhof6g,https://wandb.ai/xzy11632/dance-dev/sweeps/hy70jugh","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + 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 +",0.7860962748527527,all_total_runs:210|all_finished_runs:153|step2_total_runs:150|step2_finished_runs:115|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:72.86%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7860962748527527,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8vsayaln|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ur4raslu,https://wandb.ai/xzy11632/dance-dev/sweeps/ou3vw3yu,https://wandb.ai/xzy11632/dance-dev/sweeps/ukajfztu","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 2.1103297221164885 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 898 + n_bins: 10 + flavor: seurat +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7709447415329769,all_total_runs:150|all_finished_runs:112|step2_total_runs:90|step2_finished_runs:73|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:20|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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 +",0.7700534759358288 +d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/68dze8s6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9p2fidft,https://wandb.ai/xzy11632/dance-dev/sweeps/gfb4afks,https://wandb.ai/xzy11632/dance-dev/sweeps/rfgdltml","- type: filter.gene + target: FilterGenesScanpyOrder + params: + 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 + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.372288316488266,all_total_runs:510|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:357|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:78.24%,False,"- type: filter.gene + 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: 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+ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58nyk24l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lv24d8vj,https://wandb.ai/xzy11632/dance-dev/sweeps/ad02sli6,https://wandb.ai/xzy11632/dance-dev/sweeps/735gpode","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3179999887943268,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3179999887943268,,,,,,, +bc260987-8ee5-4b6e-8773-72805166b3f7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bjkz4jyd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/u1a19m75,https://wandb.ai/xzy11632/dance-dev/sweeps/gfs40k7c,https://wandb.ai/xzy11632/dance-dev/sweeps/nrb4cgnm","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.32850000262260437,all_total_runs:210|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:67.62%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.32850000262260437,,,,,,, +bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gih5b907|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3h8b4ia7,https://wandb.ai/xzy11632/dance-dev/sweeps/nqd9ry7o,https://wandb.ai/xzy11632/dance-dev/sweeps/vkrxl804","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.3 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2457 + span: 0.4560040203055745 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 963 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2440000027418137,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:76.19%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + 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 +",0.23849999904632568,,,,,,, +d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/en37dusf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mc3gybd1,https://wandb.ai/xzy11632/dance-dev/sweeps/mo1fgrq0,https://wandb.ai/xzy11632/dance-dev/sweeps/algcvv9n","- type: filter.gene + 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,"- 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,,,,,,, diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index 245f6a91..549fb1f6 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -47,7 +47,55 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.48350000381469727,,,,,,, +",0.4835000038146972,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8iryrobo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ki8v82q5,https://wandb.ai/xzy11632/dance-dev/sweeps/v6ql1ykl,https://wandb.ai/xzy11632/dance-dev/sweeps/mvwab59k","- 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: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- 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: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5544999837875366 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: {} @@ -70,7 +118,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.32350000739097595,all_total_runs:510|all_finished_runs:391|step2_total_runs:450|step2_finished_runs:349|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:76.67%,False,"- type: filter.gene +",0.3235000073909759,all_total_runs:510|all_finished_runs:391|step2_total_runs:450|step2_finished_runs:349|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:76.67%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -92,7 +140,70 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.32350000739097595,,,,,,, +",0.3235000073909759,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/888d5wod|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uiwmt8u5,https://wandb.ai/xzy11632/dance-dev/sweeps/rfx86so6,https://wandb.ai/xzy11632/dance-dev/sweeps/5ik43ov8","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 379 + n_bins: 22 + flavor: seurat +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 268 + 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 +",0.3714999854564667,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3675000071525574 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: @@ -157,7 +268,57 @@ 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,,,,,,, +",0.5149999856948853,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lm5mwxkq,https://wandb.ai/xzy11632/dance-dev/sweeps/ortq51x9,https://wandb.ai/xzy11632/dance-dev/sweeps/lakwxgnu","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5440000295639038,all_total_runs:182|all_finished_runs:114|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.64%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5440000295639038 52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5awnfxur|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3bspph5d,https://wandb.ai/xzy11632/dance-dev/sweeps/4wkwaao0,https://wandb.ai/xzy11632/dance-dev/sweeps/gosfxkg9","- type: filter.gene target: FilterGenesPercentile params: {} @@ -204,7 +365,79 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5485000014305115,,,,,,, +",0.5485000014305115,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzh51eku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t7mnkajx,https://wandb.ai/xzy11632/dance-dev/sweeps/4n8979b9,https://wandb.ai/xzy11632/dance-dev/sweeps/pfvyypow","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 417 + min_cells: 0.0672634037707255 + max_counts: 0.9623011565598958 + max_cells: 0.9539584138468586 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9466 + span: 0.3327063122842796 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 985 + 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 +",0.5895000100135803,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5889999866485596 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 @@ -230,7 +463,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.35499998927116394,all_total_runs:510|all_finished_runs:396|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.65%,False,"- type: filter.gene +",0.3549999892711639,all_total_runs:510|all_finished_runs:396|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.65%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -251,50 +484,100 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.34049999713897705,,,,,,, -43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njrfx2sd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d0qeq1ft,https://wandb.ai/xzy11632/dance-dev/sweeps/ao28i16e,https://wandb.ai/xzy11632/dance-dev/sweeps/1tkopoue","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 9 - max_val: 99 - mode: var +",0.340499997138977,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: - min: 1 - max: 10 - gmean_eps: - min: 1 - max: 10 - n_genes: - min: 1000 - max: 3000 - n_cells: - values: - - null - - 1 - - 10 - - 100 - bin_size: - min: 300 - max: 800 - bw_adjust: - min: 1.0 - max: 5.0 + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: HighlyVariableGenesRawCount params: - min_disp: - min: 0.05 - max: 0.5 - max_disp: - min: 1.0 - max: 100.0 - min_mean: - min: 0.0 - max: 0.0125 + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989 +43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njrfx2sd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d0qeq1ft,https://wandb.ai/xzy11632/dance-dev/sweeps/ao28i16e,https://wandb.ai/xzy11632/dance-dev/sweeps/1tkopoue","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 99 + mode: var +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: + min: 1 + max: 10 + gmean_eps: + min: 1 + max: 10 + n_genes: + min: 1000 + max: 3000 + n_cells: + values: + - null + - 1 + - 10 + - 100 + bin_size: + min: 300 + max: 800 + bw_adjust: + min: 1.0 + max: 5.0 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: + min: 0.05 + max: 0.5 + max_disp: + min: 1.0 + max: 100.0 + min_mean: + min: 0.0 + max: 0.0125 max_mean: min: 3.0 max: 20.0 @@ -348,7 +631,75 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8654999732971191,,,,,,, +",0.8654999732971191,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i9nym2ro|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ugip15uh,https://wandb.ai/xzy11632/dance-dev/sweeps/azouushu,https://wandb.ai/xzy11632/dance-dev/sweeps/fdz2z220","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033,all_total_runs:210|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:67.14%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033 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: {} @@ -393,7 +744,75 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7515000104904175,,,,,,, +",0.7515000104904175,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7710000276565552,all_total_runs:182|all_finished_runs:122|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:67.03%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7710000276565552 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: @@ -590,38 +1009,106 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7699999809265137,,,,,,, -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 +",0.7699999809265137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t969ysm5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lkr2r2zq,https://wandb.ai/xzy11632/dance-dev/sweeps/kpnyhd83,https://wandb.ai/xzy11632/dance-dev/sweeps/tzy3vv3w","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 3 - max_val: 95 - mode: rv + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: - min: 1 - max: 10 - gmean_eps: - min: 1 - max: 10 - n_genes: - min: 1000 - max: 3000 - n_cells: - values: - - null - - 1 - - 10 - - 100 - bin_size: - min: 300 - max: 800 - bw_adjust: - min: 1.0 - max: 5.0 + target: Log1P + params: {} +- type: filter.gene + target: 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 +",0.7954999804496765,all_total_runs:179|all_finished_runs:124|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:17|step3_0_finished_runs:4|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.27%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7954999804496765 +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: + min_val: 3 + max_val: 95 + mode: rv +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: + min: 1 + max: 10 + gmean_eps: + min: 1 + max: 10 + n_genes: + min: 1000 + max: 3000 + n_cells: + values: + - null + - 1 + - 10 + - 100 + bin_size: + min: 300 + max: 800 + bw_adjust: + min: 1.0 + max: 5.0 - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: @@ -687,7 +1174,79 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4169999957084656,,,,,,, +",0.4169999957084656,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/17rooerg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k5eks81i,https://wandb.ai/xzy11632/dance-dev/sweeps/tjht44xq,https://wandb.ai/xzy11632/dance-dev/sweeps/jv70jolu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - min_counts + - max_cells + min_counts: 396 + min_cells: 0.08114426717926743 + max_counts: 0.90410781757729 + max_cells: 0.9639650300380824 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2843 + span: 0.22156016971664047 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 421 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4950000047683716 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: @@ -726,7 +1285,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.31200000643730164,all_total_runs:510|all_finished_runs:346|step2_total_runs:450|step2_finished_runs:343|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:67.84%,False,"- type: filter.gene +",0.3120000064373016,all_total_runs:510|all_finished_runs:346|step2_total_runs:450|step2_finished_runs:343|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:67.84%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -748,7 +1307,60 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2800000011920929,,,,,,, +",0.2800000011920929,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hkkcbz82|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cmx0xd8z,https://wandb.ai/xzy11632/dance-dev/sweeps/x6c34300,https://wandb.ai/xzy11632/dance-dev/sweeps/5l0emjk0","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.2193874739513255 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 153 + top: false + mode: var +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 327 + feat_norm_mode: normalize +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3400000035762787,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:73.47%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3395000100135803 9372df2d-13d6-4fac-980b-919a5b7eb483,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p5149kgi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0r0wmg1f,https://wandb.ai/xzy11632/dance-dev/sweeps/549m8ddo,https://wandb.ai/xzy11632/dance-dev/sweeps/envt6ozk","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -813,31 +1425,58 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4639999866485596,,,,,,, -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 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+",0.4934999942779541,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:78.10%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD +- 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 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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: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.45500001311302185,all_total_runs:493|all_finished_runs:322|step2_total_runs:450|step2_finished_runs:301|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:65.31%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} 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params: out: feature.cell log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.5084999799728394,all_total_runs:510|all_finished_runs:319|step2_total_runs:450|step2_finished_runs:297|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.55%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 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bw_adjust: 1.1228665082399538 - type: filter.gene - target: FilterGenesRegression - params: - method: enclasc - num_genes: 9677 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell - target: FeatureCellPlaceHolder 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 -",0.5736386179924011,all_total_runs:493|all_finished_runs:342|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:69.37%,False,"- type: filter.gene 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0.3285327702328724 + n_top_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.525801956653595,all_total_runs:493|all_finished_runs:327|step2_total_runs:450|step2_finished_runs:289|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:66.33%,False,"- type: filter.gene +",0.8090000152587891,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene target: 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target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4431818127632141,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5130813717842102,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e8vlk083,https://wandb.ai/xzy11632/dance-dev/sweeps/mwggo6ee,https://wandb.ai/xzy11632/dance-dev/sweeps/33pi0zc3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5130813717842102,all_total_runs:182|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.27%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5130813717842102 +f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xzxk78ak|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n3z93yct,https://wandb.ai/xzy11632/dance-dev/sweeps/4arisd9h,https://wandb.ai/xzy11632/dance-dev/sweeps/u8gs5iqg","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 2921 + top: true + mode: cv +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 237 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6538461446762085,all_total_runs:493|all_finished_runs:370|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:75.05%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.64891517162323,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4voqq7a0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6para2wq,https://wandb.ai/xzy11632/dance-dev/sweeps/cabldqak,https://wandb.ai/xzy11632/dance-dev/sweeps/s2xpuetf","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6637080907821655 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target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4739454090595245,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zmxfvz4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5pamm1zp,https://wandb.ai/xzy11632/dance-dev/sweeps/a0z7ol9w,https://wandb.ai/xzy11632/dance-dev/sweeps/e3io8n98","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5260545611381531,all_total_runs:210|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.52%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5260545611381531 +ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9sbul8yi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/csltl4qv,https://wandb.ai/xzy11632/dance-dev/sweeps/vevuukvb,https://wandb.ai/xzy11632/dance-dev/sweeps/yky0bz21","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.468804657459259,all_total_runs:493|all_finished_runs:368|step2_total_runs:450|step2_finished_runs:345|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.65%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.468804657459259,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xghzky,https://wandb.ai/xzy11632/dance-dev/sweeps/pwxoaixd,https://wandb.ai/xzy11632/dance-dev/sweeps/1yosmcdd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.48571428656578064 +07760522-707a-4a1c-8891-dbd1226d6b27,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/flsm88dc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ggwltzko,https://wandb.ai/xzy11632/dance-dev/sweeps/6o4yy577,https://wandb.ai/xzy11632/dance-dev/sweeps/rq6r99by","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + 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 +",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + 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 +",1.0 +146216e1-ec30-4fee-a1fb-25defe801e2d,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 +700aed19-c16e-4ba8-9191-07da098a8626,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9vvinymt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0f6156l,https://wandb.ai/xzy11632/dance-dev/sweeps/fmt50h6n,https://wandb.ai/xzy11632/dance-dev/sweeps/pbhkpdsh","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,all_total_runs:194|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:18|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:74.74%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 +9813a1d4-d107-459e-9b2e-7687be935f69,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/piw9m0r4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/83fzgznu,https://wandb.ai/xzy11632/dance-dev/sweeps/k12d4bb4,https://wandb.ai/xzy11632/dance-dev/sweeps/elc05kea","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + 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 +",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,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + 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 +",1.0 diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index ae6e9478..ba701e5d 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res 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: @@ -59,7 +59,57 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.948853611946106 +",0.948853611946106,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c1y9hl9c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9gz3pmi2,https://wandb.ai/xzy11632/dance-dev/sweeps/pwb5373a,https://wandb.ai/xzy11632/dance-dev/sweeps/4kab8419","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.9506173133850098 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: @@ -90,7 +140,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.38749998807907104,all_total_runs:493|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:73.02%,False,"- type: filter.gene +",0.387499988079071,all_total_runs:493|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:73.02%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -112,7 +162,61 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.34200000762939453 +",0.3420000076293945,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gaurbw0r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5luhlhr8,https://wandb.ai/xzy11632/dance-dev/sweeps/6cvflsss,https://wandb.ai/xzy11632/dance-dev/sweeps/tdxjnsvf","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9960 + top: true + mode: rv +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 280 + feat_norm_mode: normalize +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3995000123977661 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: @@ -173,6 +277,74 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type +",0.9725000262260436,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qfzblohn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fs7r3zpn,https://wandb.ai/xzy11632/dance-dev/sweeps/cdk9uk18,https://wandb.ai/xzy11632/dance-dev/sweeps/0zjjl1n1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.9725000262260436,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type ",0.9725000262260436 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 @@ -227,7 +399,75 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6359999775886536 +",0.6359999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9nsespwt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fckv2ie6,https://wandb.ai/xzy11632/dance-dev/sweeps/23djawcn,https://wandb.ai/xzy11632/dance-dev/sweeps/nt9416y1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6399999856948853 c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i94przah|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7ruaq9f1,https://wandb.ai/xzy11632/dance-dev/sweeps/o1o45k7l,https://wandb.ai/xzy11632/dance-dev/sweeps/lnl0snl5","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -274,34 +514,41 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.836448609828949 -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 +",0.836448609828949,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n20e9pvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ahwfxqzw,https://wandb.ai/xzy11632/dance-dev/sweeps/kxkron6u,https://wandb.ai/xzy11632/dance-dev/sweeps/87hdz0un","- 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: - mode: standardize - eps: 0.1 + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 6889 - top: true - mode: var + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 107 - feat_norm_mode: l2 + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.25,all_total_runs:493|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:78.90%,False,"- type: filter.gene +",0.8317757248878479,all_total_runs:210|all_finished_runs:148|step2_total_runs:150|step2_finished_runs:114|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:15|finished_rate:70.48%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -314,54 +561,68 @@ d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.2195000052452087 -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 +",0.8317757248878479 +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 - target: NormalizeTotal + target: ScaleFeature params: - target_sum: 10000 - max_fraction: 1 + mode: standardize + eps: 0.1 - type: filter.gene target: FilterGenesTopK params: - num_genes: 399 - top: false - mode: rv + num_genes: 6889 + top: true + mode: var - type: feature.cell - target: CellSVD + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 846 + n_components: 107 + feat_norm_mode: l2 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.265500009059906,all_total_runs:510|all_finished_runs:410|step2_total_runs:450|step2_finished_runs:350|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.39%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.25,all_total_runs:493|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:78.90%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -371,46 +632,52 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2610000073909759 -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 +",0.2195000052452087,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dtijolpo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kq7ng1ob,https://wandb.ai/xzy11632/dance-dev/sweeps/ynfxrozp,https://wandb.ai/xzy11632/dance-dev/sweeps/z56oz4tj","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - min_counts - max_cells - - min_cells + - min_counts - max_counts - min_counts: 324 - min_cells: 0.0994897883945216 - max_counts: 0.9671792921176364 - max_cells: 0.952327145046576 + - min_cells + min_counts: 65 + min_cells: 0.03832924256867298 + max_counts: 0.984514560421666 + max_cells: 0.9614458802125864 - type: normalize - target: NormalizePlaceHolder + target: ScaleFeature + params: + mode: l2 + eps: 0.5 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - method: seurat3 - num_genes: 3947 + n_top_genes: 4223 + span: 0.5672352308267095 - type: feature.cell - target: GaussRandProjFeature + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 392 + n_components: 569 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.6265000104904175,all_total_runs:510|all_finished_runs:388|step2_total_runs:450|step2_finished_runs:328|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.08%,False,"- type: filter.gene +",0.2565000057220459,all_total_runs:210|all_finished_runs:154|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:8|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:73.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -423,7 +690,7 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: ScaleFeature params: {} - type: filter.gene target: HighlyVariableGenesRawCount @@ -433,21 +700,70 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + 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-",0.32499998807907104,all_total_runs:453|all_finished_runs:348|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:1|step3_0_finished_runs:0|step3_1_total_runs:1|step3_1_finished_runs:0|step3_2_total_runs:1|step3_2_finished_runs:0|finished_rate:76.82%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.29249998927116394,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene target: FilterGenesTopK params: @@ -481,46 +799,48 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.32499998807907104 -fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- type: filter.gene +",0.29249998927116394 +e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene target: FilterGenesScanpyOrder params: order: - min_counts + - max_cells - min_cells - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + min_counts: 324 + min_cells: 0.0994897883945216 + max_counts: 0.9671792921176364 + max_cells: 0.952327145046576 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: NormalizePlaceHolder - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: - num_genes: 3000 + method: seurat3 + num_genes: 3947 - type: feature.cell + target: GaussRandProjFeature params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + n_components: 392 - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6654999852180481,all_total_runs:453|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:369|step3_0_total_runs:1|step3_0_finished_runs:0|step3_1_total_runs:1|step3_1_finished_runs:0|step3_2_total_runs:1|step3_2_finished_runs:0|finished_rate:81.46%,False,"- type: filter.gene 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feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.29750001430511475,all_total_runs:459|all_finished_runs:352|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:76.69%,False,"- type: filter.gene +",0.6290000081062317,all_total_runs:196|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:61.22%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -597,61 +917,58 @@ 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target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.6359999775886536,all_total_runs:476|all_finished_runs:354|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.37%,False,"- type: filter.gene +",0.3880000114440918,all_total_runs:196|all_finished_runs:154|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:16|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:78.57%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: Log1P params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.6359999775886536 -ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fadl6x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f6na6k1n,https://wandb.ai/xzy11632/dance-dev/sweeps/1hwk0ec1,https://wandb.ai/xzy11632/dance-dev/sweeps/g73ajpao","- type: filter.gene +",0.3880000114440918 +fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- 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target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6775000095367432,all_total_runs:210|all_finished_runs:188|step2_total_runs:150|step2_finished_runs:128|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:89.52%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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FilterGenesPercentile + params: + min_val: 10 + max_val: 99 + mode: rv +- type: normalize + target: Log1P + params: + base: 9.18544800269841 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: 0.4075238200301367 + max_disp: 41.50678547261833 + min_mean: 0.00843552051034461 + max_mean: 8.182103499798425 + n_bins: 29 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 745 + 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 +",0.34450000524520874,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3434999883174896 +65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n9pv9var|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uox7hj7b,https://wandb.ai/xzy11632/dance-dev/sweeps/lghef4b7,https://wandb.ai/xzy11632/dance-dev/sweeps/16q0x97m","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 96 + mode: rv +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.3 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8619 + top: false + mode: cv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 703 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3454999923706054,all_total_runs:510|all_finished_runs:405|step2_total_runs:450|step2_finished_runs:346|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.41%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + 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type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6359999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j4vz4ws5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tecc0rt6,https://wandb.ai/xzy11632/dance-dev/sweeps/jtni6g54,https://wandb.ai/xzy11632/dance-dev/sweeps/uu6v00z6","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 95 + mode: rv +- type: normalize + target: Log1P + params: + base: 6.969521165170953 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 2223 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 167 + 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 +",0.6460000276565552,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:80.95%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + 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 +",0.6455000042915344 +ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fadl6x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f6na6k1n,https://wandb.ai/xzy11632/dance-dev/sweeps/1hwk0ec1,https://wandb.ai/xzy11632/dance-dev/sweeps/g73ajpao","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_counts + - min_cells + - max_cells + min_counts: 413 + min_cells: 0.07306060707222754 + max_counts: 0.9906711226720064 + max_cells: 0.9967104990967668 +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 4 + gmean_eps: 1 + n_genes: 2400 + n_cells: null + bin_size: 538 + bw_adjust: 2.433119961706298 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9618 + top: true + mode: var +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3149999976158142,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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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+",1.0,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:81.90%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 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+",1.0,all_total_runs:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 +bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/frisdu4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fywjox,https://wandb.ai/xzy11632/dance-dev/sweeps/dz23lu62,https://wandb.ai/xzy11632/dance-dev/sweeps/g0d29txd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 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+",1.0,all_total_runs:182|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.88%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 +f7995301-7551-4e1d-8396-ffe3c9497ace,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,all_total_runs:210|all_finished_runs:149|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.95%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index 512e728a..7c8388f9 100644 --- a/examples/atlas/sweep_results/Intestine_ans.csv +++ b/examples/atlas/sweep_results/Intestine_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res 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: @@ -29,7 +29,7 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.44999998807907104,all_total_runs:510|all_finished_runs:408|step2_total_runs:450|step2_finished_runs:349|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:80.00%,False,"- type: filter.gene +",0.449999988079071,all_total_runs:510|all_finished_runs:408|step2_total_runs:450|step2_finished_runs:349|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:80.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -59,7 +59,61 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.44999998807907104 +",0.449999988079071,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mvhlvdxl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0zk0bilm,https://wandb.ai/xzy11632/dance-dev/sweeps/z9xnldun,https://wandb.ai/xzy11632/dance-dev/sweeps/xctbkm4s","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.1 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8722 + top: true + mode: sum +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 170 + 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 +",0.4494999945163727,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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.44699999690055847 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: @@ -122,7 +176,74 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4474999904632568 +",0.4474999904632568,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dedm26ib|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/765195mr,https://wandb.ai/xzy11632/dance-dev/sweeps/4f58apli,https://wandb.ai/xzy11632/dance-dev/sweeps/fvoqt6jw","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 7 + max_val: 96 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.3 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8455 + top: false + mode: cv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 747 + 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 +",0.4900000095367432,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4889999926090241 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: {} @@ -145,7 +266,7 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.35065943002700806,all_total_runs:476|all_finished_runs:359|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:75.42%,False,"- type: filter.gene +",0.350659430027008,all_total_runs:476|all_finished_runs:359|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:75.42%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -167,7 +288,79 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.35065943002700806 +",0.350659430027008,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2ygbd0g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wa5xd2jo,https://wandb.ai/xzy11632/dance-dev/sweeps/njbvga25,https://wandb.ai/xzy11632/dance-dev/sweeps/1ueyprxc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - max_cells + - min_counts + - min_cells + min_counts: 329 + min_cells: 0.006752469050480836 + max_counts: 0.9772984468022424 + max_cells: 0.97184145489983 +- type: normalize + target: Log1P + params: + base: 1.6360071938209937 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3958 + n_bins: 13 + flavor: seurat +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 500 + 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 +",0.3653995394706726,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.36229634284973145 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: {} @@ -191,7 +384,7 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.41360294818878174,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- type: filter.gene +",0.4136029481887817,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -214,7 +407,79 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.41360294818878174 +",0.4136029481887817,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpjhyj9q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wyv5vmis,https://wandb.ai/xzy11632/dance-dev/sweeps/8qobi3e5,https://wandb.ai/xzy11632/dance-dev/sweeps/jkwnilze","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_counts + - min_cells + - max_cells + min_counts: 135 + min_cells: 0.0762385917181959 + max_counts: 0.9889394686374898 + max_cells: 0.9923759873179532 +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4877 + span: 0.12580818609215275 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 996 + 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 +",0.450367659330368,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4485294222831726 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: @@ -277,7 +542,72 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4715000092983246 +",0.4715000092983246,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n6knsnsf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6opqehxd,https://wandb.ai/xzy11632/dance-dev/sweeps/2xlryh6l,https://wandb.ai/xzy11632/dance-dev/sweeps/lz3o81dv","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 96 + mode: var +- type: normalize + target: Log1P + params: + base: 3.4792913454298 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 7286 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 770 + 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 +",0.512499988079071,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5109999775886536 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: @@ -342,4 +672,54 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5298858284950256 +",0.5298858284950256,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vim4nmzr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tp4lwwq5,https://wandb.ai/xzy11632/dance-dev/sweeps/amhduqwq,https://wandb.ai/xzy11632/dance-dev/sweeps/fmj9uxc4","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5648086071014404,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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5648086071014404 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index a54615ac..50ef0b0a 100644 --- a/examples/atlas/sweep_results/Kidney_ans.csv +++ b/examples/atlas/sweep_results/Kidney_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res 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: {} @@ -43,7 +43,57 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2630000114440918 +",0.2630000114440918,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/whvpjn2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rq2xo8wj,https://wandb.ai/xzy11632/dance-dev/sweeps/jwo7gft3,https://wandb.ai/xzy11632/dance-dev/sweeps/dbka8jop","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.27300000190734863,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.27300000190734863 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: {} @@ -90,7 +140,57 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5335000157356262 +",0.5335000157356262,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/r1y7gnbt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8z8b7s39,https://wandb.ai/xzy11632/dance-dev/sweeps/xv3zpnqo,https://wandb.ai/xzy11632/dance-dev/sweeps/9rlhjyjr","- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5799999833106995 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: @@ -151,7 +251,75 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5565000176429749 +",0.5565000176429749,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/a6rgr8w4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ssb28ejh,https://wandb.ai/xzy11632/dance-dev/sweeps/thvgw7zh,https://wandb.ai/xzy11632/dance-dev/sweeps/0a06jn63","- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + 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,"- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5964999794960022 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: @@ -222,7 +390,75 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6965000033378601 +",0.6965000033378601,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hbvj1oip|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xq06tu32,https://wandb.ai/xzy11632/dance-dev/sweeps/yiz263kv,https://wandb.ai/xzy11632/dance-dev/sweeps/b9zvve4u","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7020000219345093,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.7020000219345093 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 @@ -269,7 +505,79 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.273499995470047 +",0.273499995470047,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ltca3oim|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9oulbho9,https://wandb.ai/xzy11632/dance-dev/sweeps/ko18r05s,https://wandb.ai/xzy11632/dance-dev/sweeps/zg1qkqy0","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 269 + min_cells: 0.04017237612650692 + max_counts: 0.981578887268918 + max_cells: 0.9529854552953828 +- type: normalize + target: Log1P + params: + base: 1.0126842046864493 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3607 + n_bins: 30 + flavor: seurat +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 423 + 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 +",0.2815000116825104,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,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2809999883174896 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: {} @@ -291,7 +599,7 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22699999809265137,all_total_runs:510|all_finished_runs:398|step2_total_runs:450|step2_finished_runs:341|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:78.04%,False,"- type: filter.gene +",0.2269999980926513,all_total_runs:510|all_finished_runs:398|step2_total_runs:450|step2_finished_runs:341|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:78.04%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -312,7 +620,61 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22699999809265137 +",0.2269999980926513,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cdcv6mna|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ne54nu6k,https://wandb.ai/xzy11632/dance-dev/sweeps/0z8zj8do,https://wandb.ai/xzy11632/dance-dev/sweeps/bi91nl8w","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 4264 + n_bins: 16 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 909 + 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 +",0.25,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,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.24950000643730164 9df60c57-fdf3-4e93-828e-fe9303f20438,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c0t2tf8r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nychgnxo,https://wandb.ai/xzy11632/dance-dev/sweeps/393j00a1","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -368,7 +730,60 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2300000041723251 +",0.2300000041723251,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m28fu5e4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rd136al3,https://wandb.ai/xzy11632/dance-dev/sweeps/o1v4t50e,https://wandb.ai/xzy11632/dance-dev/sweeps/j5ef3unu","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 5123 + span: 0.4427554467674908 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 204 + 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 +",0.2639999985694885,all_total_runs:210|all_finished_runs:151|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.90%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2615000009536743 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: @@ -408,7 +823,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.42899999022483826,all_total_runs:510|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:338|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.59%,False,"- type: filter.gene +",0.4289999902248382,all_total_runs:510|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:338|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.59%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -429,7 +844,75 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.382999986410141 +",0.382999986410141,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1a0xicia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wunz1pqq,https://wandb.ai/xzy11632/dance-dev/sweeps/0n5dswxy,https://wandb.ai/xzy11632/dance-dev/sweeps/13if0wtd","- type: filter.gene + 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.43849998712539673,all_total_runs:183|all_finished_runs:139|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:75.96%,False,"- type: filter.gene + 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.43849998712539673 32b9bdce-2481-4c85-ba1b-6ad5fcea844c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wimg2shl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4y52ea9r,https://wandb.ai/xzy11632/dance-dev/sweeps/i3uqbr79,https://wandb.ai/xzy11632/dance-dev/sweeps/rfefu9nm","- type: filter.gene target: FilterGenesPercentile params: {} @@ -474,7 +957,57 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2055000066757202 +",0.2055000066757202,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8arpp0bg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kutscmkt,https://wandb.ai/xzy11632/dance-dev/sweeps/d1iadk7m,https://wandb.ai/xzy11632/dance-dev/sweeps/87cnxjeb","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.23549999296665192,all_total_runs:210|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:75.71%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.23549999296665192 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: @@ -508,7 +1041,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20499999821186063,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- type: filter.gene +",0.2049999982118606,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -538,7 +1071,57 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.19949999451637268 +",0.1994999945163726,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sk7ynfj9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/64bshk8k,https://wandb.ai/xzy11632/dance-dev/sweeps/y9l1vpb7,https://wandb.ai/xzy11632/dance-dev/sweeps/v6t2nb4k","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2294999957084656,all_total_runs:196|all_finished_runs:151|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:77.04%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2294999957084656 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: @@ -600,43 +1183,41 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.870917558670044 -6a30bf44-c490-41ac-965b-0bb58432b10a,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hn06vbc0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f0pf2vll,https://wandb.ai/xzy11632/dance-dev/sweeps/yd0s5ou6,https://wandb.ai/xzy11632/dance-dev/sweeps/8spua97g","- type: filter.gene +",0.870917558670044,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qc59eog9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/539khgz0,https://wandb.ai/xzy11632/dance-dev/sweeps/afbpb46d,https://wandb.ai/xzy11632/dance-dev/sweeps/mn356re7","- type: filter.gene target: FilterGenesScanpyOrder params: order: + - min_counts - min_cells - - max_cells - max_counts - - min_counts - min_counts: 255 - min_cells: 0.01511082364107167 - max_counts: 0.9497483701603496 - max_cells: 0.9750075182668252 + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P - params: - base: 8.039331292267493 + target: ScaleFeature + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 9640 - top: true - mode: var + n_top_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 768 - feat_norm_mode: l2 + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.2777777910232544,all_total_runs:510|all_finished_runs:438|step2_total_runs:450|step2_finished_runs:378|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.88%,False,"- type: filter.gene +",0.8755832314491272,all_total_runs:210|all_finished_runs:155|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:73.81%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -649,7 +1230,77 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8755832314491272 +6a30bf44-c490-41ac-965b-0bb58432b10a,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hn06vbc0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f0pf2vll,https://wandb.ai/xzy11632/dance-dev/sweeps/yd0s5ou6,https://wandb.ai/xzy11632/dance-dev/sweeps/8spua97g","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 255 + min_cells: 0.01511082364107167 + max_counts: 0.9497483701603496 + max_cells: 0.9750075182668252 +- type: normalize + target: Log1P + params: + base: 8.039331292267493 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9640 + top: true + mode: var +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 768 + feat_norm_mode: l2 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2777777910232544,all_total_runs:510|all_finished_runs:438|step2_total_runs:450|step2_finished_runs:378|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.88%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount @@ -666,6 +1317,74 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type +",0.2222222238779068,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nbuoq984|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v8k3ecyi,https://wandb.ai/xzy11632/dance-dev/sweeps/i30iteaa,https://wandb.ai/xzy11632/dance-dev/sweeps/wc6rut0d","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + 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 +",0.2222222238779068,all_total_runs:215|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:126|step3_0_total_runs:25|step3_0_finished_runs:24|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.07%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + 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 ",0.2222222238779068 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 @@ -711,7 +1430,69 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3564929664134979 +",0.3564929664134979,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6zzg3aev|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ti1w2l2i,https://wandb.ai/xzy11632/dance-dev/sweeps/en9xlysw,https://wandb.ai/xzy11632/dance-dev/sweeps/cbj2rjp1","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.700035243593383 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 460 + top: true + mode: var +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 520 + feat_norm_mode: standardize +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3655914068222046,all_total_runs:209|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:19|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:78.47%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3647642731666565 20d87640-4be8-487f-93d4-dce38378d00f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ajwsfjty|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m73ege01,https://wandb.ai/xzy11632/dance-dev/sweeps/tnm2ji4l,https://wandb.ai/xzy11632/dance-dev/sweeps/acrse11l","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -758,7 +1539,75 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2620115280151367 +",0.2620115280151367,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x8uut7hm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zhpozwl1,https://wandb.ai/xzy11632/dance-dev/sweeps/i43sxcxt,https://wandb.ai/xzy11632/dance-dev/sweeps/vscrpbjl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.29468289017677307,all_total_runs:209|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:19|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:75.12%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.29468289017677307 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 @@ -789,37 +1638,208 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3394160568714142,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gfl9vtdc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wqi6cztc,https://wandb.ai/xzy11632/dance-dev/sweeps/eng7tqc9,https://wandb.ai/xzy11632/dance-dev/sweeps/rz1nmsox","- 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.36496350169181824,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:79.05%,False,"- type: filter.gene + 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: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.36496350169181824 +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: + min_val: 5 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 4.533975561756228 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 4165 + top: false + mode: cv +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2730000019073486,all_total_runs:493|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:340|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.08%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2630000114440918,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fv5txyhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gftuks1f,https://wandb.ai/xzy11632/dance-dev/sweeps/vhtoxock,https://wandb.ai/xzy11632/dance-dev/sweeps/1qsjz3ai","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2759999930858612,all_total_runs:196|all_finished_runs:146|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:74.49%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.3394160568714142 -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 +",0.2759999930858612 +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: - min_val: 5 - max_val: 98 - mode: sum + order: + - max_counts + - min_cells + - min_counts + - max_cells + min_counts: 97 + min_cells: 0.008669870041697503 + max_counts: 0.9782460305842908 + max_cells: 0.9930432468421152 - type: normalize - target: Log1P - params: - base: 4.533975561756228 + target: NormalizePlaceHolder - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: - num_genes: 4165 - top: false - mode: cv + method: scmap + num_genes: 9555 - type: feature.cell target: FeatureCellPlaceHolder params: @@ -831,60 +1851,73 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.27300000190734863,all_total_runs:493|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:340|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.08%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.4275000095367432,all_total_runs:493|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.48%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2630000114440918 -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 +",0.3790000081062317,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/02te0za8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8narfff8,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2dfvtp,https://wandb.ai/xzy11632/dance-dev/sweeps/1deo7tn9","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - max_counts - - min_cells - min_counts + - min_cells + - max_counts - max_cells - min_counts: 97 - min_cells: 0.008669870041697503 - max_counts: 0.9782460305842908 - max_cells: 0.9930432468421152 + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: ScaleFeature + params: {} - type: filter.gene target: FilterGenesRegression params: - method: scmap - num_genes: 9555 + num_genes: 3000 - type: feature.cell - target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.4275000095367432,all_total_runs:493|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.48%,False,"- type: filter.gene +",0.4375,all_total_runs:182|all_finished_runs:138|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:6|step3_2_finished_runs:0|finished_rate:75.82%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -897,11 +1930,10 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -910,13 +1942,16 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell label_channel: cell_type -",0.3790000081062317 +",0.4375 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: @@ -948,7 +1983,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22499999403953552,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.18%,False,"- type: filter.gene +",0.2249999940395355,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.18%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -979,7 +2014,59 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22499999403953552 +",0.2249999940395355,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h267r9gw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gsf3qy1c,https://wandb.ai/xzy11632/dance-dev/sweeps/dzembwwg,https://wandb.ai/xzy11632/dance-dev/sweeps/iygud7ig","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.24050000309944153,all_total_runs:182|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.23%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.24050000309944153 2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/098iecnp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0a785nvw,https://wandb.ai/xzy11632/dance-dev/sweeps/05d33k6p,https://wandb.ai/xzy11632/dance-dev/sweeps/a878cw3h","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1033,7 +2120,75 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.45897436141967773 +",0.4589743614196777,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1het6p1z,https://wandb.ai/xzy11632/dance-dev/sweeps/7z429hba,https://wandb.ai/xzy11632/dance-dev/sweeps/81ikkh2i","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5,all_total_runs:182|all_finished_runs:134|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:73.63%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5 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: @@ -1098,4 +2253,72 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.870917558670044 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