diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv deleted file mode 100644 index e510bee5..00000000 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ /dev/null @@ -1,270 +0,0 @@ -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 -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0rvmzkia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e9ndxdji,https://wandb.ai/xzy11632/dance-dev/sweeps/6lndzud2,https://wandb.ai/xzy11632/dance-dev/sweeps/kboc5b0g","- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.24699999392032623,all_total_runs:493|all_finished_runs:376|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.24699999392032623 -fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lx05p3vr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iuazawqt,https://wandb.ai/xzy11632/dance-dev/sweeps/s9ckkiye,https://wandb.ai/xzy11632/dance-dev/sweeps/kval7p9y","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.9113029837608336,all_total_runs:510|all_finished_runs:347|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:68.04%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.9113029837608336 -c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/igxg3cvm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0fxcrj2d,https://wandb.ai/xzy11632/dance-dev/sweeps/ldrt5co9,https://wandb.ai/xzy11632/dance-dev/sweeps/f375yojf","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 7 - max_val: 98 - mode: cv -- type: normalize - target: ScaleFeature - params: - mode: minmax - eps: 0.5 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 7024 - top: true - mode: cv -- type: feature.cell - target: FeatureCellPlaceHolder - params: - out: feature.cell - 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target: FilterGenesPercentile - params: - min_val: 5 - max_val: 99 - mode: cv -- type: normalize - target: NormalizeTotal - params: - target_sum: 1000000 - max_fraction: 0.05 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 227 - top: false - mode: rv -- type: feature.cell - target: GaussRandProjFeature - params: - out: feature.cell - log_level: INFO - n_components: 872 -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.1655000001192093,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- 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 - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.1515000015497207 -d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgjtmzk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4lc9v41j,https://wandb.ai/xzy11632/dance-dev/sweeps/qgpqm3rx,https://wandb.ai/xzy11632/dance-dev/sweeps/l6uoduzp","- type: filter.gene - target: FilterGenesPercentile - params: {} -- 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 - 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target: FilterGenesPlaceHolder -- type: normalize - target: NormalizeTotal - params: - target_sum: 1000000 - max_fraction: 0.05 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 559 - top: true - mode: cv -- type: feature.cell - target: WeightedFeatureSVD - params: - out: feature.cell - log_level: INFO - n_components: 151 - feat_norm_mode: minmax -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.5099999904632568,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:348|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:72.35%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: NormalizeTotal - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.48350000381469727,,,,,,, -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Brain),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0fw2so56|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmr1g5de,https://wandb.ai/xzy11632/dance-dev/sweeps/7izot7qs,https://wandb.ai/xzy11632/dance-dev/sweeps/jlmorjb4","- type: filter.gene - target: FilterGenesPercentile - params: {} -- 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 -",0.32350000739097595,all_total_runs:510|all_finished_runs:391|step2_total_runs:450|step2_finished_runs:349|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:76.67%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.32350000739097595,,,,,,, -9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tjo2gadd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0h9izpy1,https://wandb.ai/xzy11632/dance-dev/sweeps/i8ghsgev,https://wandb.ai/xzy11632/dance-dev/sweeps/h1l9teot","- type: filter.gene - target: FilterGenesScanpyOrder - params: - 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 -",0.5149999856948853,all_total_runs:510|all_finished_runs:353|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:69.22%,False,"- 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 - 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target: FilterGenesPercentile - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.5485000014305115,,,,,,, -56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/om1u72x5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bfpl63bz,https://wandb.ai/xzy11632/dance-dev/sweeps/h86ptqve,https://wandb.ai/xzy11632/dance-dev/sweeps/hoc145hn","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: NormalizeTotal - params: - target_sum: 100000 - max_fraction: 0.5 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 226 - top: false - mode: rv -- type: feature.cell - 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target: FilterGenesPercentile - params: - min_val: 9 - max_val: 99 - mode: var -- type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: - min: 1 - max: 10 - gmean_eps: - min: 1 - max: 10 - n_genes: - min: 1000 - max: 3000 - n_cells: - values: - - null - - 1 - - 10 - - 100 - bin_size: - min: 300 - max: 800 - bw_adjust: - min: 1.0 - max: 5.0 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: - min_disp: - min: 0.05 - max: 0.5 - max_disp: - min: 1.0 - max: 100.0 - min_mean: - min: 0.0 - max: 0.0125 - max_mean: - min: 3.0 - max: 20.0 - n_bins: - min: 10 - max: 30 - flavor: - values: - - seurat - - cell_ranger -- type: feature.cell - target: WeightedFeatureSVD - params: - out: feature.cell - log_level: INFO - n_components: - min: 100 - max: 1000 - feat_norm_mode: - values: - - null - - normalize - - standardize - - minmax - - l2 -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.8744999766349792,all_total_runs:510|all_finished_runs:389|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False,"- type: filter.gene - 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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 -",0.2195000052452087 -d567b692-c374-4628-a508-8008f6778f22,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4raopmgl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tj8oqma7,https://wandb.ai/xzy11632/dance-dev/sweeps/j7f8tlxr,https://wandb.ai/xzy11632/dance-dev/sweeps/vo4w0lty","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: NormalizeTotal - params: - target_sum: 10000 - max_fraction: 1 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 399 - top: false - mode: rv -- type: feature.cell - target: CellSVD - params: - out: feature.cell - log_level: INFO - n_components: 846 -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.265500009059906,all_total_runs:510|all_finished_runs:410|step2_total_runs:450|step2_finished_runs:350|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.39%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- 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 -",0.2610000073909759 -e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hyf9hn73|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lmvwaqis,https://wandb.ai/xzy11632/dance-dev/sweeps/bfgvyy1a,https://wandb.ai/xzy11632/dance-dev/sweeps/e30as1qf","- type: filter.gene - 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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: 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 -",0.625 -f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/datmwta4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ri7gpq3f,https://wandb.ai/xzy11632/dance-dev/sweeps/6apaq3my,https://wandb.ai/xzy11632/dance-dev/sweeps/crgctmfi","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- 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 - 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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 -",0.29750001430511475,all_total_runs:459|all_finished_runs:352|step2_total_runs:450|step2_finished_runs:352|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:76.69%,False,"- type: filter.gene - 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 - 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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 -",0.3075000047683716 -f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8zlw0izq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/js85xigg,https://wandb.ai/xzy11632/dance-dev/sweeps/li8w1754,https://wandb.ai/xzy11632/dance-dev/sweeps/p4u94ygt","- type: filter.gene - target: FilterGenesPercentile - params: {} -- 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 - 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target: FilterGenesScanpyOrder - params: - order: - - min_counts - - max_counts - - min_cells - - max_cells - min_counts: 413 - min_cells: 0.07306060707222754 - max_counts: 0.9906711226720064 - max_cells: 0.9967104990967668 -- type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: 4 - gmean_eps: 1 - n_genes: 2400 - n_cells: null - bin_size: 538 - bw_adjust: 2.433119961706298 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 9618 - top: true - mode: var -- type: feature.cell - target: FeatureCellPlaceHolder - params: - out: feature.cell - log_level: INFO -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.3149999976158142,all_total_runs:510|all_finished_runs:340|step2_total_runs:450|step2_finished_runs:337|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:66.67%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.3084999918937683 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv deleted file mode 100644 index 512e728a..00000000 --- a/examples/atlas/sweep_results/Intestine_ans.csv +++ /dev/null @@ -1,345 +0,0 @@ -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 -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cal53l43|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6qn8k6fz,https://wandb.ai/xzy11632/dance-dev/sweeps/bk4iumv7,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwnnypr","- type: filter.gene - 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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 -",0.44999998807907104 -f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/968ejhzy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4mpkufxm,https://wandb.ai/xzy11632/dance-dev/sweeps/68q8gvfj,https://wandb.ai/xzy11632/dance-dev/sweeps/f094n1hy","- type: filter.gene - target: FilterGenesScanpyOrder - params: - 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 - 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max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.4715000092983246 -d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2efkko22|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5tshgz51,https://wandb.ai/xzy11632/dance-dev/sweeps/xj7266k8,https://wandb.ai/xzy11632/dance-dev/sweeps/hyob32ut","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 4 - max_val: 99 - mode: var -- type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: 1 - gmean_eps: 1 - n_genes: 2453 - n_cells: null - bin_size: 401 - bw_adjust: 3.4304615240549303 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 6303 - top: true - mode: sum -- 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 -",0.557421088218689,all_total_runs:493|all_finished_runs:362|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:73.43%,False,"- 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 - 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target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.2630000114440918,all_total_runs:493|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:357|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:73.02%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - 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target: FilterGenesPercentile - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.5335000157356262 -f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8kh86ent|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s95wr9an,https://wandb.ai/xzy11632/dance-dev/sweeps/vc4fkvqd,https://wandb.ai/xzy11632/dance-dev/sweeps/9cswqwn1","- type: filter.gene - target: FilterGenesScanpyOrder - params: - 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: CellPCA -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.5565000176429749,all_total_runs:476|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:344|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:76.26%,False,"- 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: CellPCA -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.5565000176429749 -105c7dad-0468-4628-a5be-2bb42c6a8ae4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ifoggvrj|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ux35adas,https://wandb.ai/xzy11632/dance-dev/sweeps/3eqw1s6m,https://wandb.ai/xzy11632/dance-dev/sweeps/g8eti0ga","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - max_counts - - max_cells - - min_cells - min_counts: 484 - min_cells: 0.0607859528781899 - max_counts: 0.9489684352815044 - max_cells: 0.9997931464413096 -- type: normalize - target: ScTransform - params: - processes_num: 8 - min_cells: 4 - gmean_eps: 1 - n_genes: 2675 - n_cells: 100 - bin_size: 687 - bw_adjust: 3.3573035291211055 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 6238 - n_bins: 28 - flavor: cell_ranger -- type: feature.cell - target: FeatureCellPlaceHolder - 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target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 8628 - n_bins: 18 - flavor: cell_ranger -- 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 -",0.42899999022483826,all_total_runs:510|all_finished_runs:360|step2_total_runs:450|step2_finished_runs:338|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.59%,False,"- type: filter.gene - 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 - 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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 -",0.2055000066757202 -0b4a15a7-4e9e-4555-9733-2423e5c66469,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nyj1bpi3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m9go9yqe,https://wandb.ai/xzy11632/dance-dev/sweeps/z7jtisk2,https://wandb.ai/xzy11632/dance-dev/sweeps/t16m4wm2","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - max_cells - - max_counts - - min_counts - - min_cells - min_counts: 195 - min_cells: 0.05756089036439415 - max_counts: 0.981004319592022 - max_cells: 0.9809071900458808 -- type: normalize - target: NormalizeTotal - params: - target_sum: 10000 - max_fraction: 0.5 -- type: filter.gene - target: FilterGenesRegression - params: - method: scmap - num_genes: 6616 -- 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 -",0.20499999821186063,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False,"- type: filter.gene - 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 - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.19949999451637268 -53d208b0-2cfd-4366-9866-c3c6114081bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/23fzd0cr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ltc7pxdm,https://wandb.ai/xzy11632/dance-dev/sweeps/lnn8aqay,https://wandb.ai/xzy11632/dance-dev/sweeps/vhcg91li","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - max_counts - - max_cells - - min_counts - - min_cells - min_counts: 417 - min_cells: 0.017197474107088717 - max_counts: 0.9777114640222584 - max_cells: 0.9742742842857086 -- type: normalize - target: NormalizePlaceHolder -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 9921 - top: false - mode: rv -- type: feature.cell - target: FeatureCellPlaceHolder - params: - out: feature.cell - log_level: INFO -- type: misc - target: SetConfig - 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- min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: NormalizeTotal - 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 -",0.2222222238779068 -f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hrylvzb1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/km714tee,https://wandb.ai/xzy11632/dance-dev/sweeps/5yr6v6hl,https://wandb.ai/xzy11632/dance-dev/sweeps/44mxsz2v","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - 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target: FilterGenesPlaceHolder -- type: normalize - target: NormalizeTotal - params: - target_sum: 1000 - max_fraction: 1 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 9315 - top: true - mode: rv -- 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 -",0.2696989178657532,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:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.28%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - 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target: FilterGenesPercentile - params: {} -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.3394160568714142 -fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58296xo1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ckbfs7l7,https://wandb.ai/xzy11632/dance-dev/sweeps/ri8pts3d,https://wandb.ai/xzy11632/dance-dev/sweeps/8i66984j","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 5 - max_val: 98 - mode: sum -- type: normalize - target: Log1P - params: - base: 4.533975561756228 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 4165 - top: false - mode: cv -- type: feature.cell - target: FeatureCellPlaceHolder - params: - 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target: FilterGenesScanpyOrder - params: - order: - - max_counts - - min_cells - - min_counts - - max_cells - min_counts: 97 - min_cells: 0.008669870041697503 - max_counts: 0.9782460305842908 - max_cells: 0.9930432468421152 -- type: normalize - target: NormalizePlaceHolder -- type: filter.gene - target: FilterGenesRegression - params: - method: scmap - num_genes: 9555 -- 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 -",0.4275000095367432,all_total_runs:493|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.48%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: 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 -",0.3790000081062317 -0b75c598-0893-4216-afe8-5414cab7739d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5j0mk5dm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qj8fwcsn,https://wandb.ai/xzy11632/dance-dev/sweeps/s1ybint1,https://wandb.ai/xzy11632/dance-dev/sweeps/np4gc8ac","- type: filter.gene - target: FilterGenesScanpyOrder - params: - 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 - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.22499999403953552,all_total_runs:510|all_finished_runs:363|step2_total_runs:450|step2_finished_runs:339|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.18%,False,"- type: filter.gene - 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 - target: FeatureCellPlaceHolder -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: feature.cell - label_channel: cell_type -",0.22499999403953552 -2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/098iecnp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0a785nvw,https://wandb.ai/xzy11632/dance-dev/sweeps/05d33k6p,https://wandb.ai/xzy11632/dance-dev/sweeps/a878cw3h","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: NormalizeTotal - params: - target_sum: 100000 - max_fraction: 1 -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 9957 - span: 0.2627532661141566 -- 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 -",0.4931623935699463,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: NormalizeTotal - 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 -",0.45897436141967773 -2423ce2c-3149-4cca-a2ff-cf682ea29b5f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3peh3ey|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pstn2il1,https://wandb.ai/xzy11632/dance-dev/sweeps/w0nlva0s,https://wandb.ai/xzy11632/dance-dev/sweeps/iw5hu22k","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_cells - - max_counts - min_counts: 499 - min_cells: 0.018131353485912372 - max_counts: 0.991161328623826 - max_cells: 0.9558836866906196 -- type: normalize - target: ScaleFeature - params: - mode: minmax - eps: 0.3 -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 9999 - top: true - mode: rv -- 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 -",0.8750647902488708,all_total_runs:510|all_finished_runs:401|step2_total_runs:450|step2_finished_runs:341|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:78.63%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: 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 -",0.870917558670044 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv deleted file mode 100644 index fb6a1786..00000000 --- a/examples/atlas/sweep_results/Pancreas_ans.csv +++ /dev/null @@ -1,931 +0,0 @@ -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 -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 - 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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 -78f10833-3e61-4fad-96c9-4bbd4f14bdfa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ile10jfv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8tfuwq6k,https://wandb.ai/xzy11632/dance-dev/sweeps/cwadf7td,https://wandb.ai/xzy11632/dance-dev/sweeps/6kx7b6kc","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - 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target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig - params: - config_dict: - label_channel: cell_type -",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: {} -- 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 - 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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 -",0.47699999809265137,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 - 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 -",0.47699999809265137 -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: {} -- 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: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig - 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 - 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 - 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 -",0.27399998903274536 -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: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig - params: - config_dict: - label_channel: cell_type -",0.4124999940395355,all_total_runs:210|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:93|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:65.24%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig - params: - config_dict: - label_channel: cell_type -",0.4124999940395355 -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: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell -- type: misc - target: SetConfig - params: - config_dict: - label_channel: cell_type -",0.3791748583316803,all_total_runs:196|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:80.61%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: 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 -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: {} -- 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:133|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:0|finished_rate:63.33%,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