diff --git a/examples/atlas/sweep_results/Lung_ans.csv b/examples/atlas/sweep_results/Lung_ans.csv new file mode 100644 index 00000000..53c10f71 --- /dev/null +++ b/examples/atlas/sweep_results/Lung_ans.csv @@ -0,0 +1,1054 @@ +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 +fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p93dumjw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0garwmxd,https://wandb.ai/xzy11632/dance-dev/sweeps/s6vapi8h,https://wandb.ai/xzy11632/dance-dev/sweeps/vjyplvr1","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.4560000002384186,all_total_runs:493|all_finished_runs:381|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:77.28%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4560000002384186 +f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cf7nubki|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0dqimbs,https://wandb.ai/xzy11632/dance-dev/sweeps/obby7pnt,https://wandb.ai/xzy11632/dance-dev/sweeps/mvohukm2","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27549999952316284,all_total_runs:510|all_finished_runs:324|step2_total_runs:450|step2_finished_runs:264|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:63.53%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27549999952316284 +3de0ad6d-4378-4f62-b37b-ec0b75a50d94,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/82wyioi1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9stmezaf,https://wandb.ai/xzy11632/dance-dev/sweeps/w5sy9d7k,https://wandb.ai/xzy11632/dance-dev/sweeps/wpjgpvr7","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.15850000083446503,all_total_runs:510|all_finished_runs:419|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.16%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.15850000083446503 +1e5bd3b8-6a0e-4959-8d69-cafed30fe814,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6tj8p155|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/81avsh07,https://wandb.ai/xzy11632/dance-dev/sweeps/buygqdt4,https://wandb.ai/xzy11632/dance-dev/sweeps/4l19utts","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.5 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 2690 + top: true + mode: cv +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 461 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33899998664855957,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3334999978542328 +4ed927e9-c099-49af-b8ce-a2652d069333(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/go3pdoh7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v5kbmzlh,https://wandb.ai/xzy11632/dance-dev/sweeps/7jrk2f6s,https://wandb.ai/xzy11632/dance-dev/sweeps/mhxt4wt6","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5975000262260437,all_total_runs:459|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:78.43%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5975000262260437 +01209dce-3575-4bed-b1df-129f57fbc031(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kqfwox7t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/y0046ayn,https://wandb.ai/xzy11632/dance-dev/sweeps/ldnjitb7,https://wandb.ai/xzy11632/dance-dev/sweeps/lt59uias","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 99 + mode: var +- type: normalize + target: NormalizePlaceHolder +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 1122 +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 476 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28450000286102295,all_total_runs:510|all_finished_runs:420|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.35%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28349998593330383 +c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uffahbta|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kce6ughj,https://wandb.ai/xzy11632/dance-dev/sweeps/a2x6wq1a,https://wandb.ai/xzy11632/dance-dev/sweeps/ahewlrh8","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6784999966621399,all_total_runs:510|all_finished_runs:375|step2_total_runs:450|step2_finished_runs:315|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:73.53%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6784999966621399 +9968be68-ab65-4a38-9e1a-c9b6abece194,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/idz72j8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zs9no5j,https://wandb.ai/xzy11632/dance-dev/sweeps/0a22jgfw,https://wandb.ai/xzy11632/dance-dev/sweeps/cqlbke6s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6570000052452087,all_total_runs:476|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.63%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6570000052452087 +1e6a6ef9-7ec9-4c90-bbfb-2ad3c3165fd1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b54i7xxa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mgw2de3q,https://wandb.ai/xzy11632/dance-dev/sweeps/jfuj5vll,https://wandb.ai/xzy11632/dance-dev/sweeps/3r9o7kkx","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + 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 +",0.14749999344348907,all_total_runs:510|all_finished_runs:420|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.35%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + 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 +",0.14749999344348907 +486486d4-9462-43e5-9249-eb43fa5a49a6,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4sue5c56|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/o8vlmct0,https://wandb.ai/xzy11632/dance-dev/sweeps/xajb94o1,https://wandb.ai/xzy11632/dance-dev/sweeps/sgh0lqbn","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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 + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4869999885559082,all_total_runs:476|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:79.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4869999885559082 +7b3368a5-c1a0-4973-9e75-d95b4150c7da,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hlkac19s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ov3ryli8,https://wandb.ai/xzy11632/dance-dev/sweeps/6obgw9bs,https://wandb.ai/xzy11632/dance-dev/sweeps/izhbqz2a","- 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 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1557970941066742,all_total_runs:510|all_finished_runs:365|step2_total_runs:450|step2_finished_runs:360|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:2|finished_rate:71.57%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1557970941066742 +e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fw95i0vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lzszad4s,https://wandb.ai/xzy11632/dance-dev/sweeps/2hg95kcf,https://wandb.ai/xzy11632/dance-dev/sweeps/ix89ykms","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.11605080962181091,all_total_runs:510|all_finished_runs:335|step2_total_runs:450|step2_finished_runs:294|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:65.69%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.11605080962181091 +e9175006-8978-4417-939f-819855eab80e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ihea1f9w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tra6ajgy,https://wandb.ai/xzy11632/dance-dev/sweeps/gpcxo6dy,https://wandb.ai/xzy11632/dance-dev/sweeps/5pbruy9a","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8007153868675232,all_total_runs:318|all_finished_runs:257|step2_total_runs:258|step2_finished_runs:255|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:80.82%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + 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 +",0.8007153868675232 +0ba16f4b-cb87-4fa3-9363-19fc51eec6e7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/v0gc7aor|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t0gcfd2b,https://wandb.ai/xzy11632/dance-dev/sweeps/o4gnu5j7,https://wandb.ai/xzy11632/dance-dev/sweeps/w8we952e","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.3 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 9080 +- 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 +",0.3712230324745178,all_total_runs:268|all_finished_runs:255|step2_total_runs:242|step2_finished_runs:239|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:95.15%,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: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.35827338695526123 +a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b76qr295|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dn8svl35,https://wandb.ai/xzy11632/dance-dev/sweeps/epc20utc,https://wandb.ai/xzy11632/dance-dev/sweeps/mg2pnd4n","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_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: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3480176329612732,all_total_runs:510|all_finished_runs:383|step2_total_runs:450|step2_finished_runs:326|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.10%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3480176329612732 +8c42cfd0-0b0a-46d5-910c-fc833d83c45e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mwjlq7a2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pt55s3l9,https://wandb.ai/xzy11632/dance-dev/sweeps/gk0raad1,https://wandb.ai/xzy11632/dance-dev/sweeps/sxex7w80","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 455 + min_cells: 0.08766785970976693 + max_counts: 0.982343433796268 + max_cells: 0.9664774788562582 +- type: normalize + target: Log1P + params: + base: 7.459782027773534 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9807 + top: true + mode: cv +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,all_total_runs:476|all_finished_runs:380|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:79.83%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22300000488758087 +2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ggmt3lbe|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gukxv9vr,https://wandb.ai/xzy11632/dance-dev/sweeps/a4gvm8jz,https://wandb.ai/xzy11632/dance-dev/sweeps/1yxm20rs","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.21649999916553497,all_total_runs:493|all_finished_runs:388|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.70%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.21649999916553497 +d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xbubo8oq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6vnfiblb,https://wandb.ai/xzy11632/dance-dev/sweeps/1rgmr3tb,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2wvt9c","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.15800000727176666,all_total_runs:493|all_finished_runs:399|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:80.93%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.15800000727176666 +4023a2bc-6325-47db-bfdf-9639e91042c2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7u7qawi2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n2403fvc,https://wandb.ai/xzy11632/dance-dev/sweeps/4jk06ql6,https://wandb.ai/xzy11632/dance-dev/sweeps/6t7sm8o0","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6186813116073608,all_total_runs:493|all_finished_runs:361|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:73.23%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6186813116073608 +71be997d-ff75-41b9-8a9f-1288c865f921(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l2wuxpnd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t17ir30r,https://wandb.ai/xzy11632/dance-dev/sweeps/boxtoi63,https://wandb.ai/xzy11632/dance-dev/sweeps/wu62crhr","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5909090638160706,all_total_runs:510|all_finished_runs:413|step2_total_runs:450|step2_finished_runs:357|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:80.98%,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 + 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 +",0.5909090638160706 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv index fb6a1786..2d8a197b 100644 --- a/examples/atlas/sweep_results/Pancreas_ans.csv +++ b/examples/atlas/sweep_results/Pancreas_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res +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 53d208b0-2cfd-4366-9866-c3c6114081bc(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g7t7xwhn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cf0x6364,https://wandb.ai/xzy11632/dance-dev/sweeps/ol212cn4,https://wandb.ai/xzy11632/dance-dev/sweeps/i688o13x","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -37,7 +37,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.40299999713897705,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 +",0.402999997138977,all_total_runs:210|all_finished_runs:126|step2_total_runs:150|step2_finished_runs:99|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:20|step3_1_finished_runs:10|step3_2_total_runs:20|step3_2_finished_runs:9|finished_rate:60.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -71,6 +71,50 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type +",0.4020000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q7l6m2qp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5go16fns,https://wandb.ai/xzy11632/dance-dev/sweeps/i63ze0b1,https://wandb.ai/xzy11632/dance-dev/sweeps/e7g4eglj","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4020000100135803,all_total_runs:510|all_finished_runs:402|step2_total_runs:450|step2_finished_runs:342|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.82%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type ",0.4020000100135803 78f10833-3e61-4fad-96c9-4bbd4f14bdfa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ile10jfv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8tfuwq6k,https://wandb.ai/xzy11632/dance-dev/sweeps/cwadf7td,https://wandb.ai/xzy11632/dance-dev/sweeps/6kx7b6kc","- type: filter.gene target: FilterGenesScanpyOrder @@ -140,7 +184,7 @@ 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,,,,,,, f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ki0b8xal,https://wandb.ai/xzy11632/dance-dev/sweeps/hzv5a32f,https://wandb.ai/xzy11632/dance-dev/sweeps/vvy7c4q9","- type: filter.gene target: FilterGenesPercentile params: {} @@ -166,7 +210,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.25999999046325684,all_total_runs:210|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:57.62%,True,"- type: filter.gene +",0.2599999904632568,all_total_runs:210|all_finished_runs:121|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:7|step3_1_total_runs:20|step3_1_finished_runs:6|step3_2_total_runs:20|step3_2_finished_runs:4|finished_rate:57.62%,True,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -191,7 +235,51 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.25999999046325684 +",0.2599999904632568,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q7pjlbgz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hn65sj20,https://wandb.ai/xzy11632/dance-dev/sweeps/0aloe2j4,https://wandb.ai/xzy11632/dance-dev/sweeps/2fp77b7l","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.257999986410141,all_total_runs:510|all_finished_runs:413|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.98%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.257999986410141 37b21763-7f0f-41ae-9001-60bad6e2841d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ertfvv8w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8r7518v2,https://wandb.ai/xzy11632/dance-dev/sweeps/hh8iu4b5,https://wandb.ai/xzy11632/dance-dev/sweeps/fd2zwr1f","- type: filter.gene target: FilterGenesPercentile params: @@ -258,7 +346,59 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.3160000145435333 +",0.3160000145435333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/njuwyfnv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nrka7j9c,https://wandb.ai/xzy11632/dance-dev/sweeps/9a520ovb,https://wandb.ai/xzy11632/dance-dev/sweeps/enxkipmk","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 1 + max_val: 95 + mode: sum +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.1 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9608 + top: false + mode: var +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 137 + feat_norm_mode: null +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3160000145435333,all_total_runs:510|all_finished_runs:415|step2_total_runs:450|step2_finished_runs:355|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.37%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3050000071525574 9c4c8515-8f82-4c72-b0c6-f87647b00bbe,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m45z81gy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/40zgwwd2,https://wandb.ai/xzy11632/dance-dev/sweeps/mrhq79ks,https://wandb.ai/xzy11632/dance-dev/sweeps/3k6f32vq","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -327,7 +467,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,, fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g8eo9qp4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/scpo55vu,https://wandb.ai/xzy11632/dance-dev/sweeps/jem8ckkq,https://wandb.ai/xzy11632/dance-dev/sweeps/qozeoh02","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -366,7 +506,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.24699999392032623,all_total_runs:178|all_finished_runs:172|step2_total_runs:118|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:96.63%,False,"- type: filter.gene +",0.2469999939203262,all_total_runs:178|all_finished_runs:172|step2_total_runs:118|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:96.63%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -391,7 +531,51 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.24549999833106995 +",0.2454999983310699,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zcjk9kzu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xa1zrlvf,https://wandb.ai/xzy11632/dance-dev/sweeps/svep9r0f,https://wandb.ai/xzy11632/dance-dev/sweeps/earmglny","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2450000047683716,all_total_runs:510|all_finished_runs:402|step2_total_runs:450|step2_finished_runs:344|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:78.82%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2450000047683716 b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/acvxgobi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/367ly4lx,https://wandb.ai/xzy11632/dance-dev/sweeps/qyt8n1ye,https://wandb.ai/xzy11632/dance-dev/sweeps/yuvualyj","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -417,7 +601,7 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.38967135548591614,all_total_runs:210|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:61.43%,False,"- type: filter.gene +",0.3896713554859161,all_total_runs:210|all_finished_runs:129|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:61.43%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -442,7 +626,49 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.38967135548591614 +",0.3896713554859161,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4y7bjr73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2bftkn2f,https://wandb.ai/xzy11632/dance-dev/sweeps/6wksp40t,https://wandb.ai/xzy11632/dance-dev/sweeps/b0igv55h","- type: filter.gene + 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 + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3849765360355377,all_total_runs:493|all_finished_runs:357|step2_total_runs:450|step2_finished_runs:319|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:72.41%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3849765360355377 c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9nfe3jei|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6v7hplqp,https://wandb.ai/xzy11632/dance-dev/sweeps/mt4za374,https://wandb.ai/xzy11632/dance-dev/sweeps/zzx2pq9v","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -515,6 +741,50 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type +",0.6593806743621826,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/91ahvamr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1b2ngpol,https://wandb.ai/xzy11632/dance-dev/sweeps/1djcluuc,https://wandb.ai/xzy11632/dance-dev/sweeps/k4aioss2","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6593806743621826,all_total_runs:510|all_finished_runs:370|step2_total_runs:450|step2_finished_runs:314|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:72.55%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type ",0.6593806743621826 a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8n01i0az|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sckhppek,https://wandb.ai/xzy11632/dance-dev/sweeps/mnx13kpn,https://wandb.ai/xzy11632/dance-dev/sweeps/t0k7akxc","- type: filter.gene target: FilterGenesPlaceHolder @@ -566,6 +836,68 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type +",0.9090909361839294,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3vagufgh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zbn2i026,https://wandb.ai/xzy11632/dance-dev/sweeps/za3zf761,https://wandb.ai/xzy11632/dance-dev/sweeps/d8thkug7","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9090909361839294,all_total_runs:510|all_finished_runs:356|step2_total_runs:450|step2_finished_runs:303|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:69.80%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type ",0.9090909361839294 5a11f879-d1ef-458a-910c-9b0bdfca5ebf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zqtpjc1h|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3o7b2xs0,https://wandb.ai/xzy11632/dance-dev/sweeps/6glysub4,https://wandb.ai/xzy11632/dance-dev/sweeps/htrki617","- type: filter.gene target: FilterGenesScanpyOrder @@ -637,7 +969,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",1.0 +",1.0,,,,,,, 3294d050-6eeb-4a00-b24c-71aacc9b777f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rq1aqcks|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w7fykvmx,https://wandb.ai/xzy11632/dance-dev/sweeps/7zg7srym,https://wandb.ai/xzy11632/dance-dev/sweeps/qgcvp9vy","- type: filter.gene target: FilterGenesPercentile params: {} @@ -663,7 +995,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.47699999809265137,all_total_runs:193|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:66.32%,False,"- type: filter.gene +",0.4769999980926513,all_total_runs:193|all_finished_runs:128|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:66.32%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -688,7 +1020,53 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.47699999809265137 +",0.4769999980926513,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/g85syyzg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cdggwljw,https://wandb.ai/xzy11632/dance-dev/sweeps/natn1hgy,https://wandb.ai/xzy11632/dance-dev/sweeps/b0eefc5r","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4670000076293946,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:341|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:71.18%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + 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 +",0.4670000076293946 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ghnlphpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qmwfsxt6,https://wandb.ai/xzy11632/dance-dev/sweeps/0bv97iz8,https://wandb.ai/xzy11632/dance-dev/sweeps/fhv7qkjx","- type: filter.gene target: FilterGenesPercentile params: {} @@ -714,7 +1092,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.27399998903274536,all_total_runs:210|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:70.00%,False,"- type: filter.gene +",0.2739999890327453,all_total_runs:210|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:70.00%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -739,7 +1117,55 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.27399998903274536 +",0.2739999890327453,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tnlms8f7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/37b6ag4h,https://wandb.ai/xzy11632/dance-dev/sweeps/drrj9j62,https://wandb.ai/xzy11632/dance-dev/sweeps/yrm085kp","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: -1 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8013 + top: false + mode: sum +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 897 + feat_norm_mode: l2 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27300000190734863,all_total_runs:510|all_finished_runs:395|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:77.45%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2644999921321869 ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xrzp33gj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/erm7pgbk,https://wandb.ai/xzy11632/dance-dev/sweeps/z5w6mxqq,https://wandb.ai/xzy11632/dance-dev/sweeps/6gwdbnnf","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -808,7 +1234,51 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4124999940395355 +",0.4124999940395355,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/li0kaahk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mftedu6f,https://wandb.ai/xzy11632/dance-dev/sweeps/05zma5yg,https://wandb.ai/xzy11632/dance-dev/sweeps/3a1vt11n","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4115000069141388,all_total_runs:510|all_finished_runs:384|step2_total_runs:450|step2_finished_runs:325|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:75.29%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4115000069141388 66d15835-5dc8-4e96-b0eb-f48971cb65e8,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vqiycw97|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mqxn1w2x,https://wandb.ai/xzy11632/dance-dev/sweeps/7xrgbuws,https://wandb.ai/xzy11632/dance-dev/sweeps/rfy7mvau","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -877,7 +1347,62 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3791748583316803 +",0.3791748583316803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p87lac44|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lfrx75bu,https://wandb.ai/xzy11632/dance-dev/sweeps/9dafryxc,https://wandb.ai/xzy11632/dance-dev/sweeps/yh7p9cq3","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_cells + - max_counts + - min_counts + min_counts: 436 + min_cells: 0.008052271855593807 + max_counts: 0.9724095836117284 + max_cells: 0.968847446724503 +- type: normalize + target: Log1P + params: + base: 5.483824101447068 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 6222 + top: true + mode: var +- type: feature.cell + target: FeatureCellPlaceHolder + params: + out: feature.cell + log_level: INFO +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3791748583316803,all_total_runs:493|all_finished_runs:344|step2_total_runs:450|step2_finished_runs:307|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:69.78%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3634577691555023 97a17473-e2b1-4f31-a544-44a60773e2dd(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5sc3ymja|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tzb3gq58,https://wandb.ai/xzy11632/dance-dev/sweeps/epie6vgv,https://wandb.ai/xzy11632/dance-dev/sweeps/w6gc0mfl","- type: filter.gene target: FilterGenesPercentile params: {} @@ -928,4 +1453,48 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6768107414245605 +",0.6768107414245605,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hikrp0lg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uazhlu4v,https://wandb.ai/xzy11632/dance-dev/sweeps/wrbzgnc1,https://wandb.ai/xzy11632/dance-dev/sweeps/kvelln8e","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6755934357643127,all_total_runs:511|all_finished_runs:385|step2_total_runs:451|step2_finished_runs:327|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:75.34%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6755934357643127