diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index c2e27da1..206b7a70 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 +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check 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 +20,32 @@ 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 +",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,"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,,,,, 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: @@ -51,7 +76,41 @@ fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.9113029837608336,all_total_runs:510|all_finished_runs:347|step2_total_runs:450|step2_finished_runs:329|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:16|finished_rate:68.04%,False +",0.9113029837608336,all_total_runs:510|all_finished_runs:347|step2_total_runs:450|step2_finished_runs:329|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:16|finished_rate:68.04%,False,"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,,,,, 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: @@ -80,7 +139,41 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2565000057220459,all_total_runs:510|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:322|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.90%,False +",0.2565000057220459,all_total_runs:510|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:322|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.90%,False,"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,,,,, 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: @@ -110,7 +203,32 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.1655000001192093,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 +",0.1655000001192093,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,"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,,,,, 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: {} @@ -133,4 +251,588 @@ 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 +",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,"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,,,,, +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,"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,"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 +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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/osyfv0bk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sni6qvye,https://wandb.ai/xzy11632/dance-dev/sweeps/zqf37ih0,https://wandb.ai/xzy11632/dance-dev/sweeps/9vy9sc81","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.1 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 7305 + top: true + mode: sum +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 188 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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cell_type +",0.3631910426871938,all_total_runs:150|all_finished_runs:130|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:86.67%,False +71be997d-ff75-41b9-8a9f-1288c865f921,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3hrf2wbb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d6vpumby,https://wandb.ai/xzy11632/dance-dev/sweeps/4ewws3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/iuubdwht","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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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 +",0.30300000309944153,all_total_runs:510|all_finished_runs:378|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.12%,False,,,,,,,,,, +01209dce-3575-4bed-b1df-129f57fbc031,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cjdtc2ag|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fzjbv8p0,https://wandb.ai/xzy11632/dance-dev/sweeps/gtz5viph,https://wandb.ai/xzy11632/dance-dev/sweeps/4l2hy0fx","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3709999918937683,all_total_runs:210|all_finished_runs:165|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:9|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:78.57%,False,,,,, +055ca631-6ffb-40de-815e-b931e10718c0,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51smdbay|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mhvqib1h,https://wandb.ai/xzy11632/dance-dev/sweeps/qpmixdis,https://wandb.ai/xzy11632/dance-dev/sweeps/j2p0o87d","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 2.12228660428801 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 4984 + n_bins: 29 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 872 + 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 +",0.2179999947547913,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.33%,False,,,,, +2a498ace-872a-4935-984b-1afa70fd9886,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51z2kmba|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/exnltfk3,https://wandb.ai/xzy11632/dance-dev/sweeps/l5tne1kz,https://wandb.ai/xzy11632/dance-dev/sweeps/5v2hyx8m","- type: filter.gene + target: FilterGenesPercentile + 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 +",0.21050000190734863,all_total_runs:210|all_finished_runs:170|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:80.95%,False,,,,, 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+",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,,,,, +4c4cd77c-8fee-4836-9145-16562a8782fe,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9despcsl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ezmsqc0q,https://wandb.ai/xzy11632/dance-dev/sweeps/wplvjtme,https://wandb.ai/xzy11632/dance-dev/sweeps/c3we0q6d","- type: filter.gene + target: FilterGenesPercentile + 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 +",0.27300000190734863,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:10|finished_rate:78.57%,False,,,,, +ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58nyk24l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lv24d8vj,https://wandb.ai/xzy11632/dance-dev/sweeps/ad02sli6,https://wandb.ai/xzy11632/dance-dev/sweeps/735gpode","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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,,,,, +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,,,,, +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,,,,, +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,,,,, diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index 264410d5..65011f78 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -25,7 +25,31 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5099999904632568,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:348|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:2|finished_rate:72.35%,False,,,,, +",0.5099999904632568,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:348|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:2|finished_rate:72.35%,False,"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 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: {} @@ -48,7 +72,36 @@ 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,,,,, +",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,"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 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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 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: {} @@ -105,7 +183,45 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5485000014305115,all_total_runs:476|all_finished_runs:348|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:73.11%,False,,,,, +",0.5485000014305115,all_total_runs:476|all_finished_runs:348|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:73.11%,False,"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 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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 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: @@ -206,7 +347,41 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8744999766349792,all_total_runs:510|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,,,,, +",0.8744999766349792,all_total_runs:510|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"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 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: {} @@ -229,7 +404,41 @@ 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,all_total_runs:510|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:63.33%,False,,,,, +",0.7515000104904175,all_total_runs:510|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:321|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:63.33%,False,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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 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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 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: @@ -405,7 +648,45 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4715000092983246,all_total_runs:486|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:309|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:4|step3_1_finished_runs:3|step3_2_total_runs:12|step3_2_finished_runs:11|finished_rate:66.46%,False,,,,, +",0.4715000092983246,all_total_runs:486|all_finished_runs:323|step2_total_runs:450|step2_finished_runs:309|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:4|step3_1_finished_runs:3|step3_2_total_runs:12|step3_2_finished_runs:11|finished_rate:66.46%,False,"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 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label_channel: cell_type +",0.4934999942779541,all_total_runs:210|all_finished_runs:164|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:78.10%,False 94c41723-b2c4-4b59-a49a-64c9b851903e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fxkuovhw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5je4ee5m,https://wandb.ai/xzy11632/dance-dev/sweeps/u8uc0m16,https://wandb.ai/xzy11632/dance-dev/sweeps/ljbofqhi","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -501,7 +835,32 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: feature.cell label_channel: cell_type 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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 +",0.5055000185966492,all_total_runs:182|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.48%,False c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w1v0bvs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8s7p9moq,https://wandb.ai/xzy11632/dance-dev/sweeps/on8m4hqo,https://wandb.ai/xzy11632/dance-dev/sweeps/ssor6fhj","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -533,7 +892,33 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: 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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 +",0.6389999985694885,all_total_runs:210|all_finished_runs:135|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:64.29%,False e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gbqweu7x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eo0n8lpt,https://wandb.ai/xzy11632/dance-dev/sweeps/dtisosl6,https://wandb.ai/xzy11632/dance-dev/sweeps/c3h0t2hl","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -556,7 +941,41 @@ 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min_counts + - min_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 +",0.8090000152587891,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 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+",0.4740000069141388,all_total_runs:182|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.53%,False 93cb76aa-a84b-4a92-8e6c-66a914e26d4c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7d180py8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yskxemo0,https://wandb.ai/xzy11632/dance-dev/sweeps/0t8yh7s0,https://wandb.ai/xzy11632/dance-dev/sweeps/7s7n24pt","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -609,7 +1053,41 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5115000009536743,all_total_runs:168|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/996q4lqs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/itvecyve,https://wandb.ai/xzy11632/dance-dev/sweeps/b8xy9cpt,https://wandb.ai/xzy11632/dance-dev/sweeps/4vxpqar7","- type: filter.gene target: 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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: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5748762488365173,all_total_runs:196|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.45%,False 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params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5355648398399353,all_total_runs:196|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:64.80%,False 3d044b52-140a-4528-bf0d-a2dbef9e1f40,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9hu1w69n|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uirvntb0,https://wandb.ai/xzy11632/dance-dev/sweeps/vkaj6z6p,https://wandb.ai/xzy11632/dance-dev/sweeps/tyw2zheq","- type: filter.gene target: FilterGenesPercentile params: {} @@ -699,7 +1236,32 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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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: + 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 f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qphd8ocy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/x4rsitxd,https://wandb.ai/xzy11632/dance-dev/sweeps/4f2tamuu,https://wandb.ai/xzy11632/dance-dev/sweeps/y585p279","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -721,7 +1283,41 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: 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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 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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 576f193c-75d0-4a11-bd25-8676587e6dc2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5wuups73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6py3oklg,https://wandb.ai/xzy11632/dance-dev/sweeps/dktteowl,https://wandb.ai/xzy11632/dance-dev/sweeps/smtg82tq","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -767,7 +1389,32 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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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 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: {} @@ -790,4 +1437,159 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: 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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 +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 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+",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 +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 +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 diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index 51a87b4d..7e0faff6 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 +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check 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: @@ -29,7 +29,32 @@ 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,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:303|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:71.18%,False +",0.948853611946106,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:303|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:71.18%,False,"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 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: @@ -60,7 +85,36 @@ 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 +",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,"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 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: @@ -91,7 +145,41 @@ 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,all_total_runs:493|all_finished_runs:382|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:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:77.48%,False +",0.9725000262260436,all_total_runs:493|all_finished_runs:382|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:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:77.48%,False,"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 a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1128huxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/98s1vpgx,https://wandb.ai/xzy11632/dance-dev/sweeps/dkxsnzmu,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6fvur7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -124,7 +212,41 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.637499988079071,all_total_runs:510|all_finished_runs:367|step2_total_runs:450|step2_finished_runs:307|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:71.96%,False +",0.637499988079071,all_total_runs:510|all_finished_runs:367|step2_total_runs:450|step2_finished_runs:307|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:71.96%,False,"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 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: {} @@ -148,7 +270,41 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.836448609828949,all_total_runs:494|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:4|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.91%,False +",0.836448609828949,all_total_runs:494|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:334|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:4|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.91%,False,"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: {} +- 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 +",0.8317757248878479,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 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 @@ -175,7 +331,45 @@ d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 +",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,"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: + - max_cells + - min_counts + - max_counts + - min_cells + min_counts: 65 + min_cells: 0.03832924256867298 + max_counts: 0.984514560421666 + max_cells: 0.9614458802125864 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4223 + span: 0.5672352308267095 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + 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: + label_channel: cell_type +",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 d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4raopmgl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tj8oqma7,https://wandb.ai/xzy11632/dance-dev/sweeps/j7f8tlxr,https://wandb.ai/xzy11632/dance-dev/sweeps/vo4w0lty","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -201,7 +395,32 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ 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 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+",0.29249998927116394,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -233,7 +452,41 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",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 f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/datmwta4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ri7gpq3f,https://wandb.ai/xzy11632/dance-dev/sweeps/6apaq3my,https://wandb.ai/xzy11632/dance-dev/sweeps/crgctmfi","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -257,7 +510,32 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",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 +",0.324999988079071,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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5myhddto|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sy7is0by,https://wandb.ai/xzy11632/dance-dev/sweeps/hhagx1i4,https://wandb.ai/xzy11632/dance-dev/sweeps/3xb10het","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",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 fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cnp2of1r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vqejchrw,https://wandb.ai/xzy11632/dance-dev/sweeps/ppkzgb1v,https://wandb.ai/xzy11632/dance-dev/sweeps/31caw0fv","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -290,7 +568,40 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6654999852180481,all_total_runs:453|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:369|step3_0_total_runs:1|step3_0_finished_runs:0|step3_1_total_runs:1|step3_1_finished_runs:0|step3_2_total_runs:1|step3_2_finished_runs:0|finished_rate:81.46%,False +",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypo5xler|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/75anan67,https://wandb.ai/xzy11632/dance-dev/sweeps/js80dvkm,https://wandb.ai/xzy11632/dance-dev/sweeps/uqz1gvwh","- type: 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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 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+ config_dict: + label_channel: cell_type +",0.35499998927116394,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.90%,False f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8zlw0izq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/js85xigg,https://wandb.ai/xzy11632/dance-dev/sweeps/li8w1754,https://wandb.ai/xzy11632/dance-dev/sweeps/p4u94ygt","- type: filter.gene target: FilterGenesPercentile params: {} @@ -376,7 +750,38 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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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 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: @@ -416,4 +821,380 @@ 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CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2824999988079071,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:76.19%,False +83b5e943-a1d5-4164-b3f2-f7a37f01b524,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ozba1990|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/338v3aw4,https://wandb.ai/xzy11632/dance-dev/sweeps/ptrrovoq,https://wandb.ai/xzy11632/dance-dev/sweeps/uln7yltc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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:156|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:74.29%,False +97a17473-e2b1-4f31-a544-44a60773e2dd,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5n3rvy41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/863btck9,https://wandb.ai/xzy11632/dance-dev/sweeps/2eikroc1,https://wandb.ai/xzy11632/dance-dev/sweeps/ga9o1zyj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:64.80%,False 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+",1.0,all_total_runs:196|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:127|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:81.12%,False +1062c0f2-2a44-4cf9-a7c8-b5ed58b4728d,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6dw5iyg7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/06k4gi1t,https://wandb.ai/xzy11632/dance-dev/sweeps/le8r1zi4,https://wandb.ai/xzy11632/dance-dev/sweeps/ocpspe17","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:81.90%,False +1252c5fb-945f-42d6-b1a8-8a3bd864384b,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False +bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/frisdu4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0fywjox,https://wandb.ai/xzy11632/dance-dev/sweeps/dz23lu62,https://wandb.ai/xzy11632/dance-dev/sweeps/g0d29txd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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 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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 +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 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index c8d99ad5..2fe1b8a7 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 +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check 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 +29,36 @@ 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 +",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,"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 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: @@ -61,7 +90,40 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4474999904632568,all_total_runs:476|all_finished_runs:361|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:2|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:75.84%,False +",0.4474999904632568,all_total_runs:476|all_finished_runs:361|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:2|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:75.84%,False,"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 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: {} @@ -84,7 +146,45 @@ 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 +",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,"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 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: {} @@ -108,7 +208,45 @@ 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 +",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,"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 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: @@ -140,7 +278,38 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4715000092983246,all_total_runs:510|all_finished_runs:364|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:71.37%,False +",0.4715000092983246,all_total_runs:510|all_finished_runs:364|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:71.37%,False,"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 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: @@ -174,4 +343,29 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.557421088218689,all_total_runs:493|all_finished_runs:362|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:73.43%,False +",0.557421088218689,all_total_runs:493|all_finished_runs:362|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:73.43%,False,"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 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index ce4a326d..ed01dbcc 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 +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check 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: {} @@ -21,7 +21,32 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2630000114440918,all_total_runs:493|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:357|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:73.02%,False +",0.2630000114440918,all_total_runs:493|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:357|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:73.02%,False,"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 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: {} @@ -45,7 +70,32 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5335000157356262,all_total_runs:476|all_finished_runs:325|step2_total_runs:450|step2_finished_runs:325|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:68.28%,False +",0.5335000157356262,all_total_runs:476|all_finished_runs:325|step2_total_runs:450|step2_finished_runs:325|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:68.28%,False,"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 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: @@ -76,7 +126,41 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.5565000176429749,all_total_runs:476|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:344|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:19|finished_rate:76.26%,False +",0.5565000176429749,all_total_runs:476|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:344|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:19|finished_rate:76.26%,False,"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 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: @@ -116,7 +200,41 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.6995000243186951,all_total_runs:476|all_finished_runs:340|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:71.43%,False +",0.6995000243186951,all_total_runs:476|all_finished_runs:340|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:71.43%,False,"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 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 @@ -142,7 +260,45 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2759999930858612,all_total_runs:477|all_finished_runs:372|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:4|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:77.99%,False 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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 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: {} @@ -164,7 +320,36 @@ 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 +",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,"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 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: @@ -198,7 +383,35 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2434999942779541,all_total_runs:490|all_finished_runs:362|step2_total_runs:450|step2_finished_runs:341|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|finished_rate:73.88%,False +",0.2434999942779541,all_total_runs:490|all_finished_runs:362|step2_total_runs:450|step2_finished_runs:341|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|finished_rate:73.88%,False,"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 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: @@ -238,7 +451,41 @@ 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 +",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,"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 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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 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: @@ -295,7 +567,32 @@ 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 +",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,"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 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: @@ -327,7 +624,41 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.8745464086532593,all_total_runs:510|all_finished_runs:402|step2_total_runs:450|step2_finished_runs:342|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.82%,False +",0.8745464086532593,all_total_runs:510|all_finished_runs:402|step2_total_runs:450|step2_finished_runs:342|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.82%,False,"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_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8755832314491272,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 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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 f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hrylvzb1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/km714tee,https://wandb.ai/xzy11632/dance-dev/sweeps/5yr6v6hl,https://wandb.ai/xzy11632/dance-dev/sweeps/44mxsz2v","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -386,7 +751,35 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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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 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 @@ -411,7 +804,41 @@ 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min_counts + - min_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 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target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: 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 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 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+ params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",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 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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 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 @@ -550,7 +1096,41 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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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 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 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