diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index 0049978b..bb1a4a42 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 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: @@ -168,7 +168,69 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.7700534759358288 +",0.7700534759358288,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/iprfvp38|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sfsccz7u,https://wandb.ai/xzy11632/dance-dev/sweeps/sauccnk6,https://wandb.ai/xzy11632/dance-dev/sweeps/rxsuxkxm","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7584670186042786,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7584670186042786 d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/68dze8s6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9p2fidft,https://wandb.ai/xzy11632/dance-dev/sweeps/gfb4afks,https://wandb.ai/xzy11632/dance-dev/sweeps/rfgdltml","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -346,7 +408,67 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3631910426871938 +",0.3631910426871938,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pyjligel|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m0a71zdj,https://wandb.ai/xzy11632/dance-dev/sweeps/kd7wlkd6,https://wandb.ai/xzy11632/dance-dev/sweeps/490xe7ht","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3596920967102051,all_total_runs:600|all_finished_runs:453|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:75.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3596920967102051 71be997d-ff75-41b9-8a9f-1288c865f921,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3hrf2wbb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d6vpumby,https://wandb.ai/xzy11632/dance-dev/sweeps/4ewws3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/iuubdwht","- type: filter.gene target: FilterGenesPercentile params: {} @@ -389,7 +511,45 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4636363685131073,,,,,,,,,,,,,, +",0.4636363685131073,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6x20gszq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zt8h2u2q,https://wandb.ai/xzy11632/dance-dev/sweeps/6u6zlhu5,https://wandb.ai/xzy11632/dance-dev/sweeps/mclm6mgq","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4545454545454546,all_total_runs:150|all_finished_runs:81|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:54.00%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4545454545454546,,,,,,, a5d95a42-0137-496f-8a60-101e17f263c8,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vp004sgu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ndsnj28d,https://wandb.ai/xzy11632/dance-dev/sweeps/zyn1nzj3,https://wandb.ai/xzy11632/dance-dev/sweeps/g578uurw","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -412,7 +572,7 @@ a5d95a42-0137-496f-8a60-101e17f263c8,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.43396225571632385,all_total_runs:510|all_finished_runs:355|step2_total_runs:450|step2_finished_runs:322|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:69.61%,False,"- type: filter.gene +",0.4339622557163238,all_total_runs:510|all_finished_runs:355|step2_total_runs:450|step2_finished_runs:322|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:69.61%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -434,7 +594,47 @@ a5d95a42-0137-496f-8a60-101e17f263c8,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.43396225571632385,,,,,,,,,,,,,, +",0.4339622557163238,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3suyx48|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9tktvcgh,https://wandb.ai/xzy11632/dance-dev/sweeps/6ss7fdt3,https://wandb.ai/xzy11632/dance-dev/sweeps/3gob5ntf","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 95 + mode: var +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2851 + span: 0.16719280450405202 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4113207547169811,all_total_runs:150|all_finished_runs:88|step2_total_runs:90|step2_finished_runs:50|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:58.67%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3962264150943397,,,,,,, c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y14kg9m4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zxn6dvhn,https://wandb.ai/xzy11632/dance-dev/sweeps/sw3khaut,https://wandb.ai/xzy11632/dance-dev/sweeps/9h4fnk3e","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -477,7 +677,61 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.1835000067949295,,,,,,,,,,,,,, +",0.1835000067949295,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/67nc05qo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/968h8p8g,https://wandb.ai/xzy11632/dance-dev/sweeps/fuzr2xth,https://wandb.ai/xzy11632/dance-dev/sweeps/u6dg202m","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.206,all_total_runs:150|all_finished_runs:106|step2_total_runs:90|step2_finished_runs:52|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:70.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.206,,,,,,, 456e8b9b-f872-488b-871d-94534090a865,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wri3w9ug|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9c166tcq,https://wandb.ai/xzy11632/dance-dev/sweeps/0j1n56kx,https://wandb.ai/xzy11632/dance-dev/sweeps/3761sh9x","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -499,7 +753,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20100000500679016,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.29%,False,"- type: filter.gene +",0.2010000050067901,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.29%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -520,95 +774,96 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.20100000500679016,,,,,,,,,,,,,, -738942eb-ac72-44ff-a64b-8943b5ecd8d9,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pk55qst3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ikkth34p,https://wandb.ai/xzy11632/dance-dev/sweeps/33eivzhs,https://wandb.ai/xzy11632/dance-dev/sweeps/0iyvi4uj","- type: filter.gene +",0.2010000050067901,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lv0fx66b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ddug6xp,https://wandb.ai/xzy11632/dance-dev/sweeps/idxr1y9z,https://wandb.ai/xzy11632/dance-dev/sweeps/0iz6wobo","- type: filter.gene target: FilterGenesScanpyOrder params: order: - - max_cells - - min_counts - min_cells + - max_cells - max_counts - min_counts: 78 - min_cells: 0.010918863730631823 - max_counts: 0.9529126141448788 - max_cells: 0.9571952580883056 + - min_counts + min_counts: 466 + min_cells: 0.0660564715580836 + max_counts: 0.9574165855780944 + max_cells: 0.956786246060403 - type: normalize target: NormalizeTotal params: - target_sum: 100000 - max_fraction: 0.5 + target_sum: 1000 + max_fraction: 0.05 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 8304 - top: false - mode: var + n_top_genes: 2925 + span: 0.4795559241062898 - type: feature.cell - target: FeatureCellPlaceHolder - params: - out: feature.cell - log_level: INFO + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature 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,"- type: filter.gene +",0.2295,all_total_runs:150|all_finished_runs:109|step2_total_runs:90|step2_finished_runs:69|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:72.67%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScTransform - params: - processes_num: 8 + target: NormalizeTotal + params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder + target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: SCNFeature label_channel: cell_type -",0.289000004529953,,,,,,,,,,,,,, -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: {} +",0.229,,,,,,, +738942eb-ac72-44ff-a64b-8943b5ecd8d9,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pk55qst3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ikkth34p,https://wandb.ai/xzy11632/dance-dev/sweeps/33eivzhs,https://wandb.ai/xzy11632/dance-dev/sweeps/0iyvi4uj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_counts + - min_cells + - max_counts + min_counts: 78 + min_cells: 0.010918863730631823 + max_counts: 0.9529126141448788 + max_cells: 0.9571952580883056 - type: normalize target: NormalizeTotal - params: {} + params: + target_sum: 100000 + max_fraction: 0.5 - type: filter.gene target: FilterGenesTopK params: - num_genes: 3000 + num_genes: 8304 + top: false + mode: var - type: feature.cell + target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3709999918937683,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,"- type: filter.gene +",0.3030000030994415,all_total_runs:510|all_finished_runs:378|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:74.12%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizeTotal - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: FilterGenesTopK params: @@ -617,77 +872,62 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3709999918937683,,,,,,, -055ca631-6ffb-40de-815e-b931e10718c0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51smdbay|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mhvqib1h,https://wandb.ai/xzy11632/dance-dev/sweeps/qpmixdis,https://wandb.ai/xzy11632/dance-dev/sweeps/j2p0o87d","- type: filter.gene +",0.289000004529953,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/538iyppx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fj7pyf1f,https://wandb.ai/xzy11632/dance-dev/sweeps/es7cum5d,https://wandb.ai/xzy11632/dance-dev/sweeps/o5ozuhv2","- type: filter.gene target: FilterGenesPlaceHolder + params: {} - type: normalize target: Log1P - params: - base: 2.12228660428801 + params: {} - type: filter.gene - target: 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FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -724,21 +970,17 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.21050000190734863,,,,,,, -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,,,,,,,,"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 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feature_channel: SCNFeature + label_channel: cell_type +",0.3635,all_total_runs:150|all_finished_runs:106|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:70.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount params: - cell_feature_channel: feature.cell + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,"- type: filter.gene +",0.3585,,,,,,, +055ca631-6ffb-40de-815e-b931e10718c0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dooszu50|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ot9m5uei,https://wandb.ai/xzy11632/dance-dev/sweeps/latzm9d1,https://wandb.ai/xzy11632/dance-dev/sweeps/tqrr3dft","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -830,33 +1082,37 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.23999999463558197,,,,,,, -4c4cd77c-8fee-4836-9145-16562a8782fe,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9despcsl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ezmsqc0q,https://wandb.ai/xzy11632/dance-dev/sweeps/wplvjtme,https://wandb.ai/xzy11632/dance-dev/sweeps/c3we0q6d","- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.19699999690055847,all_total_runs:510|all_finished_runs:401|step2_total_runs:450|step2_finished_runs:351|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.63%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene target: FilterGenesTopK @@ -866,8 +1122,32 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - split_name: train + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.19699999690055847,"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: @@ -877,8 +1157,8 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:10|finished_rate:78.57%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.2179999947547913,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize target: Log1P @@ -902,8 +1182,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,,,,,,, -ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58nyk24l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lv24d8vj,https://wandb.ai/xzy11632/dance-dev/sweeps/ad02sli6,https://wandb.ai/xzy11632/dance-dev/sweeps/735gpode","- type: filter.gene +",0.2125000059604644,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bhbayrqz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g75vkdn5,https://wandb.ai/xzy11632/dance-dev/sweeps/0hn8a45n,https://wandb.ai/xzy11632/dance-dev/sweeps/jf6af7rq","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -916,27 +1195,1093 @@ ae29ebd0-1973-40a4-a6af-d15a5f77a80f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P - params: {} -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2105,all_total_runs:150|all_finished_runs:85|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:56.67%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2105,,,,,,, +2a498ace-872a-4935-984b-1afa70fd9886,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bq07gszd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bktx311f,https://wandb.ai/xzy11632/dance-dev/sweeps/5mdhsnx2,https://wandb.ai/xzy11632/dance-dev/sweeps/fcfzcmn5","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 1587 + top: true + mode: cv +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 291 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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+",0.3714999854564667,all_total_runs:510|all_finished_runs:278|step2_total_runs:450|step2_finished_runs:278|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:54.51%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3714999854564667,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/en37dusf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mc3gybd1,https://wandb.ai/xzy11632/dance-dev/sweeps/mo1fgrq0,https://wandb.ai/xzy11632/dance-dev/sweeps/algcvv9n","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1074,8 +2595,7 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.23849999904632568,,,,,,, -d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/en37dusf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mc3gybd1,https://wandb.ai/xzy11632/dance-dev/sweeps/mo1fgrq0,https://wandb.ai/xzy11632/dance-dev/sweeps/algcvv9n","- type: filter.gene +",0.4535000026226044,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.62%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1100,32 +2620,105 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.4535000026226044,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.62%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} 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+",0.452,all_total_runs:150|all_finished_runs:75|step2_total_runs:90|step2_finished_runs:71|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:50.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig params: - num_genes: 3000 + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.452,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m6m2bupx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/l1zrtkhn,https://wandb.ai/xzy11632/dance-dev/sweeps/ht752ldv,https://wandb.ai/xzy11632/dance-dev/sweeps/bdlp03ds","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph + target: WeightedFeatureSVD +- type: misc + target: SetConfig params: - cell_feature_channel: feature.cell + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4325000047683716,all_total_runs:600|all_finished_runs:464|step2_total_runs:540|step2_finished_runs:425|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:77.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.4535000026226044,,,,,,, +",0.4325000047683716 fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"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: @@ -1194,7 +2787,59 @@ fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.9113029837608336,,,,,,, +",0.9113029837608336,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kdroab03|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/03u2wz8j,https://wandb.ai/xzy11632/dance-dev/sweeps/axsgwcx0,https://wandb.ai/xzy11632/dance-dev/sweeps/j8ds8gtj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.923861852433281,all_total_runs:150|all_finished_runs:107|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.923861852433281,,,,,,, c2a461b1-0c15-4047-9fcb-1f966fe55100,,,,,,,,"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: @@ -1229,7 +2874,7 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.27149999141693115,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene +",0.2714999914169311,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1263,7 +2908,61 @@ c2a461b1-0c15-4047-9fcb-1f966fe55100,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.27149999141693115,,,,,,, +",0.2714999914169311,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y431lfy9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dq1c78iq,https://wandb.ai/xzy11632/dance-dev/sweeps/4n2extwx,https://wandb.ai/xzy11632/dance-dev/sweeps/pl4hig09","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.284,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.284,,,,,,, b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7s03jiel|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dvxln80t,https://wandb.ai/xzy11632/dance-dev/sweeps/xcsvburm,https://wandb.ai/xzy11632/dance-dev/sweeps/3rm9yv2h","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1292,7 +2991,7 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.17399999499320984,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:77.14%,False,"- type: filter.gene +",0.1739999949932098,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:77.14%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1317,7 +3016,43 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.17249999940395355,,,,,,, +",0.1724999994039535,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/06p1lum5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dh1b7ovm,https://wandb.ai/xzy11632/dance-dev/sweeps/bjql1aor","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.169,all_total_runs:130|all_finished_runs:71|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:13|finished_rate:54.62%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.169,,,,,,, d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"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: @@ -1351,7 +3086,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.18799999356269836,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene +",0.1879999935626983,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1376,4 +3111,38 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.17649999260902405,,,,,,, +",0.176499992609024,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/r5o2z89s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zdzqqtvz,https://wandb.ai/xzy11632/dance-dev/sweeps/xp9872vg,https://wandb.ai/xzy11632/dance-dev/sweeps/74ynsvg4","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.1715,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.1715,,,,,,, diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index fd57ec1a..d214440b 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 0bc7235a-ae5a-479d-a487-510435377e55,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: {} @@ -47,7 +47,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5544999837875366 +",0.5544999837875366,,,,,,,,,,,,,, 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Brain),"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 @@ -111,7 +111,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3675000071525574 +",0.3675000071525574,,,,,,,,,,,,,, 9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lm5mwxkq,https://wandb.ai/xzy11632/dance-dev/sweeps/ortq51x9,https://wandb.ai/xzy11632/dance-dev/sweeps/lakwxgnu","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -162,7 +162,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5440000295639038 +",0.5440000295639038,,,,,,,,,,,,,, 52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"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: @@ -235,7 +235,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5889999866485596 +",0.5889999866485596,,,,,,,,,,,,,, 56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -286,7 +286,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3580000102519989 +",0.3580000102519989,,,,,,,,,,,,,, 43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"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: @@ -355,7 +355,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.8740000128746033 +",0.8740000128746033,,,,,,,,,,,,,, 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: @@ -422,7 +422,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 146216e1-ec30-4fee-a1fb-25defe801e2d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -491,7 +491,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 22658f4f-9268-41ad-8828-cc53f4baa9fa,"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: @@ -560,7 +560,61 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.7710000276565552 +",0.7710000276565552,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vo5e6hw9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5w7eenvp,https://wandb.ai/xzy11632/dance-dev/sweeps/jz7dz1rv,https://wandb.ai/xzy11632/dance-dev/sweeps/zaq3sba8","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7735,all_total_runs:150|all_finished_runs:126|step2_total_runs:90|step2_finished_runs:70|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7735 595c9010-99ec-462d-b6a1-2b2fe5407871,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t969ysm5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lkr2r2zq,https://wandb.ai/xzy11632/dance-dev/sweeps/kpnyhd83,https://wandb.ai/xzy11632/dance-dev/sweeps/tzy3vv3w","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -629,7 +683,61 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.7954999804496765 +",0.7954999804496765,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nxmpirmv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uav0gqma,https://wandb.ai/xzy11632/dance-dev/sweeps/0c6gmy6y,https://wandb.ai/xzy11632/dance-dev/sweeps/gm2eowtj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7595,all_total_runs:150|all_finished_runs:68|step2_total_runs:90|step2_finished_runs:68|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:45.33%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.7595 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: @@ -698,6 +806,42 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/veqwly0p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m5no45rs,https://wandb.ai/xzy11632/dance-dev/sweeps/s3krb2sa,https://wandb.ai/xzy11632/dance-dev/sweeps/3js0dhw4","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0,all_total_runs:150|all_finished_runs:13|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:8.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type ",1.0 70e4f35b-c98c-45a1-9aa9-2053b07315dd,"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 @@ -737,7 +881,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.49549999833106995,all_total_runs:182|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.33%,False,"- type: filter.gene +",0.4954999983310699,all_total_runs:182|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -771,7 +915,63 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.4950000047683716 +",0.4950000047683716,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1dxe2l0w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ab7lhlo3,https://wandb.ai/xzy11632/dance-dev/sweeps/7yjr744v,https://wandb.ai/xzy11632/dance-dev/sweeps/4u07d9ec","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - max_cells + - min_counts + min_counts: 64 + min_cells: 0.09731136945676208 + max_counts: 0.9966478293559916 + max_cells: 0.9887500429224624 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 8255 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4845,all_total_runs:150|all_finished_runs:116|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:77.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.484 72822932-10f6-466f-baf3-a2c1d89364bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hkkcbz82|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cmx0xd8z,https://wandb.ai/xzy11632/dance-dev/sweeps/x6c34300,https://wandb.ai/xzy11632/dance-dev/sweeps/5l0emjk0","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -825,7 +1025,55 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3395000100135803 +",0.3395000100135803,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/66gvcj96|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dfkmrl1i,https://wandb.ai/xzy11632/dance-dev/sweeps/ciietvtw,https://wandb.ai/xzy11632/dance-dev/sweeps/f1mqyetb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 309 + min_cells: 0.03282765645433316 + max_counts: 0.9979696820991064 + max_cells: 0.9842200110060252 +- type: normalize + target: NormalizeTotal + params: + target_sum: null + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 858 + span: 0.1494170169182795 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3445,all_total_runs:150|all_finished_runs:104|step2_total_runs:90|step2_finished_runs:69|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:69.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3435 9372df2d-13d6-4fac-980b-919a5b7eb483,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nmy20c1k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vk37x3sb,https://wandb.ai/xzy11632/dance-dev/sweeps/2ygn08c2,https://wandb.ai/xzy11632/dance-dev/sweeps/0omklbn8","- type: filter.gene target: FilterGenesPercentile params: {} @@ -876,7 +1124,45 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.4934999942779541 +",0.4934999942779541,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vugxebv6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iqwj2j8c,https://wandb.ai/xzy11632/dance-dev/sweeps/tta7mfwk,https://wandb.ai/xzy11632/dance-dev/sweeps/zmiplrsx","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 96 + mode: rv +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.3 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5035,all_total_runs:150|all_finished_runs:83|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:55.33%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5 94c41723-b2c4-4b59-a49a-64c9b851903e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uc3r74ot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s3l0vrwm,https://wandb.ai/xzy11632/dance-dev/sweeps/9vj7bbi4,https://wandb.ai/xzy11632/dance-dev/sweeps/mwg2kekc","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -927,33 +1213,56 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5055000185966492 -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: {} +",0.5055000185966492,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ol3ztzsp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4y8mkdbc,https://wandb.ai/xzy11632/dance-dev/sweeps/227yfu9d,https://wandb.ai/xzy11632/dance-dev/sweeps/p7ic9i6t","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - min_counts + - max_cells + min_counts: 464 + min_cells: 0.08771271564181772 + max_counts: 0.9772928029677204 + max_cells: 0.9973074494435608 - type: normalize - target: NormalizeTotal - params: {} + target: ScaleFeature + params: + mode: standardize + eps: 0.1 - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesRegression params: - n_top_genes: 3000 + method: seurat3 + num_genes: 4103 - type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.521,all_total_runs:150|all_finished_runs:91|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:60.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform params: - cell_feature_channel: feature.cell + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",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,"- 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cell_type -",0.6389999985694885 -e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pnrn8w7g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bpgm4640,https://wandb.ai/xzy11632/dance-dev/sweeps/8y4as678,https://wandb.ai/xzy11632/dance-dev/sweeps/9s7cwjsk","- type: filter.gene +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uot5zwd7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ic3r42l1,https://wandb.ai/xzy11632/dance-dev/sweeps/6uyjhppn,https://wandb.ai/xzy11632/dance-dev/sweeps/vsm4o34t","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1045,28 +1325,21 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.8090000152587891,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:12|step2_total_runs:90|step2_finished_runs:6|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:8.00%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1079,18 +1352,38 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: NormalizeTotal params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0 +c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ojpcn5g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z9bpiv2r,https://wandb.ai/xzy11632/dance-dev/sweeps/d3yy3133,https://wandb.ai/xzy11632/dance-dev/sweeps/pbn9c42i","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -1100,17 +1393,17 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8090000152587891 -364348b4-bc34-4fe1-a851-60d99e36cafa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rtybof1t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8i4spm76,https://wandb.ai/xzy11632/dance-dev/sweeps/s2fldxlp,https://wandb.ai/xzy11632/dance-dev/sweeps/ew7a4p33","- type: filter.gene +",0.6389999985694885,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,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -1126,33 +1419,44 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4740000069141388,all_total_runs:182|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.53%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.6389999985694885,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m9ewkyjd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yvjbuz2i,https://wandb.ai/xzy11632/dance-dev/sweeps/83qmid0p,https://wandb.ai/xzy11632/dance-dev/sweeps/wncozogi","- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6525,all_total_runs:150|all_finished_runs:109|step2_total_runs:90|step2_finished_runs:53|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:72.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount params: - cell_feature_channel: feature.cell + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.4740000069141388 -93cb76aa-a84b-4a92-8e6c-66a914e26d4c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/aqfmsmpx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sxj7ndgn,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6pxhij,https://wandb.ai/xzy11632/dance-dev/sweeps/kfpas6cb","- type: filter.gene +",0.6525 +e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pnrn8w7g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bpgm4640,https://wandb.ai/xzy11632/dance-dev/sweeps/8y4as678,https://wandb.ai/xzy11632/dance-dev/sweeps/9s7cwjsk","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1186,7 +1490,7 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.5748762488365173,all_total_runs:196|all_finished_runs:142|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.45%,False,"- type: filter.gene +",0.7944999933242798,all_total_runs:510|all_finished_runs:338|step2_total_runs:450|step2_finished_runs:335|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.27%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P - params: {} -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.5748762488365173 -774c18c5-efa1-4dc5-9e5e-2c824bab2e34,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2b6ovf5e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/p16tpv7x,https://wandb.ai/xzy11632/dance-dev/sweeps/3sk7tq5f,https://wandb.ai/xzy11632/dance-dev/sweeps/c2j4hpev","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 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3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.5355648398399353 -3d044b52-140a-4528-bf0d-a2dbef9e1f40,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/32erao2o|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d907a0yd,https://wandb.ai/xzy11632/dance-dev/sweeps/goiqwztt,https://wandb.ai/xzy11632/dance-dev/sweeps/ihj7vn5a","- type: filter.gene +",0.8025 +364348b4-bc34-4fe1-a851-60d99e36cafa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rtybof1t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8i4spm76,https://wandb.ai/xzy11632/dance-dev/sweeps/s2fldxlp,https://wandb.ai/xzy11632/dance-dev/sweeps/ew7a4p33","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell @@ -1366,14 +1630,14 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4431818127632141,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"- type: filter.gene +",0.4740000069141388,all_total_runs:182|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.53%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell @@ -1391,8 +1655,7 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4431818127632141 -f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e8vlk083,https://wandb.ai/xzy11632/dance-dev/sweeps/mwggo6ee,https://wandb.ai/xzy11632/dance-dev/sweeps/33pi0zc3","- type: filter.gene +",0.4740000069141388,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9ulcm4zs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lc65vlu9,https://wandb.ai/xzy11632/dance-dev/sweeps/102sw7wh,https://wandb.ai/xzy11632/dance-dev/sweeps/xg2gclj5","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1405,28 +1668,21 @@ 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+",0.5355648398399353,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ayv8er0u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iz7l716f,https://wandb.ai/xzy11632/dance-dev/sweeps/au13vzvx,https://wandb.ai/xzy11632/dance-dev/sweeps/89kft6qm","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4825662482566248,all_total_runs:150|all_finished_runs:103|step2_total_runs:90|step2_finished_runs:48|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:68.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4825662482566248 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+",0.4431818127632141,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4431818127632141,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/miscnge3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/23lpopcy,https://wandb.ai/xzy11632/dance-dev/sweeps/b41qby5x,https://wandb.ai/xzy11632/dance-dev/sweeps/tyxa0naz","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 9.242037197483024 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 107 + span: 0.4291184002623445 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4090909090909091,all_total_runs:150|all_finished_runs:112|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4053030303030303 +f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e8vlk083,https://wandb.ai/xzy11632/dance-dev/sweeps/mwggo6ee,https://wandb.ai/xzy11632/dance-dev/sweeps/33pi0zc3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5130813717842102,all_total_runs:182|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.27%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -1460,7 +2216,64 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5130813717842102 +",0.5130813717842102,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6dd8f769|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rzk9xa5x,https://wandb.ai/xzy11632/dance-dev/sweeps/onruvxox","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 500 + min_cells: 0.06393007765980539 + max_counts: 0.976667396355037 + max_cells: 0.9642353149258592 +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 7772 + span: 0.4864283691327307 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5188953488372093,all_total_runs:130|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:54|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|finished_rate:68.46%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5159883720930233 f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4voqq7a0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6para2wq,https://wandb.ai/xzy11632/dance-dev/sweeps/cabldqak,https://wandb.ai/xzy11632/dance-dev/sweeps/s2xpuetf","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1513,7 +2326,43 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6637080907821655 +",0.6637080907821655,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bti6u79m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nr43xqu5,https://wandb.ai/xzy11632/dance-dev/sweeps/ol7bbm2a,https://wandb.ai/xzy11632/dance-dev/sweeps/hvb1fsf0","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6617357001972387,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6617357001972387 576f193c-75d0-4a11-bd25-8676587e6dc2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zmxfvz4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5pamm1zp,https://wandb.ai/xzy11632/dance-dev/sweeps/a0z7ol9w,https://wandb.ai/xzy11632/dance-dev/sweeps/e3io8n98","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1564,8 +2413,44 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5260545611381531 -ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xghzky,https://wandb.ai/xzy11632/dance-dev/sweeps/pwxoaixd,https://wandb.ai/xzy11632/dance-dev/sweeps/1yosmcdd","- type: filter.gene +",0.5260545611381531,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zzzd70pb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jykr43e9,https://wandb.ai/xzy11632/dance-dev/sweeps/gyjktfxe,https://wandb.ai/xzy11632/dance-dev/sweeps/s06xv871","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5268817204301075,all_total_runs:150|all_finished_runs:74|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:49.33%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5268817204301075 +ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wsvx4b09,https://wandb.ai/xzy11632/dance-dev/sweeps/onnj2wg3,https://wandb.ai/xzy11632/dance-dev/sweeps/lgf5xaby","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1590,7 +2475,7 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.48571428656578064,all_total_runs:210|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:66.67%,False,"- type: filter.gene +",0.48571428656578064,all_total_runs:182|all_finished_runs:130|step2_total_runs:150|step2_finished_runs:119|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:71.43%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1615,4 +2500,161 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.48571428656578064 +",0.48571428656578064,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d2u4p3ti|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mbb5jpgc,https://wandb.ai/xzy11632/dance-dev/sweeps/1anx19g8,https://wandb.ai/xzy11632/dance-dev/sweeps/igfltnzc","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4921282798833819,all_total_runs:150|all_finished_runs:133|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:88.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4921282798833819 +421e5f54-5de7-425f-b399-34ead0651ce1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2v3pfqs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/exctgkg7,https://wandb.ai/xzy11632/dance-dev/sweeps/0ilextij,https://wandb.ai/xzy11632/dance-dev/sweeps/hxwj0qn7","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.92849999666214,all_total_runs:208|all_finished_runs:120|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:7|step3_2_total_runs:19|step3_2_finished_runs:8|finished_rate:57.69%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.92849999666214,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fdskrg67|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v4hxj53u,https://wandb.ai/xzy11632/dance-dev/sweeps/59sb97va,https://wandb.ai/xzy11632/dance-dev/sweeps/69x4485s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9265,all_total_runs:150|all_finished_runs:101|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:67.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9265 diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index 0a66308b..f4c4dfd3 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res 5a11f879-d1ef-458a-910c-9b0bdfca5ebf,"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: {} @@ -49,7 +49,51 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.9506173133850098 +",0.9506173133850098,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uvd74lau|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j8nt0tvf,https://wandb.ai/xzy11632/dance-dev/sweeps/30givefv,https://wandb.ai/xzy11632/dance-dev/sweeps/ce943o71","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9365079402923584,all_total_runs:600|all_finished_runs:432|step2_total_runs:540|step2_finished_runs:395|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:72.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9365079402923584,,,,,,, 1c739a3e-c3f5-49d5-98e0-73975e751201,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pe7wrxhx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bjghjlj5,https://wandb.ai/xzy11632/dance-dev/sweeps/wahyq279,https://wandb.ai/xzy11632/dance-dev/sweeps/33b4rte8","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -103,7 +147,65 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3370000123977661 +",0.3370000123977661,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z2v6lwrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zebalczl,https://wandb.ai/xzy11632/dance-dev/sweeps/av6xm0h7,https://wandb.ai/xzy11632/dance-dev/sweeps/lx1ky4rl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - max_counts + - min_cells + min_counts: 226 + min_cells: 0.047663500071270286 + max_counts: 0.9287568186013924 + max_cells: 0.991629947014312 +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 10 + gmean_eps: 1 + n_genes: 1261 + n_cells: 100 + bin_size: 528 + bw_adjust: 1.8575579429886373 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 7844 +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.304500013589859,all_total_runs:510|all_finished_runs:397|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:77.84%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28450000286102295 4ed927e9-c099-49af-b8ce-a2652d069333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gl8a9d5v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nrpkd1s1,https://wandb.ai/xzy11632/dance-dev/sweeps/i4ot3t4a,https://wandb.ai/xzy11632/dance-dev/sweeps/1off7yhe","- type: filter.gene target: FilterGenesPercentile params: @@ -170,7 +272,59 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.2770000100135803 +",0.2770000100135803,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lxi0z80g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spk2mp9z,https://wandb.ai/xzy11632/dance-dev/sweeps/xwvu3aat,https://wandb.ai/xzy11632/dance-dev/sweeps/ssfi4ars","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 6.02274143830023 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 8532 +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.24899999797344208,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:72.35%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.24699999392032623 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: @@ -239,7 +393,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 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: @@ -308,7 +462,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 572f3f3e-d3e4-4d13-8e2b-88215e508481,"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 @@ -363,7 +517,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3995000123977661 +",0.3995000123977661,,,,,,,,,,,,,, 1009f384-b12d-448e-ba9f-1b7d2ecfbb4e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/amviyxfs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ix2rrweg,https://wandb.ai/xzy11632/dance-dev/sweeps/xapwqo4n,https://wandb.ai/xzy11632/dance-dev/sweeps/f4x92sq0","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -432,7 +586,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 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: @@ -501,7 +655,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 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: @@ -570,7 +724,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, 9434b020-de42-43eb-bcc4-542b2be69015,"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: @@ -639,7 +793,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.9725000262260436 +",0.9725000262260436,,,,,,,,,,,,,, a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"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: @@ -708,7 +862,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6399999856948853 +",0.6399999856948853,,,,,,,,,,,,,, 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: @@ -777,7 +931,7 @@ bdf69f8d-5a96-4d6f-a9f5-9ee0e33597b7,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, c5d88abe-f23a-45fa-a534-788985e93dad,"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: @@ -846,7 +1000,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8317757248878479 +",0.8317757248878479,,,,,,,,,,,,,, d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"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: @@ -919,7 +1073,7 @@ d4e69e01-3ba2-4d6b-a15d-e7048f78f22e,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.25600001215934753 +",0.2560000121593475,,,,,,,,,,,,,, d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6j8pm34t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qx2374ds,https://wandb.ai/xzy11632/dance-dev/sweeps/o4kcwds1,https://wandb.ai/xzy11632/dance-dev/sweeps/xo5xdpan","- type: filter.gene target: FilterGenesPercentile params: {} @@ -945,7 +1099,7 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29249998927116394,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False,"- type: filter.gene +",0.2924999892711639,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:75.24%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -970,7 +1124,7 @@ d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29249998927116394 +",0.2924999892711639,,,,,,,,,,,,,, e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c2luijzg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ohzu189d,https://wandb.ai/xzy11632/dance-dev/sweeps/xk206l8b,https://wandb.ai/xzy11632/dance-dev/sweeps/j5aozig6","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1039,7 +1193,7 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6290000081062317 +",0.6290000081062317,,,,,,,,,,,,,, f15e263b-6544-46cb-a46e-e33ab7ce8347,"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: {} @@ -1090,7 +1244,7 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3880000114440918 +",0.3880000114440918,,,,,,,,,,,,,, f75f2ff4-2884-4c2d-b375-70de37a34507,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/as6ivetf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/icsk75i5,https://wandb.ai/xzy11632/dance-dev/sweeps/vtlcraw8,https://wandb.ai/xzy11632/dance-dev/sweeps/qjov7ai7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1159,7 +1313,7 @@ f75f2ff4-2884-4c2d-b375-70de37a34507,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, f7995301-7551-4e1d-8396-ffe3c9497ace,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1228,7 +1382,7 @@ f7995301-7551-4e1d-8396-ffe3c9497ace,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,,,,,,,,, fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypo5xler|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/75anan67,https://wandb.ai/xzy11632/dance-dev/sweeps/js80dvkm,https://wandb.ai/xzy11632/dance-dev/sweeps/uqz1gvwh","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1295,7 +1449,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6775000095367432 +",0.6775000095367432,,,,,,,,,,,,,, 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Heart),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nrlo0chb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/itw8aeyv,https://wandb.ai/xzy11632/dance-dev/sweeps/gpjulqb6,https://wandb.ai/xzy11632/dance-dev/sweeps/c1at5qua","- type: filter.gene target: FilterGenesPercentile params: @@ -1331,7 +1485,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.34450000524520874,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene +",0.3445000052452087,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1355,7 +1509,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3434999883174896 +",0.3434999883174896,,,,,,,,,,,,,, 65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s66g7ypd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kuznrzx4,https://wandb.ai/xzy11632/dance-dev/sweeps/t9vtfezo,https://wandb.ai/xzy11632/dance-dev/sweeps/adq7j7mn","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1384,7 +1538,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: 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,"- type: filter.gene +",0.3549999892711639,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.90%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1409,7 +1563,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.35350000858306885 +",0.3535000085830688,,,,,,,,,,,,,, f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j4vz4ws5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tecc0rt6,https://wandb.ai/xzy11632/dance-dev/sweeps/jtni6g54,https://wandb.ai/xzy11632/dance-dev/sweeps/uu6v00z6","- type: filter.gene target: FilterGenesPercentile params: @@ -1475,7 +1629,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6455000042915344 +",0.6455000042915344,,,,,,,,,,,,,, ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b47t3rbw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xf8y2bet,https://wandb.ai/xzy11632/dance-dev/sweeps/60mja5m8,https://wandb.ai/xzy11632/dance-dev/sweeps/y27ceukr","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1544,4 +1698,4 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3409999907016754 +",0.3409999907016754,,,,,,,,,,,,,, diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index 0ebbf1d3..ff57eb09 100644 --- a/examples/atlas/sweep_results/Intestine_ans.csv +++ b/examples/atlas/sweep_results/Intestine_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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 @@ -53,7 +53,45 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.44699999690055847 +",0.4469999969005584,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yjg75eb2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6n6m09lu,https://wandb.ai/xzy11632/dance-dev/sweeps/5o2qlh8l,https://wandb.ai/xzy11632/dance-dev/sweeps/is374gfu","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4595,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:58.00%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4595 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -121,7 +159,43 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.4889999926090241 +",0.4889999926090241,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kxkmzv41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rwswn0ja,https://wandb.ai/xzy11632/dance-dev/sweeps/cayifo99,https://wandb.ai/xzy11632/dance-dev/sweeps/y40of4uy","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.496,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:58.00%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.496 e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -194,7 +268,46 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36229634284973145 +",0.3622963428497314,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lydev3fk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q4cn3mtb,https://wandb.ai/xzy11632/dance-dev/sweeps/3rx39oxw,https://wandb.ai/xzy11632/dance-dev/sweeps/xhgs2c15","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 99 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3840186190845617,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:61.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3770364623739333 6a270451-b4d9-43e0-aa89-e33aac1ac74b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -267,7 +380,51 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4485294222831726 +",0.4485294222831726,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2w7qh6m9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/orery7et,https://wandb.ai/xzy11632/dance-dev/sweeps/w60mlkdg,https://wandb.ai/xzy11632/dance-dev/sweeps/gmdyzho8","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScTransform + params: + processes_num: 8 + min_cells: 3 + gmean_eps: 1 + n_genes: 2584 + n_cells: null + bin_size: 380 + bw_adjust: 4.122403001571971 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 9393 + n_bins: 15 + flavor: cell_ranger +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4522058823529412,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.44485294117647056 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -333,7 +490,43 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 params: config_dict: label_channel: cell_type -",0.5109999775886536 +",0.5109999775886536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jocmyjw4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zo3i9mg9,https://wandb.ai/xzy11632/dance-dev/sweeps/cx6569af,https://wandb.ai/xzy11632/dance-dev/sweeps/o8jyq6rr","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.506,all_total_runs:150|all_finished_runs:95|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.506 d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: {} @@ -384,4 +577,42 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5648086071014404 +",0.5648086071014404,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/f0izdcdt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cp84ljtg,https://wandb.ai/xzy11632/dance-dev/sweeps/6tb70g8g,https://wandb.ai/xzy11632/dance-dev/sweeps/oa5ayktp","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5601074546675622,all_total_runs:150|all_finished_runs:76|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:50.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5601074546675622 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index 742bc11c..b44f4b7f 100644 --- a/examples/atlas/sweep_results/Kidney_ans.csv +++ b/examples/atlas/sweep_results/Kidney_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: {} @@ -24,7 +24,7 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"- type: filter.gene +",0.2730000019073486,all_total_runs:196|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:6|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:73.47%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -49,7 +49,45 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.27300000190734863 +",0.2730000019073486,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l0ayhmzb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tus9enye,https://wandb.ai/xzy11632/dance-dev/sweeps/72p9xtzb,https://wandb.ai/xzy11632/dance-dev/sweeps/6djo4d5d","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2725,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2725 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: {} @@ -100,7 +138,43 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5799999833106995 +",0.5799999833106995,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q6fawkyp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ygkup2y2,https://wandb.ai/xzy11632/dance-dev/sweeps/2fu1tsj8,https://wandb.ai/xzy11632/dance-dev/sweeps/fu62rjas","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5945,all_total_runs:150|all_finished_runs:66|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:44.00%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5945 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -169,7 +243,43 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.5964999794960022 +",0.5964999794960022,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wm8pq6ig|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/csv3mlbn,https://wandb.ai/xzy11632/dance-dev/sweeps/885assxx,https://wandb.ai/xzy11632/dance-dev/sweeps/fgeio7m9","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5705,all_total_runs:150|all_finished_runs:68|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:45.33%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5705 105c7dad-0468-4628-a5be-2bb42c6a8ae4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -238,7 +348,59 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.7020000219345093 +",0.7020000219345093,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bwld9xlk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6sopj3bj,https://wandb.ai/xzy11632/dance-dev/sweeps/6xqavd24,https://wandb.ai/xzy11632/dance-dev/sweeps/528j1po3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6975,all_total_runs:150|all_finished_runs:93|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:62.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6975 5af90777-6760-4003-9dba-8f945fec6fdf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ltca3oim|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9oulbho9,https://wandb.ai/xzy11632/dance-dev/sweeps/ko18r05s,https://wandb.ai/xzy11632/dance-dev/sweeps/zg1qkqy0","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -311,7 +473,45 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da params: config_dict: label_channel: cell_type -",0.2809999883174896 +",0.2809999883174896,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jnktyajr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5eigq4mq,https://wandb.ai/xzy11632/dance-dev/sweeps/b5lw76u0,https://wandb.ai/xzy11632/dance-dev/sweeps/bfchr0lr","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2625,all_total_runs:151|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:67|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:21|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:58.94%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2625 dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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 @@ -366,7 +566,61 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24950000643730164 +",0.2495000064373016,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ubj3byxy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vj3djhsu,https://wandb.ai/xzy11632/dance-dev/sweeps/sfz5a11n,https://wandb.ai/xzy11632/dance-dev/sweeps/7k9birau","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.229,all_total_runs:150|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:66.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.229 9df60c57-fdf3-4e93-828e-fe9303f20438,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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 @@ -420,7 +674,43 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2615000009536743 +",0.2615000009536743,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mb2cyn4c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uha7jepq,https://wandb.ai/xzy11632/dance-dev/sweeps/nq1sd8jx,https://wandb.ai/xzy11632/dance-dev/sweeps/fhvkz6ju","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2735,all_total_runs:150|all_finished_runs:122|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2735 be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -455,7 +745,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.43849998712539673,all_total_runs:183|all_finished_runs:139|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:75.96%,False,"- type: filter.gene +",0.4384999871253967,all_total_runs:183|all_finished_runs:139|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:75.96%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -489,21 +779,57 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.43849998712539673 -32b9bdce-2481-4c85-ba1b-6ad5fcea844c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8arpp0bg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kutscmkt,https://wandb.ai/xzy11632/dance-dev/sweeps/d1iadk7m,https://wandb.ai/xzy11632/dance-dev/sweeps/87cnxjeb","- type: filter.gene +",0.4384999871253967,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xl2nwacs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qhr4km04,https://wandb.ai/xzy11632/dance-dev/sweeps/7vqnpicq,https://wandb.ai/xzy11632/dance-dev/sweeps/t8ovlamf","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount + target: ScTransform params: - n_top_genes: 3000 + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig params: - out: feature.cell - log_level: INFO + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.451,all_total_runs:150|all_finished_runs:76|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:50.67%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.451 +32b9bdce-2481-4c85-ba1b-6ad5fcea844c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8arpp0bg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kutscmkt,https://wandb.ai/xzy11632/dance-dev/sweeps/d1iadk7m,https://wandb.ai/xzy11632/dance-dev/sweeps/87cnxjeb","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO split_name: train target: WeightedFeaturePCA - type: graph.cell @@ -515,7 +841,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.23549999296665192,all_total_runs:210|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:75.71%,False,"- type: filter.gene +",0.2354999929666519,all_total_runs:210|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:75.71%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -540,7 +866,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.23549999296665192 +",0.2354999929666519,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/abphixpv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/46zj4ous,https://wandb.ai/xzy11632/dance-dev/sweeps/ql3ox0ee,https://wandb.ai/xzy11632/dance-dev/sweeps/oaiwrhfs","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - max_cells + - min_counts + min_counts: 132 + min_cells: 0.045921635815448794 + max_counts: 0.9851254486346562 + max_cells: 0.9786632198872888 +- type: normalize + target: Log1P + params: + base: 4.927714595143703 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.249,all_total_runs:150|all_finished_runs:116|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.247 0b4a15a7-4e9e-4555-9733-2423e5c66469,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: {} @@ -591,7 +961,55 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2294999957084656 +",0.2294999957084656,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s6rn5ps8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mg255re6,https://wandb.ai/xzy11632/dance-dev/sweeps/45j03ilz,https://wandb.ai/xzy11632/dance-dev/sweeps/701eayg8","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_cells + - max_counts + - min_counts + min_counts: 263 + min_cells: 0.023032742875690015 + max_counts: 0.9761189040538616 + max_cells: 0.9659085418084716 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 4654 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2395,all_total_runs:150|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:66.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2355 53d208b0-2cfd-4366-9866-c3c6114081bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/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: @@ -660,7 +1078,63 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8755832314491272 +",0.8755832314491272,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/onc0rdcc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fle277i2,https://wandb.ai/xzy11632/dance-dev/sweeps/v1vpz6gs,https://wandb.ai/xzy11632/dance-dev/sweeps/jo5s8o6z","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8657335406946605,all_total_runs:150|all_finished_runs:105|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:70.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8657335406946605 6a30bf44-c490-41ac-965b-0bb58432b10a,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nbuoq984|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v8k3ecyi,https://wandb.ai/xzy11632/dance-dev/sweeps/i30iteaa,https://wandb.ai/xzy11632/dance-dev/sweeps/wc6rut0d","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -729,7 +1203,43 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2222222238779068 +",0.2222222238779068,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ulj3xxmi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/22ifljz1,https://wandb.ai/xzy11632/dance-dev/sweeps/jqzc266f","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.16666666666666666,all_total_runs:130|all_finished_runs:99|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|finished_rate:76.15%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.16666666666666666 f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6zzg3aev|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ti1w2l2i,https://wandb.ai/xzy11632/dance-dev/sweeps/en9xlysw,https://wandb.ai/xzy11632/dance-dev/sweeps/cbj2rjp1","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -792,7 +1302,43 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3647642731666565 +",0.3647642731666565,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qoaxxv3r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/scykgn20,https://wandb.ai/xzy11632/dance-dev/sweeps/n8btsi9f,https://wandb.ai/xzy11632/dance-dev/sweeps/z5tkx4n0","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.34491315136476425,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.34491315136476425 20d87640-4be8-487f-93d4-dce38378d00f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x8uut7hm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zhpozwl1,https://wandb.ai/xzy11632/dance-dev/sweeps/i43sxcxt,https://wandb.ai/xzy11632/dance-dev/sweeps/vscrpbjl","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -827,7 +1373,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29468289017677307,all_total_runs:209|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:19|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:75.12%,False,"- type: filter.gene +",0.294682890176773,all_total_runs:209|all_finished_runs:157|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:19|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:75.12%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -861,7 +1407,59 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.29468289017677307 +",0.294682890176773,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xx97kth1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2ij5ijlv,https://wandb.ai/xzy11632/dance-dev/sweeps/euzr7ujg,https://wandb.ai/xzy11632/dance-dev/sweeps/dlrnxq72","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3042921204356182,all_total_runs:150|all_finished_runs:131|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:87.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3042921204356182 2d31c0ca-0233-41ce-bd1a-05aa8404b073,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gfl9vtdc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wqi6cztc,https://wandb.ai/xzy11632/dance-dev/sweeps/eng7tqc9,https://wandb.ai/xzy11632/dance-dev/sweeps/rz1nmsox","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -887,7 +1485,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36496350169181824,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:79.05%,False,"- type: filter.gene +",0.3649635016918182,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:79.05%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -912,7 +1510,62 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.36496350169181824 +",0.3649635016918182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x7o546sk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xoxj0wu3,https://wandb.ai/xzy11632/dance-dev/sweeps/fp7afgvx,https://wandb.ai/xzy11632/dance-dev/sweeps/oo1am6pb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_counts + - min_cells + - max_cells + min_counts: 22 + min_cells: 0.05741156858919219 + max_counts: 0.91367665193381 + max_cells: 0.9829848013655572 +- type: normalize + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.01 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.37664233576642336,all_total_runs:150|all_finished_runs:96|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:64.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3759124087591241 fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fv5txyhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gftuks1f,https://wandb.ai/xzy11632/dance-dev/sweeps/vhtoxock,https://wandb.ai/xzy11632/dance-dev/sweeps/1qsjz3ai","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -981,7 +1634,41 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2759999930858612 +",0.2759999930858612,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rfy7muvr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0pdtdvge,https://wandb.ai/xzy11632/dance-dev/sweeps/7qoqqm29,https://wandb.ai/xzy11632/dance-dev/sweeps/z3tsakmq","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2915,all_total_runs:150|all_finished_runs:115|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:76.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2915 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/02te0za8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8narfff8,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2dfvtp,https://wandb.ai/xzy11632/dance-dev/sweeps/1deo7tn9","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1050,7 +1737,61 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4375 +",0.4375,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2xlnu6s7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ged3jw2n,https://wandb.ai/xzy11632/dance-dev/sweeps/au2t88g0,https://wandb.ai/xzy11632/dance-dev/sweeps/z6zqb0ij","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4125,all_total_runs:150|all_finished_runs:121|step2_total_runs:90|step2_finished_runs:68|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:80.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4125 0b75c598-0893-4216-afe8-5414cab7739d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h267r9gw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gsf3qy1c,https://wandb.ai/xzy11632/dance-dev/sweeps/dzembwwg,https://wandb.ai/xzy11632/dance-dev/sweeps/iygud7ig","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1077,7 +1818,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24050000309944153,all_total_runs:182|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.23%,False,"- type: filter.gene +",0.2405000030994415,all_total_runs:182|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:114|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:69.23%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1103,32 +1844,69 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.24050000309944153 -2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1het6p1z,https://wandb.ai/xzy11632/dance-dev/sweeps/7z429hba,https://wandb.ai/xzy11632/dance-dev/sweeps/81ikkh2i","- type: filter.gene - target: FilterGenesScanpyOrder +",0.2405000030994415,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wcb9vpq4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4bgd5dkd,https://wandb.ai/xzy11632/dance-dev/sweeps/ap5p1ejx,https://wandb.ai/xzy11632/dance-dev/sweeps/8vpkidbc","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2465,all_total_runs:150|all_finished_runs:85|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:56.67%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize - target: Log1P + target: NormalizePlaceHolder params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2465 +2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r6m7zdo1,https://wandb.ai/xzy11632/dance-dev/sweeps/rvpunccy,https://wandb.ai/xzy11632/dance-dev/sweeps/50vokx7l","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 98 + mode: cv +- type: normalize + target: Log1P + params: + base: 1.0842803516615516 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: 0.06377687896770325 + max_disp: 41.939375689351905 + min_mean: 0.0025444527190867693 + max_mean: 17.950279292657427 + n_bins: 21 + flavor: seurat +- type: feature.cell + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + n_components: 664 + feat_norm_mode: standardize - type: graph.cell target: CellFeatureGraph params: @@ -1138,7 +1916,7 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5,all_total_runs:182|all_finished_runs:134|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:73.63%,False,"- type: filter.gene +",0.5051282048225403,all_total_runs:210|all_finished_runs:161|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:76.67%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1172,7 +1950,43 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5 +",0.5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ebnsel1o|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hzm9cmea,https://wandb.ai/xzy11632/dance-dev/sweeps/im8zzzed,https://wandb.ai/xzy11632/dance-dev/sweeps/0v22gcsp","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.488034188034188,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:62.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.488034188034188 2423ce2c-3149-4cca-a2ff-cf682ea29b5f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z3v3k8xa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rxf8w4kk,https://wandb.ai/xzy11632/dance-dev/sweeps/oq5yjvcy,https://wandb.ai/xzy11632/dance-dev/sweeps/g644vduv","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1241,4 +2055,60 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.8755832314491272 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b/examples/atlas/sweep_results/Lung_ans.csv @@ -0,0 +1,1410 @@ +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/31p1jl13|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jv0qygxw,https://wandb.ai/xzy11632/dance-dev/sweeps/3k1x4ael,https://wandb.ai/xzy11632/dance-dev/sweeps/0drfyazl","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4790000021457672,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:82.38%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.4790000021457672,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/umip8col|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8rbu9tz5,https://wandb.ai/xzy11632/dance-dev/sweeps/s2x3klie,https://wandb.ai/xzy11632/dance-dev/sweeps/xq1tygx9","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.486,all_total_runs:150|all_finished_runs:111|step2_total_runs:90|step2_finished_runs:56|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.486 +f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/u66vt0zy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0e4fl2ig,https://wandb.ai/xzy11632/dance-dev/sweeps/26t9dcb3,https://wandb.ai/xzy11632/dance-dev/sweeps/6er1nf7y","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.30799999833106995,all_total_runs:225|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:35|step3_0_finished_runs:26|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:80.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3055 +3de0ad6d-4378-4f62-b37b-ec0b75a50d94,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cztlwh8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xnekcm5a,https://wandb.ai/xzy11632/dance-dev/sweeps/92k8gjvn,https://wandb.ai/xzy11632/dance-dev/sweeps/ebwccpe0","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.34 +4ed927e9-c099-49af-b8ce-a2652d069333(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/up1qmjf2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xlh552ry,https://wandb.ai/xzy11632/dance-dev/sweeps/w64bnq3j,https://wandb.ai/xzy11632/dance-dev/sweeps/t7nbjgz0","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 95 + mode: cv +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: -1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9736 + span: 0.25241821131495124 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 891 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6175000071525574,all_total_runs:220|all_finished_runs:184|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:40|step3_1_finished_runs:35|step3_2_total_runs:10|step3_2_finished_runs:10|finished_rate:83.64%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6169999837875366,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3d1v8h2t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/c1w0za8n,https://wandb.ai/xzy11632/dance-dev/sweeps/6bzf7x2w,https://wandb.ai/xzy11632/dance-dev/sweeps/28wpkbwl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4014388489208633 +a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ugznmank|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zv9lzme,https://wandb.ai/xzy11632/dance-dev/sweeps/8ptyl7c3","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 2 + max_val: 98 + mode: rv +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.265,all_total_runs:149|all_finished_runs:113|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.84%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.265 +2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Lung),,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8wu00rrs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emkgdv7m,https://wandb.ai/xzy11632/dance-dev/sweeps/yz3ptmyb,https://wandb.ai/xzy11632/dance-dev/sweeps/8zpy4daf","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2355,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2355 +d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qpyso58s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n9xhwciz,https://wandb.ai/xzy11632/dance-dev/sweeps/zb5fdqlj,https://wandb.ai/xzy11632/dance-dev/sweeps/gdl97dnb","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.1705,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.1705 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+",0.65,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.65 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+",0.4393939393939394,all_total_runs:150|all_finished_runs:129|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:86.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.42424242424242425 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv new file mode 100644 index 00000000..870281cd --- /dev/null +++ b/examples/atlas/sweep_results/Pancreas_ans.csv @@ -0,0 +1,1630 @@ +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +53d208b0-2cfd-4366-9866-c3c6114081bc(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g7t7xwhn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cf0x6364,https://wandb.ai/xzy11632/dance-dev/sweeps/ol212cn4,https://wandb.ai/xzy11632/dance-dev/sweeps/i688o13x","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_cells + - min_counts + - max_counts + min_counts: 482 + min_cells: 0.08359667621587258 + max_counts: 0.984260099671448 + max_cells: 0.9831967316325464 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4805 + span: 0.59331455825036 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 541 + 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 +",0.40299999713897705,all_total_runs:210|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:99|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:20|step3_1_finished_runs:10|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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 +",0.4020000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gpj4i6jb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pqpwvbcl,https://wandb.ai/xzy11632/dance-dev/sweeps/hc0zyrsm,https://wandb.ai/xzy11632/dance-dev/sweeps/oqeg7gt6","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 95 + mode: cv +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000 + max_fraction: 0.7 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3006 + span: 0.3081446146760134 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4035,all_total_runs:150|all_finished_runs:91|step2_total_runs:90|step2_finished_runs:57|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.402 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+",1.0,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:77.62%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mjxq9wbz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mb64lqt6,https://wandb.ai/xzy11632/dance-dev/sweeps/gaeji3wq,https://wandb.ai/xzy11632/dance-dev/sweeps/jdxyftrd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0,all_total_runs:150|all_finished_runs:33|step2_total_runs:90|step2_finished_runs:16|step3_0_total_runs:20|step3_0_finished_runs:9|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:22.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0 +f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pncdq2k1,https://wandb.ai/xzy11632/dance-dev/sweeps/z1tnppgo,https://wandb.ai/xzy11632/dance-dev/sweeps/s4ka2u4s","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + 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 +",0.25999999046325684,all_total_runs:210|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:62.86%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + 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 +",0.25999999046325684,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/szccibek|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ncv8d9cl,https://wandb.ai/xzy11632/dance-dev/sweeps/9c2q16tc,https://wandb.ai/xzy11632/dance-dev/sweeps/t3jzvjsd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_cells + - min_cells + - max_counts + min_counts: 290 + min_cells: 0.09769546522542771 + max_counts: 0.9875755318917276 + max_cells: 0.9902514987938889 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.3 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 7878 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 2997 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 645 + 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 +",0.3165000081062317,all_total_runs:210|all_finished_runs:139|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:66.19%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.47699999809265137,all_total_runs:210|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:59.52%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + 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: + 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max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3791748583316803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0tpkjxr3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dxjir4oa,https://wandb.ai/xzy11632/dance-dev/sweeps/ozctmfyc,https://wandb.ai/xzy11632/dance-dev/sweeps/ie0fgnbo","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: 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filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6768107414245605,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:10|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:69.05%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.6768107414245605,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/09vtppjh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/l5fovbpb,https://wandb.ai/xzy11632/dance-dev/sweeps/utu1c0zt,https://wandb.ai/xzy11632/dance-dev/sweeps/689d3b91","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - min_counts + - max_counts + - max_cells + min_counts: 327 + min_cells: 0.08986191604520012 + max_counts: 0.9467699188647029 + max_cells: 0.9545870083635444 +- type: normalize + target: NormalizeTotal + params: + target_sum: 1000000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 571 + top: true + mode: sum +- type: feature.cell + 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