From cf402bd24e6a668309dcf046e657bf234c92471a Mon Sep 17 00:00:00 2001 From: xzy Date: Wed, 15 Jan 2025 12:55:45 +0800 Subject: [PATCH] update ans --- examples/atlas/sweep_results/Blood_ans.csv | 2374 +++++++++++-- examples/atlas/sweep_results/Brain_ans.csv | 2224 +++++++++++- examples/atlas/sweep_results/Heart_ans.csv | 3019 +++++++++++++++-- .../atlas/sweep_results/Intestine_ans.csv | 316 +- examples/atlas/sweep_results/Kidney_ans.csv | 1088 +++++- examples/atlas/sweep_results/Lung_ans.csv | 2467 ++++++++++++-- examples/atlas/sweep_results/Pancreas_ans.csv | 880 ++++- 7 files changed, 11194 insertions(+), 1174 deletions(-) diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv index bb1a4a42..8b45331c 100644 --- a/examples/atlas/sweep_results/Blood_ans.csv +++ b/examples/atlas/sweep_results/Blood_ans.csv @@ -511,7 +511,59 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4636363685131073,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6x20gszq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zt8h2u2q,https://wandb.ai/xzy11632/dance-dev/sweeps/6u6zlhu5,https://wandb.ai/xzy11632/dance-dev/sweeps/mclm6mgq","- type: filter.gene +",0.4636363685131073,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ofw1llkf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uge2k7vi,https://wandb.ai/xzy11632/dance-dev/sweeps/qn85rgjd,https://wandb.ai/xzy11632/dance-dev/sweeps/kcp8pt1y","- 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 + 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 +",0.4272727370262146,all_total_runs:168|all_finished_runs:103|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:61.31%,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 + 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 +",0.4272727370262146,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6x20gszq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zt8h2u2q,https://wandb.ai/xzy11632/dance-dev/sweeps/6u6zlhu5,https://wandb.ai/xzy11632/dance-dev/sweeps/mclm6mgq","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -549,7 +601,49 @@ d3566d6a-a455-4a15-980f-45eb29114cab,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4545454545454546,,,,,,, +",0.4545454545454546,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/owszihkr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f49c7zeb,https://wandb.ai/xzy11632/dance-dev/sweeps/3l7yyix3,https://wandb.ai/xzy11632/dance-dev/sweeps/3hwiq1ug","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4636363685131073,all_total_runs:600|all_finished_runs:448|step2_total_runs:540|step2_finished_runs:390|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4636363685131073 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feature.cell + log_level: INFO + n_components: 840 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4377358555793762,all_total_runs:600|all_finished_runs:419|step2_total_runs:540|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:69.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + 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 +",0.4226415157318115 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FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.20600000023841855 +456e8b9b-f872-488b-871d-94534090a865,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wri3w9ug|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9c166tcq,https://wandb.ai/xzy11632/dance-dev/sweeps/0j1n56kx,https://wandb.ai/xzy11632/dance-dev/sweeps/3761sh9x","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal params: {} - type: filter.gene target: FilterGenesRegression @@ -774,7 +1092,63 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.2010000050067901,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lv0fx66b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ddug6xp,https://wandb.ai/xzy11632/dance-dev/sweeps/idxr1y9z,https://wandb.ai/xzy11632/dance-dev/sweeps/0iz6wobo","- type: filter.gene +",0.2010000050067901,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51cpr0d9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/95hn1egh,https://wandb.ai/xzy11632/dance-dev/sweeps/peld3u5u,https://wandb.ai/xzy11632/dance-dev/sweeps/on2ik08p","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 95 + mode: sum +- type: normalize + target: Log1P + params: + base: 9.417934904058548 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9808 + span: 0.19479949862140847 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 505 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.23399999737739563,all_total_runs:210|all_finished_runs:175|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2335000038146973,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lv0fx66b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ddug6xp,https://wandb.ai/xzy11632/dance-dev/sweeps/idxr1y9z,https://wandb.ai/xzy11632/dance-dev/sweeps/0iz6wobo","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -822,7 +1196,51 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.229,,,,,,, +",0.229,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w9issa4d|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/b06p6hx8,https://wandb.ai/xzy11632/dance-dev/sweeps/1i8tao7g,https://wandb.ai/xzy11632/dance-dev/sweeps/5l53xzqj","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2345000058412552,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2345000058412552 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Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -991,21 +1484,27 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3709999918937683,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:78.57%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} 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label_channel: cell_type +",0.3400000035762787,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cjdtc2ag|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fzjbv8p0,https://wandb.ai/xzy11632/dance-dev/sweeps/gtz5viph,https://wandb.ai/xzy11632/dance-dev/sweeps/4l2hy0fx","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3709999918937683,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:78.57%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: @@ -1068,7 +1614,67 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3585,,,,,,, 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+",0.1969999969005584,all_total_runs:510|all_finished_runs:401|step2_total_runs:450|step2_finished_runs:351|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.63%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1129,7 +1735,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.19699999690055847,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51smdbay|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mhvqib1h,https://wandb.ai/xzy11632/dance-dev/sweeps/qpmixdis,https://wandb.ai/xzy11632/dance-dev/sweeps/j2p0o87d","- type: filter.gene 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INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22349999845027924,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:428|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:81.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22349999845027924 2a498ace-872a-4935-984b-1afa70fd9886,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bq07gszd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bktx311f,https://wandb.ai/xzy11632/dance-dev/sweeps/5mdhsnx2,https://wandb.ai/xzy11632/dance-dev/sweeps/fcfzcmn5","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1264,7 +1914,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.19200000166893005,all_total_runs:510|all_finished_runs:390|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:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:76.47%,False,"- type: filter.gene +",0.19200000166893,all_total_runs:510|all_finished_runs:390|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:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:76.47%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1389,7 +2039,69 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.188,,,,,,, +",0.188,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b9mqelgd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3v1qtxjw,https://wandb.ai/xzy11632/dance-dev/sweeps/ww8lnegz,https://wandb.ai/xzy11632/dance-dev/sweeps/4o928ijc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.19499999284744263,all_total_runs:600|all_finished_runs:477|step2_total_runs:540|step2_finished_runs:427|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:13|finished_rate:79.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.19499999284744263 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bym68vxb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ecznwhs3,https://wandb.ai/xzy11632/dance-dev/sweeps/kqtogj5m,https://wandb.ai/xzy11632/dance-dev/sweeps/w9mcnr87","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1411,7 +2123,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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-3faad104-2ab8-4434-816d-474d8d2641db,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fizus47n|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/opykbimx,https://wandb.ai/xzy11632/dance-dev/sweeps/i46fxdho,https://wandb.ai/xzy11632/dance-dev/sweeps/0rpl7b1w","- type: filter.gene +",0.2635,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/965m42b6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2yalgnau,https://wandb.ai/xzy11632/dance-dev/sweeps/8t32838i,https://wandb.ai/xzy11632/dance-dev/sweeps/vudu58gr","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1532,7 +2243,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -1542,14 +2253,15 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22200000286102295,all_total_runs:510|all_finished_runs:408|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:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.00%,False,"- type: filter.gene +",0.289000004529953,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:439|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1562,7 +2274,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: Log1P params: {} - type: filter.gene target: FilterGenesTopK @@ -1572,46 +2284,108 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ params: out: feature.cell log_level: INFO - target: GaussRandProjFeature + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22200000286102295,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j9vqmqzc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/78oimcb2,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bv7omo,https://wandb.ai/xzy11632/dance-dev/sweeps/v818bxqg","- type: filter.gene - target: FilterGenesPercentile +",0.289000004529953 +3faad104-2ab8-4434-816d-474d8d2641db,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fizus47n|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/opykbimx,https://wandb.ai/xzy11632/dance-dev/sweeps/i46fxdho,https://wandb.ai/xzy11632/dance-dev/sweeps/0rpl7b1w","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 4 - max_val: 95 - mode: cv + 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: - base: 3.32067047306569 + target: NormalizeTotal + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesTopK params: - n_top_genes: 9665 - n_bins: 29 - flavor: cell_ranger + num_genes: 3000 - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 106 - feat_norm_mode: minmax -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: GaussRandProjFeature - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,"- type: filter.gene +",0.2220000028610229,all_total_runs:510|all_finished_runs:408|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:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: 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 +",0.2220000028610229,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j9vqmqzc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/78oimcb2,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bv7omo,https://wandb.ai/xzy11632/dance-dev/sweeps/v818bxqg","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 95 + mode: cv +- type: normalize + target: Log1P + params: + base: 3.32067047306569 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 9665 + n_bins: 29 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 106 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2440000027418137,all_total_runs:210|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:98|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.24%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1679,7 +2453,49 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2265,,,,,,, +",0.2265,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ho5r2gc4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kcxv2i8c,https://wandb.ai/xzy11632/dance-dev/sweeps/8wib619r,https://wandb.ai/xzy11632/dance-dev/sweeps/wbcfkea5","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.23849999904632568,all_total_runs:600|all_finished_runs:496|step2_total_runs:540|step2_finished_runs:436|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:82.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.23849999904632568 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+",0.2649999856948852,all_total_runs:510|all_finished_runs:397|step2_total_runs:450|step2_finished_runs:359|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:77.84%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1722,7 +2538,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.26499998569488525,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9despcsl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ezmsqc0q,https://wandb.ai/xzy11632/dance-dev/sweeps/wplvjtme,https://wandb.ai/xzy11632/dance-dev/sweeps/c3we0q6d","- type: filter.gene +",0.2649999856948852,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9despcsl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ezmsqc0q,https://wandb.ai/xzy11632/dance-dev/sweeps/wplvjtme,https://wandb.ai/xzy11632/dance-dev/sweeps/c3we0q6d","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1837,7 +2653,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.26249998807907104,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:76.17%,False,"- type: filter.gene +",0.262499988079071,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:429|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:76.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1868,7 +2684,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.26249998807907104 +",0.262499988079071 ae29ebd0-1973-40a4-a6af-d15a5f77a80f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nwvswg5l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ffiy65ls,https://wandb.ai/xzy11632/dance-dev/sweeps/schg2dj5,https://wandb.ai/xzy11632/dance-dev/sweeps/uqfhre10","- type: filter.gene target: FilterGenesPercentile params: @@ -1896,7 +2712,7 @@ ae29ebd0-1973-40a4-a6af-d15a5f77a80f,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.29499998688697815,all_total_runs:510|all_finished_runs:395|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:77.45%,False,"- type: filter.gene +",0.2949999868869781,all_total_runs:510|all_finished_runs:395|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:77.45%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2121,7 +2937,7 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type 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-",0.34299999475479126,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.83%,False,"- type: filter.gene +",0.3429999947547912,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.83%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2309,10 +3125,836 @@ bc260987-8ee5-4b6e-8773-72805166b3f7,"step2:https://wandb.ai/xzy11632/dance-dev/ target: SetConfig params: config_dict: - feature_channel: feature.cell + feature_channel: feature.cell + label_channel: cell_type +",0.3429999947547912 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normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- 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 +",0.2879999876022339 +b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7s03jiel|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dvxln80t,https://wandb.ai/xzy11632/dance-dev/sweeps/xcsvburm,https://wandb.ai/xzy11632/dance-dev/sweeps/3rm9yv2h","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.3 +- type: filter.gene + target: FilterGenesRegression + params: + method: enclasc + num_genes: 9151 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 773 + feat_norm_mode: null 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target: FilterGenesPercentile + params: + min_val: 2 + max_val: 95 + mode: rv +- type: normalize + target: NormalizeTotal + params: + target_sum: 100000 + max_fraction: 0.01 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 230 + top: true + mode: rv - type: feature.cell + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - target: FeatureCellPlaceHolder + n_components: 842 + feat_norm_mode: minmax - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22100000083446503,all_total_runs:510|all_finished_runs:371|step2_total_runs:450|step2_finished_runs:353|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:72.75%,False,"- type: filter.gene - target: FilterGenesPlaceHolder 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-",0.22100000083446503,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gih5b907|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3h8b4ia7,https://wandb.ai/xzy11632/dance-dev/sweeps/nqd9ry7o,https://wandb.ai/xzy11632/dance-dev/sweeps/vkrxl804","- type: filter.gene - target: FilterGenesPlaceHolder +",0.1665000021457672 +d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/viqji691|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/djfq0kbd,https://wandb.ai/xzy11632/dance-dev/sweeps/07jhuvad,https://wandb.ai/xzy11632/dance-dev/sweeps/um5kl8ak","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 99 + mode: rv - type: normalize target: ScaleFeature params: - mode: minmax - eps: 0.3 + mode: standardize + eps: 0.7 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 2457 - span: 0.4560040203055745 + n_top_genes: 2010 + n_bins: 28 + flavor: cell_ranger - type: feature.cell target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 963 - feat_norm_mode: minmax + n_components: 719 + feat_norm_mode: l2 - type: graph.cell target: CellFeatureGraph params: @@ -2384,14 +4058,14 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.2440000027418137,all_total_runs:210|all_finished_runs:160|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:6|finished_rate:76.19%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.1879999935626983,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -2399,7 +4073,7 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -2409,11 +4083,11 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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-",0.242,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jhrb659k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4414dhzk,https://wandb.ai/xzy11632/dance-dev/sweeps/annv74ih,https://wandb.ai/xzy11632/dance-dev/sweeps/sebccxo2","- type: filter.gene +",0.1715,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/khimppcz|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7dum9r3k,https://wandb.ai/xzy11632/dance-dev/sweeps/ecn9djtg,https://wandb.ai/xzy11632/dance-dev/sweeps/ncce9e88","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2456,12 +4130,12 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2474,7 +4148,7 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22849999368190765,all_total_runs:600|all_finished_runs:464|step2_total_runs:540|step2_finished_runs:433|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:77.33%,False,"- type: filter.gene +",0.1655000001192093,all_total_runs:601|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:21|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:84.53%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2487,12 +4161,12 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2505,81 +4179,71 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: feature.cell label_channel: cell_type -",0.22849999368190765 -d9b4bc69-ed90-4f5f-99b2-61b0681ba436,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jr5laoce|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/g2zr0j9a,https://wandb.ai/xzy11632/dance-dev/sweeps/qw5dtkuz,https://wandb.ai/xzy11632/dance-dev/sweeps/j6qftai2","- type: filter.gene - target: FilterGenesScanpyOrder +",0.1655000001192093 +471647b3-04fe-4c76-8372-3264feb950e8,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/294cixrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/82nqs7xy,https://wandb.ai/xzy11632/dance-dev/sweeps/sr152dog,https://wandb.ai/xzy11632/dance-dev/sweeps/9db3oova","- type: filter.gene + target: FilterGenesPercentile 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 + min_val: 4 + max_val: 96 + mode: cv - type: normalize target: ScTransform params: processes_num: 8 + min_cells: 6 + gmean_eps: 1 + n_genes: 2483 + n_cells: null + bin_size: 600 + bw_adjust: 2.93757162686828 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 5146 + span: 0.3488075399257312 - type: feature.cell + target: FeatureCellPlaceHolder params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type 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n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeaturePCA + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.3714999854564667,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/en37dusf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mc3gybd1,https://wandb.ai/xzy11632/dance-dev/sweeps/mo1fgrq0,https://wandb.ai/xzy11632/dance-dev/sweeps/algcvv9n","- type: filter.gene - target: FilterGenesPlaceHolder +",0.45391303300857544,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b2sjyq38|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mmw9arqn,https://wandb.ai/xzy11632/dance-dev/sweeps/j3manvbb,https://wandb.ai/xzy11632/dance-dev/sweeps/p3ar3r8e","- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2595,16 +4259,16 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4535000026226044,all_total_runs:210|all_finished_runs:163|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:77.62%,False,"- type: filter.gene - target: FilterGenesPlaceHolder +",0.4626086950302124,all_total_runs:210|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:95|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:62.86%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2620,7 +4284,7 @@ d9b4bc69-ed90-4f5f-99b2-61b0681ba436,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4535000026226044,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wtafbrz1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z6kwq1p8,https://wandb.ai/xzy11632/dance-dev/sweeps/6aybiwne,https://wandb.ai/xzy11632/dance-dev/sweeps/wttjwc6j","- type: filter.gene +",0.4626086950302124,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xsnur0f9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2r2wyqzg,https://wandb.ai/xzy11632/dance-dev/sweeps/fmc6g0fd,https://wandb.ai/xzy11632/dance-dev/sweeps/03yxho1k","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2633,11 +4297,10 @@ 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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 +",0.4365217387676239,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell @@ -2696,30 +4398,68 @@ 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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 +",0.8536009192466736,all_total_runs:511|all_finished_runs:361|step2_total_runs:451|step2_finished_runs:339|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:3|finished_rate:70.65%,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: FilterGenesNumberPlaceHolder + 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 + target: FeatureCellPlaceHolder - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.4325000047683716 -fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4oz0cf4p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2da7462h,https://wandb.ai/xzy11632/dance-dev/sweeps/heevau0y,https://wandb.ai/xzy11632/dance-dev/sweeps/x6elpm0s","- type: filter.gene +",0.8536009192466736,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nqd73gpc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0vkv2rcm,https://wandb.ai/xzy11632/dance-dev/sweeps/guwhe3e7,https://wandb.ai/xzy11632/dance-dev/sweeps/p9citqd9","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2732,18 +4472,18 @@ 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config_dict: label_channel: cell_type -",0.9113029837608336,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kdroab03|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/03u2wz8j,https://wandb.ai/xzy11632/dance-dev/sweeps/axsgwcx0,https://wandb.ai/xzy11632/dance-dev/sweeps/j8ds8gtj","- type: filter.gene +",0.8547815680503845,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ehzrgrvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fun57502,https://wandb.ai/xzy11632/dance-dev/sweeps/vt0nrjd6,https://wandb.ai/xzy11632/dance-dev/sweeps/iagsk9eg","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2803,8 +4543,9 @@ fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -2813,7 +4554,7 @@ fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.923861852433281,all_total_runs:150|all_finished_runs:107|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:71.33%,False,"- type: filter.gene +",0.8429752066115702,all_total_runs:150|all_finished_runs:90|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:60.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2829,8 +4570,9 @@ fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -2839,76 +4581,50 @@ fe52003e-1460-4a65-a213-2bb1a508332f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.923861852433281,,,,,,, -c2a461b1-0c15-4047-9fcb-1f966fe55100,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/com9229b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ix6500p3,https://wandb.ai/xzy11632/dance-dev/sweeps/ui6izi4v,https://wandb.ai/xzy11632/dance-dev/sweeps/ensewqbq","- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 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-",0.2714999914169311,all_total_runs:210|all_finished_runs:143|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:2|finished_rate:68.10%,False,"- type: filter.gene - target: FilterGenesScanpyOrder - params: - order: - - min_counts - - min_cells - - max_counts - - max_cells - min_counts: 0.01 - max_counts: 0.99 - min_cells: 0.01 - max_cells: 0.99 +",0.8453364968299866,all_total_runs:586|all_finished_runs:467|step2_total_runs:540|step2_finished_runs:427|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:20|finished_rate:79.69%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: FilterGenesNumberPlaceHolder params: {} - type: feature.cell params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: CellPCA - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2714999914169311,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y431lfy9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dq1c78iq,https://wandb.ai/xzy11632/dance-dev/sweeps/4n2extwx,https://wandb.ai/xzy11632/dance-dev/sweeps/pl4hig09","- type: filter.gene +",0.8453364968299866 +eeacb0c1-2217-4cf6-b8ce-1f0fedf1b569,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8ixv1rhg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r9jacav6,https://wandb.ai/xzy11632/dance-dev/sweeps/q6cmvwu6,https://wandb.ai/xzy11632/dance-dev/sweeps/t5aju4tb","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2921,21 +4637,26 @@ 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-",0.284,,,,,,, -b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7s03jiel|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dvxln80t,https://wandb.ai/xzy11632/dance-dev/sweeps/xcsvburm,https://wandb.ai/xzy11632/dance-dev/sweeps/3rm9yv2h","- type: filter.gene +",0.4641327559947967,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7bo3ceh1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dtijfdv0,https://wandb.ai/xzy11632/dance-dev/sweeps/hdzrhugh,https://wandb.ai/xzy11632/dance-dev/sweeps/41dsr5zv","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize - target: ScaleFeature + target: Log1P params: - mode: normalize - eps: 0.3 + base: 2.104951608085805 - type: filter.gene - target: FilterGenesRegression + target: FilterGenesTopK params: - method: enclasc - num_genes: 9151 + num_genes: 3803 + top: true + mode: cv - type: feature.cell target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 773 - feat_norm_mode: null + n_components: 127 + feat_norm_mode: minmax - type: graph.cell target: CellFeatureGraph params: @@ -2991,14 +4716,14 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.1739999949932098,all_total_runs:210|all_finished_runs:162|step2_total_runs:150|step2_finished_runs:112|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:77.14%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.5342612266540527,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -3006,7 +4731,7 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -3016,7 +4741,7 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: config_dict: label_channel: cell_type -",0.1724999994039535,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/06p1lum5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dh1b7ovm,https://wandb.ai/xzy11632/dance-dev/sweeps/bjql1aor","- type: filter.gene +",0.533725917339325,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c3yy5fd3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dr1ls28c,https://wandb.ai/xzy11632/dance-dev/sweeps/7rl62qzb,https://wandb.ai/xzy11632/dance-dev/sweeps/33lvyrau","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -3024,8 +4749,9 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -3034,7 +4760,7 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.169,all_total_runs:130|all_finished_runs:71|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:13|finished_rate:54.62%,True,"- type: filter.gene +",0.5187366167023555,all_total_runs:150|all_finished_runs:79|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:52.67%,True,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -3042,8 +4768,9 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -3052,45 +4779,51 @@ b0e547f0-462b-4f81-b31b-5b0a5d96f537,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.169,,,,,,, -d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/viqji691|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/djfq0kbd,https://wandb.ai/xzy11632/dance-dev/sweeps/07jhuvad,https://wandb.ai/xzy11632/dance-dev/sweeps/um5kl8ak","- type: filter.gene - target: FilterGenesPercentile +",0.5187366167023555,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rf2i7twp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/85j5c24x,https://wandb.ai/xzy11632/dance-dev/sweeps/kwna8mqg,https://wandb.ai/xzy11632/dance-dev/sweeps/8tvxcuym","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 6 - max_val: 99 - mode: rv + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature - params: - mode: standardize - eps: 0.7 + target: Log1P + params: {} - type: filter.gene target: HighlyVariableGenesLogarithmizedByTopGenes params: - n_top_genes: 2010 - n_bins: 28 - flavor: cell_ranger + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 719 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.1879999935626983,all_total_runs:210|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.57%,False,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.5251606106758118,all_total_runs:600|all_finished_runs:492|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:82.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene target: HighlyVariableGenesLogarithmizedByTopGenes @@ -3102,47 +4835,10 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,,,,,,,,"step2:https://wandb.ai/xzy11632/dan 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 -",0.176499992609024,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/r5o2z89s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zdzqqtvz,https://wandb.ai/xzy11632/dance-dev/sweeps/xp9872vg,https://wandb.ai/xzy11632/dance-dev/sweeps/74ynsvg4","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: NormalizeTotal - params: {} -- type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} -- type: feature.cell - target: SCNFeature -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: SCNFeature - label_channel: cell_type -",0.1715,all_total_runs:150|all_finished_runs:94|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:62.67%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: NormalizeTotal - params: {} -- type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} -- type: feature.cell - target: SCNFeature - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.1715,,,,,,, +",0.5251606106758118 diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv index d214440b..cabda022 100644 --- a/examples/atlas/sweep_results/Brain_ans.csv +++ b/examples/atlas/sweep_results/Brain_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 0bc7235a-ae5a-479d-a487-510435377e55,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8iryrobo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ki8v82q5,https://wandb.ai/xzy11632/dance-dev/sweeps/v6ql1ykl,https://wandb.ai/xzy11632/dance-dev/sweeps/mvwab59k","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -47,7 +47,123 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5544999837875366,,,,,,,,,,,,,, +",0.5544999837875366,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xuu3n6fc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fin2t33m,https://wandb.ai/xzy11632/dance-dev/sweeps/77fw5o6f,https://wandb.ai/xzy11632/dance-dev/sweeps/aqsvve2s","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5315,all_total_runs:150|all_finished_runs:61|step2_total_runs:90|step2_finished_runs:61|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:40.67%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5315,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/oxjgrsrd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w5pscp3d,https://wandb.ai/xzy11632/dance-dev/sweeps/s6b7bfmw,https://wandb.ai/xzy11632/dance-dev/sweeps/x51l7r3s","- 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5509999990463257,all_total_runs:600|all_finished_runs:504|step2_total_runs:540|step2_finished_runs:445|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: 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 +",0.5509999990463257 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Brain),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/888d5wod|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uiwmt8u5,https://wandb.ai/xzy11632/dance-dev/sweeps/rfx86so6,https://wandb.ai/xzy11632/dance-dev/sweeps/5ik43ov8","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -111,23 +227,109 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3675000071525574,,,,,,,,,,,,,, -9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lm5mwxkq,https://wandb.ai/xzy11632/dance-dev/sweeps/ortq51x9,https://wandb.ai/xzy11632/dance-dev/sweeps/lakwxgnu","- type: filter.gene - target: FilterGenesPlaceHolder +",0.3675000071525574,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o748tsyg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/py2yh3r8,https://wandb.ai/xzy11632/dance-dev/sweeps/cdz2iob0,https://wandb.ai/xzy11632/dance-dev/sweeps/ax6j7ylt","- type: filter.gene + target: FilterGenesPercentile params: {} - type: normalize - target: ScaleFeature + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3795,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesPercentile params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: FilterGenesRegression params: - n_top_genes: 3000 + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3795,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q84d43mh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7kx3k7oq,https://wandb.ai/xzy11632/dance-dev/sweeps/euoz4xtn,https://wandb.ai/xzy11632/dance-dev/sweeps/2mr5ac2i","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.382999986410141,all_total_runs:600|all_finished_runs:506|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.382999986410141 +9c63201d-bfd9-41a8-bbbc-18d947556f3d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bon88ucg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ml42ca0j,https://wandb.ai/xzy11632/dance-dev/sweeps/nsx84eyz,https://wandb.ai/xzy11632/dance-dev/sweeps/3k71zgrp","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 2467 + n_bins: 23 + flavor: cell_ranger +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 490 + feat_norm_mode: null - type: graph.cell target: CellFeatureGraph params: @@ -137,7 +339,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5440000295639038,all_total_runs:182|all_finished_runs:114|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.64%,False,"- type: filter.gene +",0.5460000038146973,all_total_runs:215|all_finished_runs:165|step2_total_runs:150|step2_finished_runs:110|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:26|step3_1_finished_runs:20|step3_2_total_runs:19|step3_2_finished_runs:15|finished_rate:76.74%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -162,36 +364,607 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5440000295639038,,,,,,,,,,,,,, -52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzh51eku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t7mnkajx,https://wandb.ai/xzy11632/dance-dev/sweeps/4n8979b9,https://wandb.ai/xzy11632/dance-dev/sweeps/pfvyypow","- type: filter.gene 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+",0.5295,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:58|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:78.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: - min_counts - min_cells - min_counts: 417 - min_cells: 0.0672634037707255 - max_counts: 0.9623011565598958 - max_cells: 0.9539584138468586 + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes params: - mode: minmax - eps: 0.1 + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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+",0.5335000157356262,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:444|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.83%,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 + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5335000157356262 +52f18bc3-52d9-487b-bf8f-f0b7aa684b09,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bzh51eku|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t7mnkajx,https://wandb.ai/xzy11632/dance-dev/sweeps/4n8979b9,https://wandb.ai/xzy11632/dance-dev/sweeps/pfvyypow","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_counts + - min_cells + min_counts: 417 + min_cells: 0.0672634037707255 + max_counts: 0.9623011565598958 + max_cells: 0.9539584138468586 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9466 + span: 0.3327063122842796 +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 985 + feat_norm_mode: minmax +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5895000100135803,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.5889999866485596,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/obu7ohqs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuwhe23l,https://wandb.ai/xzy11632/dance-dev/sweeps/mje7v676,https://wandb.ai/xzy11632/dance-dev/sweeps/30rb0den","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 9.81581694983002 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 8533 + span: 0.5476309362757072 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5825,all_total_runs:150|all_finished_runs:121|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:80.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.582,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h5sox1qq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tkk37137,https://wandb.ai/xzy11632/dance-dev/sweeps/8kuofdmo,https://wandb.ai/xzy11632/dance-dev/sweeps/v8plc2lh","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5895000100135803,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:439|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:83.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5895000100135803 +56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3580000102519989,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpa8itbf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yxhw6hrg,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwvhde7,https://wandb.ai/xzy11632/dance-dev/sweeps/1mzn11g0","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.373,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:71|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:61.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.373,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0xq25wc4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vmop7pif,https://wandb.ai/xzy11632/dance-dev/sweeps/8tn7yvjs,https://wandb.ai/xzy11632/dance-dev/sweeps/1dpu33ih","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3544999957084656,all_total_runs:600|all_finished_runs:502|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3544999957084656 +43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i9nym2ro|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ugip15uh,https://wandb.ai/xzy11632/dance-dev/sweeps/azouushu,https://wandb.ai/xzy11632/dance-dev/sweeps/fdz2z220","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033,all_total_runs:210|all_finished_runs:141|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:67.14%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.8740000128746033,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/887k1rjt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/oioj5d4q,https://wandb.ai/xzy11632/dance-dev/sweeps/i59rya2f,https://wandb.ai/xzy11632/dance-dev/sweeps/j210fgqq","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.873,all_total_runs:150|all_finished_runs:125|step2_total_runs:90|step2_finished_runs:68|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.33%,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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.873,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1t63xurp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uvq676zh,https://wandb.ai/xzy11632/dance-dev/sweeps/mfu80ue4,https://wandb.ai/xzy11632/dance-dev/sweeps/czug79hi","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8619999885559082,all_total_runs:600|all_finished_runs:500|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8619999885559082 +07760522-707a-4a1c-8891-dbd1226d6b27,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/flsm88dc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ggwltzko,https://wandb.ai/xzy11632/dance-dev/sweeps/6o4yy577,https://wandb.ai/xzy11632/dance-dev/sweeps/rq6r99by","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} - type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 9466 - span: 0.3327063122842796 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell - target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - n_components: 985 - feat_norm_mode: minmax + split_name: train + target: WeightedFeatureSVD - type: graph.cell target: CellFeatureGraph params: @@ -201,7 +974,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5895000100135803,all_total_runs:196|all_finished_runs:140|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:71.43%,False,"- type: filter.gene +",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -214,12 +987,11 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature + target: Log1P params: {} - type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell params: out: feature.cell @@ -235,59 +1007,61 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.5889999866485596,,,,,,,,,,,,,, -56c4912d-2bae-4b64-98f2-af8a84389208,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zfh6jo5f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/j4yerlyf,https://wandb.ai/xzy11632/dance-dev/sweeps/cupn87u2,https://wandb.ai/xzy11632/dance-dev/sweeps/k4amkwmq","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kygmspb8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lgj6yg3p,https://wandb.ai/xzy11632/dance-dev/sweeps/2kgqnf6r,https://wandb.ai/xzy11632/dance-dev/sweeps/j7yqtdud","- 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 + target: FilterGenesRegression params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.3580000102519989,all_total_runs:210|all_finished_runs:145|step2_total_runs:150|step2_finished_runs:106|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:8|finished_rate:69.05%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",1.0,all_total_runs:150|all_finished_runs:15|step2_total_runs:90|step2_finished_runs:7|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:10.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesRegression params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.3580000102519989,,,,,,,,,,,,,, -43b7e156-65b3-4a7b-8c7a-08528e4b21d0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i9nym2ro|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ugip15uh,https://wandb.ai/xzy11632/dance-dev/sweeps/azouushu,https://wandb.ai/xzy11632/dance-dev/sweeps/fdz2z220","- type: filter.gene 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filter.gene +",1.0 +146216e1-ec30-4fee-a1fb-25defe801e2d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -369,8 +1137,9 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: {} @@ -379,7 +1148,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -389,7 +1158,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:93|step2_total_runs:150|step2_finished_runs:85|step3_0_total_runs:20|step3_0_finished_runs:8|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:51.10%,True,"- type: filter.gene +",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -402,8 +1171,9 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: {} @@ -412,7 +1182,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -422,8 +1192,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,,,,,,,,,,,,,, -146216e1-ec30-4fee-a1fb-25defe801e2d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/wbnner7m|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ljivap3,https://wandb.ai/xzy11632/dance-dev/sweeps/omevjf6c,https://wandb.ai/xzy11632/dance-dev/sweeps/czvtu1mx","- type: filter.gene 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+",1.0,all_total_runs:150|all_finished_runs:18|step2_total_runs:90|step2_finished_runs:14|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:12.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/94jlkvhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pwo0mfuv,https://wandb.ai/xzy11632/dance-dev/sweeps/d1zcq1f3,https://wandb.ai/xzy11632/dance-dev/sweeps/45ment3z","- 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: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:168|all_finished_runs:107|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:63.69%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:436|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:81.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -470,28 +1290,25 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp + 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 + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,,,,,,,,, +",1.0 22658f4f-9268-41ad-8828-cc53f4baa9fa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t0uj441u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bhl2shvy,https://wandb.ai/xzy11632/dance-dev/sweeps/ce1n3vno,https://wandb.ai/xzy11632/dance-dev/sweeps/u9cpiusu","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -612,9 +1429,71 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: SCNFeature + label_channel: cell_type +",0.7735,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/iimj1dz0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yrrc1i9f,https://wandb.ai/xzy11632/dance-dev/sweeps/pqzc3r5k,https://wandb.ai/xzy11632/dance-dev/sweeps/fdwokoxq","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7609999775886536,all_total_runs:600|all_finished_runs:509|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.83%,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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.7735 +",0.7609999775886536 595c9010-99ec-462d-b6a1-2b2fe5407871,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t969ysm5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lkr2r2zq,https://wandb.ai/xzy11632/dance-dev/sweeps/kpnyhd83,https://wandb.ai/xzy11632/dance-dev/sweeps/tzy3vv3w","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -737,7 +1616,69 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.7595 +",0.7595,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/crxrjodt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s31c4wq8,https://wandb.ai/xzy11632/dance-dev/sweeps/ard4f4u9,https://wandb.ai/xzy11632/dance-dev/sweeps/6mriem5a","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7795000076293945,all_total_runs:600|all_finished_runs:488|step2_total_runs:540|step2_finished_runs:437|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7795000076293945 700aed19-c16e-4ba8-9191-07da098a8626,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9vvinymt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z0f6156l,https://wandb.ai/xzy11632/dance-dev/sweeps/fmt50h6n,https://wandb.ai/xzy11632/dance-dev/sweeps/pbhkpdsh","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -842,6 +1783,68 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/15mt3eq3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3pcc3teq,https://wandb.ai/xzy11632/dance-dev/sweeps/vsssu6xu,https://wandb.ai/xzy11632/dance-dev/sweeps/k69a11h0","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:438|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type ",1.0 70e4f35b-c98c-45a1-9aa9-2053b07315dd,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/17rooerg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k5eks81i,https://wandb.ai/xzy11632/dance-dev/sweeps/tjht44xq,https://wandb.ai/xzy11632/dance-dev/sweeps/jv70jolu","- type: filter.gene target: FilterGenesScanpyOrder @@ -971,7 +1974,51 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.484 +",0.484,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/grhvlnli|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pr5mnq0v,https://wandb.ai/xzy11632/dance-dev/sweeps/160tm6oy,https://wandb.ai/xzy11632/dance-dev/sweeps/o05jmzta","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4884999990463257,all_total_runs:600|all_finished_runs:502|step2_total_runs:540|step2_finished_runs:442|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:83.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4884999990463257 72822932-10f6-466f-baf3-a2c1d89364bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hkkcbz82|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cmx0xd8z,https://wandb.ai/xzy11632/dance-dev/sweeps/x6c34300,https://wandb.ai/xzy11632/dance-dev/sweeps/5l0emjk0","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1073,7 +2120,73 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3435 +",0.3435,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1ztr9p35|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z8modqe0,https://wandb.ai/xzy11632/dance-dev/sweeps/tdgslsq6,https://wandb.ai/xzy11632/dance-dev/sweeps/5ir3n8zd","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - max_counts + - min_cells + - min_counts + min_counts: 40 + min_cells: 0.08125217299144956 + max_counts: 0.9080661177583162 + max_cells: 0.9518281878428064 +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.5 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 1510 + n_bins: 15 + flavor: cell_ranger +- type: feature.cell + target: CellPCA + params: + out: feature.cell + log_level: INFO + n_components: 110 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.34150001406669617,all_total_runs:600|all_finished_runs:483|step2_total_runs:540|step2_finished_runs:423|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:80.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3409999907016754 9372df2d-13d6-4fac-980b-919a5b7eb483,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nmy20c1k|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vk37x3sb,https://wandb.ai/xzy11632/dance-dev/sweeps/2ygn08c2,https://wandb.ai/xzy11632/dance-dev/sweeps/0omklbn8","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1127,42 +2240,108 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s ",0.4934999942779541,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vugxebv6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iqwj2j8c,https://wandb.ai/xzy11632/dance-dev/sweeps/tta7mfwk,https://wandb.ai/xzy11632/dance-dev/sweeps/zmiplrsx","- type: filter.gene target: FilterGenesPercentile params: - min_val: 4 - max_val: 96 - mode: rv + min_val: 4 + max_val: 96 + mode: rv +- type: normalize + target: ScaleFeature + params: + mode: normalize + eps: 0.3 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5035,all_total_runs:150|all_finished_runs:83|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:55.33%,True,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ixh7uwhg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9ichlmte,https://wandb.ai/xzy11632/dance-dev/sweeps/akgvfhvf,https://wandb.ai/xzy11632/dance-dev/sweeps/0yr2q39w","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - max_cells + - min_counts + min_counts: 490 + min_cells: 0.0799339187017819 + max_counts: 0.9194196815998212 + max_cells: 0.9645400767614664 - type: normalize target: ScaleFeature params: - mode: normalize - eps: 0.3 + mode: minmax + eps: 0.7 - type: filter.gene - target: FilterGenesNumberPlaceHolder + target: HighlyVariableGenesRawCount + params: + n_top_genes: 9664 + span: 0.1714636071756561 - type: feature.cell - target: SCNFeature + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 279 + feat_norm_mode: standardize - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.5035,all_total_runs:150|all_finished_runs:83|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:55.33%,True,"- type: filter.gene - target: FilterGenesPercentile - params: {} +",0.5130000114440918,all_total_runs:600|all_finished_runs:486|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:81.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.5 +",0.5120000243186951 94c41723-b2c4-4b59-a49a-64c9b851903e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uc3r74ot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/s3l0vrwm,https://wandb.ai/xzy11632/dance-dev/sweeps/9vj7bbi4,https://wandb.ai/xzy11632/dance-dev/sweeps/mwg2kekc","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1261,7 +2440,51 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.52 +",0.52,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4bmyn7k4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ylbgm0wn,https://wandb.ai/xzy11632/dance-dev/sweeps/4fpuzvk1,https://wandb.ai/xzy11632/dance-dev/sweeps/3pqtwqki","- 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 + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5214999914169312,all_total_runs:600|all_finished_runs:508|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.67%,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 + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5214999914169312 9813a1d4-d107-459e-9b2e-7687be935f69,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/piw9m0r4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/83fzgznu,https://wandb.ai/xzy11632/dance-dev/sweeps/k12d4bb4,https://wandb.ai/xzy11632/dance-dev/sweeps/elc05kea","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1366,6 +2589,68 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lqheset7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxs7x3pm,https://wandb.ai/xzy11632/dance-dev/sweeps/zlciejor,https://wandb.ai/xzy11632/dance-dev/sweeps/x840lvth","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:478|step2_total_runs:540|step2_finished_runs:430|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:14|finished_rate:79.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: 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 ",1.0 c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ojpcn5g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/z9bpiv2r,https://wandb.ai/xzy11632/dance-dev/sweeps/d3yy3133,https://wandb.ai/xzy11632/dance-dev/sweeps/pbn9c42i","- type: filter.gene target: FilterGenesPlaceHolder @@ -1455,7 +2740,51 @@ c893ddc3-f25b-45e2-8c9e-155918b4261c,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.6525 +",0.6525,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sj7b58nh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nwnyv0md,https://wandb.ai/xzy11632/dance-dev/sweeps/63eiq8x8","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.640999972820282,all_total_runs:580|all_finished_runs:460|step2_total_runs:540|step2_finished_runs:420|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|finished_rate:79.31%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.640999972820282 e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pnrn8w7g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bpgm4640,https://wandb.ai/xzy11632/dance-dev/sweeps/8y4as678,https://wandb.ai/xzy11632/dance-dev/sweeps/9s7cwjsk","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1561,50 +2890,112 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ out: feature.cell log_level: INFO split_name: train - target: WeightedFeaturePCA + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7944999933242798,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/k94ikq6w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2sifydjq,https://wandb.ai/xzy11632/dance-dev/sweeps/muqarbip,https://wandb.ai/xzy11632/dance-dev/sweeps/p255tp2y","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8025,all_total_runs:150|all_finished_runs:96|step2_total_runs:90|step2_finished_runs:59|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:0|finished_rate:64.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.8025,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7v3lwalo|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kw2ikhb8,https://wandb.ai/xzy11632/dance-dev/sweeps/0m9yh1l4,https://wandb.ai/xzy11632/dance-dev/sweeps/6qay03k2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: feature_channel: feature.cell label_channel: cell_type -",0.7944999933242798,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/k94ikq6w|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2sifydjq,https://wandb.ai/xzy11632/dance-dev/sweeps/muqarbip,https://wandb.ai/xzy11632/dance-dev/sweeps/p255tp2y","- type: filter.gene - target: FilterGenesPercentile - params: {} -- type: normalize - target: Log1P - params: {} -- type: filter.gene - target: HighlyVariableGenesRawCount - params: - n_top_genes: 3000 -- type: feature.cell - target: SCNFeature -- type: misc - target: SetConfig +",0.7954999804496765,all_total_runs:600|all_finished_runs:505|step2_total_runs:540|step2_finished_runs:446|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder params: - config_dict: - feature_channel: SCNFeature - label_channel: cell_type 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364348b4-bc34-4fe1-a851-60d99e36cafa,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rtybof1t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8i4spm76,https://wandb.ai/xzy11632/dance-dev/sweeps/s2fldxlp,https://wandb.ai/xzy11632/dance-dev/sweeps/ew7a4p33","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1709,7 +3100,55 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4675 +",0.4675,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gsqa6qn6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hp6az7jq,https://wandb.ai/xzy11632/dance-dev/sweeps/9i3b010j,https://wandb.ai/xzy11632/dance-dev/sweeps/ysm8mfqg","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 5 + max_val: 97 + mode: rv +- type: normalize + target: NormalizeTotal + params: + target_sum: 10000 + max_fraction: 0.05 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 532 + feat_norm_mode: minmax +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.47200000286102295,all_total_runs:600|all_finished_runs:484|step2_total_runs:540|step2_finished_runs:425|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:80.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4715000092983246 93cb76aa-a84b-4a92-8e6c-66a914e26d4c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/aqfmsmpx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sxj7ndgn,https://wandb.ai/xzy11632/dance-dev/sweeps/kf6pxhij,https://wandb.ai/xzy11632/dance-dev/sweeps/kfpas6cb","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1832,7 +3271,71 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5005 +",0.5005,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6mib6vb3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rrbcza8h,https://wandb.ai/xzy11632/dance-dev/sweeps/84l9elo3,https://wandb.ai/xzy11632/dance-dev/sweeps/j16ha10r","- 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 +",0.5139999985694885,all_total_runs:587|all_finished_runs:458|step2_total_runs:540|step2_finished_runs:424|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:21|step3_2_finished_runs:14|finished_rate:78.02%,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 +",0.5139999985694885 d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rl05x7ci|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zrcomei,https://wandb.ai/xzy11632/dance-dev/sweeps/bt85t5r6,https://wandb.ai/xzy11632/dance-dev/sweeps/pt4fsfec","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1939,7 +3442,49 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5983910891089109 +",0.5983910891089109,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/58chvobl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qnjsie2l,https://wandb.ai/xzy11632/dance-dev/sweeps/nvedfna7,https://wandb.ai/xzy11632/dance-dev/sweeps/h3mv5jvv","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5866336822509766,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:434|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:75.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5866336822509766 774c18c5-efa1-4dc5-9e5e-2c824bab2e34,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2b6ovf5e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/p16tpv7x,https://wandb.ai/xzy11632/dance-dev/sweeps/3sk7tq5f,https://wandb.ai/xzy11632/dance-dev/sweeps/c2j4hpev","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2060,7 +3605,49 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4825662482566248 +",0.4825662482566248,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n18bq62d|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m9mopes9,https://wandb.ai/xzy11632/dance-dev/sweeps/xyehmf38,https://wandb.ai/xzy11632/dance-dev/sweeps/edu8cxmh","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5299860239028931,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:389|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5299860239028931 3d044b52-140a-4528-bf0d-a2dbef9e1f40,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/32erao2o|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/d907a0yd,https://wandb.ai/xzy11632/dance-dev/sweeps/goiqwztt,https://wandb.ai/xzy11632/dance-dev/sweeps/ihj7vn5a","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -2145,10 +3732,40 @@ d5452b83-7c3d-4d7c-ab7a-c7fece7196c5,"step2:https://wandb.ai/xzy11632/dance-dev/ target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: SCNFeature + label_channel: cell_type +",0.4053030303030303,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ar7vpgcg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lekzswh7,https://wandb.ai/xzy11632/dance-dev/sweeps/8hdww3lf,https://wandb.ai/xzy11632/dance-dev/sweeps/96ciucvt","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.4053030303030303 -f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e8vlk083,https://wandb.ai/xzy11632/dance-dev/sweeps/mwggo6ee,https://wandb.ai/xzy11632/dance-dev/sweeps/33pi0zc3","- type: filter.gene +",0.3901515007019043,all_total_runs:600|all_finished_runs:482|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2161,18 +3778,57 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + 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 +",0.3901515007019043 +f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kvawc25y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9sheweny,https://wandb.ai/xzy11632/dance-dev/sweeps/b0rongi3,https://wandb.ai/xzy11632/dance-dev/sweeps/ekmf487e","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_counts + - min_cells + - min_counts + - max_cells + min_counts: 263 + min_cells: 0.09338611959221152 + max_counts: 0.9103664063089278 + max_cells: 0.9776450063364456 +- type: normalize + target: Log1P + params: + base: 9.78567214435452 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: + min_disp: 0.42152838507294543 + max_disp: 90.25784555274645 + min_mean: 0.003754725333592855 + max_mean: 13.674551723139253 + n_bins: 13 + flavor: seurat +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 484 + feat_norm_mode: minmax - type: graph.cell target: CellFeatureGraph params: @@ -2182,7 +3838,7 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.5130813717842102,all_total_runs:182|all_finished_runs:137|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.27%,False,"- type: filter.gene +",0.5167151093482971,all_total_runs:210|all_finished_runs:176|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.81%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -2273,7 +3929,69 @@ f6d9f2ad-5ec7-4d53-b7f0-ceb0e7bcd181,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5159883720930233 +",0.5159883720930233,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c6dubcot|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6h51vv85,https://wandb.ai/xzy11632/dance-dev/sweeps/3wbf935e,https://wandb.ai/xzy11632/dance-dev/sweeps/eaxe9v47","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5254360437393188,all_total_runs:600|all_finished_runs:495|step2_total_runs:540|step2_finished_runs:435|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:82.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5254360437393188 f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4voqq7a0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6para2wq,https://wandb.ai/xzy11632/dance-dev/sweeps/cabldqak,https://wandb.ai/xzy11632/dance-dev/sweeps/s2xpuetf","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -2362,7 +4080,49 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.6617357001972387 +",0.6617357001972387,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/983ind0g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jcaz6527,https://wandb.ai/xzy11632/dance-dev/sweeps/wfvyft6a,https://wandb.ai/xzy11632/dance-dev/sweeps/c947lcfl","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6814595460891724,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:423|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.83%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6814595460891724 576f193c-75d0-4a11-bd25-8676587e6dc2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zmxfvz4r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5pamm1zp,https://wandb.ai/xzy11632/dance-dev/sweeps/a0z7ol9w,https://wandb.ai/xzy11632/dance-dev/sweeps/e3io8n98","- type: filter.gene target: FilterGenesPercentile params: {} @@ -2449,7 +4209,51 @@ f64e1be1-de15-4d27-8da4-82225cd4c035,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5268817204301075 +",0.5268817204301075,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hczkf4io|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6hi8qvm1,https://wandb.ai/xzy11632/dance-dev/sweeps/lgckqg0v,https://wandb.ai/xzy11632/dance-dev/sweeps/t06qe0t3","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5136476159095764,all_total_runs:600|all_finished_runs:493|step2_total_runs:540|step2_finished_runs:433|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:82.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5136476159095764 ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/933n8vho|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wsvx4b09,https://wandb.ai/xzy11632/dance-dev/sweeps/onnj2wg3,https://wandb.ai/xzy11632/dance-dev/sweeps/lgf5xaby","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -2534,7 +4338,51 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4921282798833819 +",0.4921282798833819,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/3yr6bmem|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2jjcov9j,https://wandb.ai/xzy11632/dance-dev/sweeps/frj335ws,https://wandb.ai/xzy11632/dance-dev/sweeps/e0ceayft","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5026239156723022,all_total_runs:600|all_finished_runs:485|step2_total_runs:540|step2_finished_runs:425|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:80.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5026239156723022 421e5f54-5de7-425f-b399-34ead0651ce1,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2v3pfqs3|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/exctgkg7,https://wandb.ai/xzy11632/dance-dev/sweeps/0ilextij,https://wandb.ai/xzy11632/dance-dev/sweeps/hxwj0qn7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2657,4 +4505,46 @@ ed11cc3e-2947-407c-883c-c53b043917c3,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.9265 +",0.9265,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mtgx8qhv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wllx4ks3,https://wandb.ai/xzy11632/dance-dev/sweeps/u1ypef2p,https://wandb.ai/xzy11632/dance-dev/sweeps/hsa4s4fk","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9419999718666076,all_total_runs:600|all_finished_runs:498|step2_total_runs:540|step2_finished_runs:443|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.9419999718666076 diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv index f4c4dfd3..de4dd679 100644 --- a/examples/atlas/sweep_results/Heart_ans.csv +++ b/examples/atlas/sweep_results/Heart_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_celltypist_step2_best_yaml,cta_celltypist_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res 5a11f879-d1ef-458a-910c-9b0bdfca5ebf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c1y9hl9c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9gz3pmi2,https://wandb.ai/xzy11632/dance-dev/sweeps/pwb5373a,https://wandb.ai/xzy11632/dance-dev/sweeps/4kab8419","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -93,7 +93,61 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.9365079402923584,,,,,,, +",0.9365079402923584,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wl63ncu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tyhv65th,https://wandb.ai/xzy11632/dance-dev/sweeps/0d2njqgp,https://wandb.ai/xzy11632/dance-dev/sweeps/nmhbwu4c","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9435626102292768,all_total_runs:150|all_finished_runs:102|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:68.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9435626102292768 1c739a3e-c3f5-49d5-98e0-73975e751201,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/pe7wrxhx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bjghjlj5,https://wandb.ai/xzy11632/dance-dev/sweeps/wahyq279,https://wandb.ai/xzy11632/dance-dev/sweeps/33b4rte8","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -147,7 +201,58 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.3370000123977661,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z2v6lwrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zebalczl,https://wandb.ai/xzy11632/dance-dev/sweeps/av6xm0h7,https://wandb.ai/xzy11632/dance-dev/sweeps/lx1ky4rl","- type: filter.gene +",0.3370000123977661,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nc4mh2qv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/l6b41sk3,https://wandb.ai/xzy11632/dance-dev/sweeps/2n26rwm1,https://wandb.ai/xzy11632/dance-dev/sweeps/bs2h91ra","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 10 + max_val: 98 + mode: var +- type: normalize + target: Log1P + params: + base: 9.926418705617555 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 546 + top: true + mode: cv +- type: feature.cell + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 733 + feat_norm_mode: null +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3294999897480011,all_total_runs:600|all_finished_runs:436|step2_total_runs:540|step2_finished_runs:389|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:12|finished_rate:72.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.32850000262260437,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z2v6lwrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zebalczl,https://wandb.ai/xzy11632/dance-dev/sweeps/av6xm0h7,https://wandb.ai/xzy11632/dance-dev/sweeps/lx1ky4rl","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -205,7 +310,41 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.28450000286102295 +",0.2845000028610229,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cz5nv4k7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7y02zy49,https://wandb.ai/xzy11632/dance-dev/sweeps/2osv7399,https://wandb.ai/xzy11632/dance-dev/sweeps/zo9ku2lg","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.353,all_total_runs:150|all_finished_runs:106|step2_total_runs:90|step2_finished_runs:63|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:70.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.353 4ed927e9-c099-49af-b8ce-a2652d069333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gl8a9d5v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nrpkd1s1,https://wandb.ai/xzy11632/dance-dev/sweeps/i4ot3t4a,https://wandb.ai/xzy11632/dance-dev/sweeps/1off7yhe","- type: filter.gene target: FilterGenesPercentile params: @@ -272,7 +411,51 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.2770000100135803,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lxi0z80g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spk2mp9z,https://wandb.ai/xzy11632/dance-dev/sweeps/xwvu3aat,https://wandb.ai/xzy11632/dance-dev/sweeps/ssfi4ars","- type: filter.gene +",0.2770000100135803,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hw7iu7r7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/nq363zvg,https://wandb.ai/xzy11632/dance-dev/sweeps/q9ttsvw9,https://wandb.ai/xzy11632/dance-dev/sweeps/tb6ulcb5","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2605000138282776,all_total_runs:586|all_finished_runs:422|step2_total_runs:540|step2_finished_runs:391|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:72.01%,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: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2605000138282776,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lxi0z80g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spk2mp9z,https://wandb.ai/xzy11632/dance-dev/sweeps/xwvu3aat,https://wandb.ai/xzy11632/dance-dev/sweeps/ssfi4ars","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: Log1P @@ -294,7 +477,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.24899999797344208,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:72.35%,False,"- type: filter.gene +",0.248999997973442,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:72.35%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -324,7 +507,53 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: feature.cell label_channel: cell_type -",0.24699999392032623 +",0.2469999939203262,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/98f9waz4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pnvn9x31,https://wandb.ai/xzy11632/dance-dev/sweeps/ptnisndu,https://wandb.ai/xzy11632/dance-dev/sweeps/b5708jv5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_counts + - min_cells + - max_cells + min_counts: 74 + min_cells: 0.09669474709406638 + max_counts: 0.960778034561404 + max_cells: 0.9605326701065215 +- type: normalize + target: Log1P + params: + base: 4.732515014862363 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 8735 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.2755,all_total_runs:150|all_finished_runs:103|step2_total_runs:90|step2_finished_runs:59|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:5|finished_rate:68.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.27 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type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -419,16 +647,13 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:64.80%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:465|step2_total_runs:540|step2_finished_runs:413|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:77.50%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -453,72 +678,70 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,,,,,,,,, -572f3f3e-d3e4-4d13-8e2b-88215e508481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gaurbw0r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5luhlhr8,https://wandb.ai/xzy11632/dance-dev/sweeps/6cvflsss,https://wandb.ai/xzy11632/dance-dev/sweeps/tdxjnsvf","- type: filter.gene - target: FilterGenesPlaceHolder +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y0qtxk9j|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bl395yon,https://wandb.ai/xzy11632/dance-dev/sweeps/adza96q3,https://wandb.ai/xzy11632/dance-dev/sweeps/g9bz7g6m","- 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 + target: ScTransform params: - mode: l2 - eps: 0.5 + processes_num: 8 - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 9960 - top: true - mode: rv + n_top_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA - params: - out: feature.cell - log_level: INFO - n_components: 280 - feat_norm_mode: normalize -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.4004999995231629,all_total_runs:210|all_finished_runs:178|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.76%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} -- type: normalize - target: ScaleFeature - params: {} -- type: filter.gene - target: FilterGenesTopK - params: - num_genes: 3000 -- type: feature.cell +",1.0,all_total_runs:150|all_finished_runs:3|step2_total_runs:90|step2_finished_runs:3|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:2.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph + 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: - cell_feature_channel: feature.cell + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.3995000123977661,,,,,,,,,,,,,, -1009f384-b12d-448e-ba9f-1b7d2ecfbb4e,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/amviyxfs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ix2rrweg,https://wandb.ai/xzy11632/dance-dev/sweeps/xapwqo4n,https://wandb.ai/xzy11632/dance-dev/sweeps/f4x92sq0","- type: filter.gene +",1.0 +97a17473-e2b1-4f31-a544-44a60773e2dd,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5n3rvy41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/863btck9,https://wandb.ai/xzy11632/dance-dev/sweeps/2eikroc1,https://wandb.ai/xzy11632/dance-dev/sweeps/ga9o1zyj","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -552,7 +775,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,all_total_runs:196|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:127|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:81.12%,False,"- type: filter.gene +",1.0,all_total_runs:196|all_finished_runs:127|step2_total_runs:150|step2_finished_runs:107|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:7|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:64.80%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -586,8 +809,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,,,,,,,,,,,,,, -1062c0f2-2a44-4cf9-a7c8-b5ed58b4728d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6dw5iyg7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/06k4gi1t,https://wandb.ai/xzy11632/dance-dev/sweeps/le8r1zi4,https://wandb.ai/xzy11632/dance-dev/sweeps/ocpspe17","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/twupybq1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fhdtfxvs,https://wandb.ai/xzy11632/dance-dev/sweeps/p0i060ck,https://wandb.ai/xzy11632/dance-dev/sweeps/rdft757u","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -612,16 +834,13 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:81.90%,False,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:404|step2_total_runs:540|step2_finished_runs:373|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:67.33%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -646,17 +865,13 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",1.0,,,,,,,,,,,,,, -1252c5fb-945f-42d6-b1a8-8a3bd864384b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jfnzokgb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ca7a5g7f,https://wandb.ai/xzy11632/dance-dev/sweeps/h30t1cml,https://wandb.ai/xzy11632/dance-dev/sweeps/mnapim92","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -672,25 +887,18 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,all_total_runs:182|all_finished_runs:144|step2_total_runs:150|step2_finished_runs:131|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.12%,False,"- type: filter.gene +",1.0,all_total_runs:150|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:40|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:59.33%,True,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -706,15 +914,38 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0 +572f3f3e-d3e4-4d13-8e2b-88215e508481,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gaurbw0r|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5luhlhr8,https://wandb.ai/xzy11632/dance-dev/sweeps/6cvflsss,https://wandb.ai/xzy11632/dance-dev/sweeps/tdxjnsvf","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.5 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 9960 + top: true + mode: rv +- type: feature.cell + target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD + n_components: 280 + feat_norm_mode: normalize - type: graph.cell target: CellFeatureGraph params: @@ -724,32 +955,22 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",1.0,,,,,,,,,,,,,, -9434b020-de42-43eb-bcc4-542b2be69015,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qfzblohn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fs7r3zpn,https://wandb.ai/xzy11632/dance-dev/sweeps/cdk9uk18,https://wandb.ai/xzy11632/dance-dev/sweeps/0zjjl1n1","- type: filter.gene - target: FilterGenesScanpyOrder - params: - 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 +",0.4004999995231629,all_total_runs:210|all_finished_runs:178|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.76%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} - type: normalize target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesTopK params: - n_top_genes: 3000 + num_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -759,7 +980,95 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.9725000262260436,all_total_runs:196|all_finished_runs:156|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:79.59%,False,"- type: filter.gene +",0.3995000123977661,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dllmfk0t|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pdu1htvk,https://wandb.ai/xzy11632/dance-dev/sweeps/9mfsvnog,https://wandb.ai/xzy11632/dance-dev/sweeps/fohrpha2","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3944999873638153,all_total_runs:558|all_finished_runs:349|step2_total_runs:540|step2_finished_runs:349|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:62.54%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3944999873638153,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/uwriv450|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9hfqgivj,https://wandb.ai/xzy11632/dance-dev/sweeps/hp8z8z34,https://wandb.ai/xzy11632/dance-dev/sweeps/ejfw0jpu","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - max_cells + - min_counts + - max_counts + - min_cells + min_counts: 346 + min_cells: 0.0694734963763344 + max_counts: 0.9289519358097762 + max_cells: 0.9793397916743596 +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.5 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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@@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s params: config_dict: label_channel: cell_type -",0.9725000262260436,,,,,,,,,,,,,, -a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9nsespwt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fckv2ie6,https://wandb.ai/xzy11632/dance-dev/sweeps/23djawcn,https://wandb.ai/xzy11632/dance-dev/sweeps/nt9416y1","- type: filter.gene +",1.0,all_total_runs:196|all_finished_runs:159|step2_total_runs:150|step2_finished_runs:127|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:81.12%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -810,7 +1118,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/ target: ScaleFeature params: {} - type: filter.gene - target: HighlyVariableGenesLogarithmizedByTopGenes + target: 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WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.2924999892711639,,,,,,,,,,,,,, -e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/c2luijzg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ohzu189d,https://wandb.ai/xzy11632/dance-dev/sweeps/xk206l8b,https://wandb.ai/xzy11632/dance-dev/sweeps/j5aozig6","- type: filter.gene +",1.0 +1252c5fb-945f-42d6-b1a8-8a3bd864384b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sno8i9gr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emiq1b6f,https://wandb.ai/xzy11632/dance-dev/sweeps/gsm0u3kf,https://wandb.ai/xzy11632/dance-dev/sweeps/ciumcc4l","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1159,7 +1416,7 @@ e6a11140-2545-46bc-929e-da243eed2cae,"step2:https://wandb.ai/xzy11632/dance-dev/ 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CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3880000114440918,all_total_runs:196|all_finished_runs:154|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:78.57%,False,"- type: filter.gene - target: FilterGenesPercentile +",1.0,all_total_runs:558|all_finished_runs:168|step2_total_runs:540|step2_finished_runs:168|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:30.11%,True,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize - target: Log1P + target: NormalizeTotal params: {} - type: filter.gene - target: FilterGenesTopK + target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell @@ -1235,17 +1488,13 @@ f15e263b-6544-46cb-a46e-e33ab7ce8347,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3880000114440918,,,,,,,,,,,,,, -f75f2ff4-2884-4c2d-b375-70de37a34507,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/as6ivetf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/icsk75i5,https://wandb.ai/xzy11632/dance-dev/sweeps/vtlcraw8,https://wandb.ai/xzy11632/dance-dev/sweeps/qjov7ai7","- type: filter.gene +",1.0,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gw31w8jw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/byh0a3yl,https://wandb.ai/xzy11632/dance-dev/sweeps/44fxvkm1,https://wandb.ai/xzy11632/dance-dev/sweeps/qwzcemto","- type: filter.gene target: FilterGenesScanpyOrder params: 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-",1.0,,,,,,,,,,,,,, -f7995301-7551-4e1d-8396-ffe3c9497ace,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/on56q36a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1z4xejov,https://wandb.ai/xzy11632/dance-dev/sweeps/dmtgt30u,https://wandb.ai/xzy11632/dance-dev/sweeps/jra56t1o","- type: filter.gene +",1.0 +9434b020-de42-43eb-bcc4-542b2be69015,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qfzblohn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fs7r3zpn,https://wandb.ai/xzy11632/dance-dev/sweeps/cdk9uk18,https://wandb.ai/xzy11632/dance-dev/sweeps/0zjjl1n1","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1348,7 +1585,7 @@ f7995301-7551-4e1d-8396-ffe3c9497ace,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type 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-fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ypo5xler|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/75anan67,https://wandb.ai/xzy11632/dance-dev/sweeps/js80dvkm,https://wandb.ai/xzy11632/dance-dev/sweeps/uqz1gvwh","- type: filter.gene +",0.9725000262260436,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ljcbdxpa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cd3jmhod,https://wandb.ai/xzy11632/dance-dev/sweeps/iuk576pz,https://wandb.ai/xzy11632/dance-dev/sweeps/xgyejfld","- 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 + - min_cells + - min_counts + min_counts: 464 + min_cells: 0.03355997076275901 + max_counts: 0.9675911149628488 + max_cells: 0.956159811249128 - type: normalize - target: Log1P - params: {} + target: ScaleFeature + params: + mode: minmax + eps: 0.5 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 4104 + span: 0.5225329617640444 - type: feature.cell + target: WeightedFeatureSVD params: out: feature.cell log_level: INFO - split_name: train - target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + n_components: 662 + feat_norm_mode: standardize - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6775000095367432,all_total_runs:210|all_finished_runs:188|step2_total_runs:150|step2_finished_runs:128|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:89.52%,False,"- type: filter.gene 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label_channel: cell_type -",0.6775000095367432,,,,,,,,,,,,,, -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Heart),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nrlo0chb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/itw8aeyv,https://wandb.ai/xzy11632/dance-dev/sweeps/gpjulqb6,https://wandb.ai/xzy11632/dance-dev/sweeps/c1at5qua","- type: filter.gene +",0.9664999842643738,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cyx8x2ef|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cm2y2e85,https://wandb.ai/xzy11632/dance-dev/sweeps/znjdtv6p,https://wandb.ai/xzy11632/dance-dev/sweeps/46gbjbvk","- type: filter.gene target: FilterGenesPercentile - params: - min_val: 10 - max_val: 99 - mode: rv + params: {} - type: normalize - target: Log1P + target: ScTransform params: - base: 9.18544800269841 + processes_num: 8 - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: - min_disp: 0.4075238200301367 - max_disp: 41.50678547261833 - min_mean: 0.00843552051034461 - max_mean: 8.182103499798425 - n_bins: 29 - flavor: cell_ranger + params: {} - type: feature.cell - target: WeightedFeatureSVD - params: - out: feature.cell - log_level: INFO - n_components: 745 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.3445000052452087,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene +",0.9405,all_total_runs:150|all_finished_runs:89|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:59.33%,True,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize - target: Log1P - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.9405 +a68b64d8-aee3-4947-81b7-36b8fe5a44d2,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9nsespwt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fckv2ie6,https://wandb.ai/xzy11632/dance-dev/sweeps/23djawcn,https://wandb.ai/xzy11632/dance-dev/sweeps/nt9416y1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train - target: WeightedFeatureSVD + target: WeightedFeaturePCA - type: graph.cell target: CellFeatureGraph params: @@ -1509,61 +1756,1936 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3434999883174896,,,,,,,,,,,,,, -65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s66g7ypd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kuznrzx4,https://wandb.ai/xzy11632/dance-dev/sweeps/t9vtfezo,https://wandb.ai/xzy11632/dance-dev/sweeps/adq7j7mn","- type: filter.gene - target: FilterGenesPlaceHolder -- type: normalize - target: Log1P - params: - base: 7.954575208692654 -- type: filter.gene - target: FilterGenesTopK 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FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6345000267028809,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/evq18crq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hlqtxu6d,https://wandb.ai/xzy11632/dance-dev/sweeps/ijgh3h21,https://wandb.ai/xzy11632/dance-dev/sweeps/pwgh6hr9","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6355,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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cell_type +",0.3445000052452087,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3434999883174896,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9gykotmw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/erompt6i,https://wandb.ai/xzy11632/dance-dev/sweeps/egu5uugr,https://wandb.ai/xzy11632/dance-dev/sweeps/mld787ay","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + 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 +",0.3395000100135803,all_total_runs:600|all_finished_runs:501|step2_total_runs:540|step2_finished_runs:442|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.50%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3395000100135803,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qckzvsgm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q0dzg8at,https://wandb.ai/xzy11632/dance-dev/sweeps/d1jd1aip,https://wandb.ai/xzy11632/dance-dev/sweeps/0riym8d4","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.353035738226729 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3613 + span: 0.5980502565579662 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3535,all_total_runs:150|all_finished_runs:135|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:90.00%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: NormalizePlaceHolder + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.351 +65badd7a-9262-4fd1-9ce2-eb5dc0ca8039,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s66g7ypd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kuznrzx4,https://wandb.ai/xzy11632/dance-dev/sweeps/t9vtfezo,https://wandb.ai/xzy11632/dance-dev/sweeps/adq7j7mn","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 7.954575208692654 +- type: filter.gene + target: FilterGenesTopK params: num_genes: 1124 top: false mode: sum - type: feature.cell - target: WeightedFeatureSVD + target: WeightedFeatureSVD + params: + out: feature.cell + log_level: INFO + n_components: 224 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3549999892711639,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.90%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3535000085830688,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/iyzgg8qc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2g6gclgm,https://wandb.ai/xzy11632/dance-dev/sweeps/v8ut5hbp,https://wandb.ai/xzy11632/dance-dev/sweeps/j0a5a1y8","- 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 - n_components: 224 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3549999892711639,all_total_runs:210|all_finished_runs:172|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:81.90%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.3695000112056732,all_total_runs:600|all_finished_runs:497|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:82.83%,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 + target: HighlyVariableGenesLogarithmizedByTopGenes params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell params: out: feature.cell log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph +- type: misc + target: SetConfig params: - cell_feature_channel: feature.cell + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3695000112056732,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vxnzgy15|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3xj9qbbu,https://wandb.ai/xzy11632/dance-dev/sweeps/d6z821hx,https://wandb.ai/xzy11632/dance-dev/sweeps/0lbam9m7","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_cells + - max_counts + - max_cells + - min_counts + min_counts: 255 + min_cells: 0.05512632013510902 + max_counts: 0.9512421884020308 + max_cells: 0.9944368835063409 +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: 0.7 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 5517 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.3475,all_total_runs:150|all_finished_runs:85|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:56.67%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",0.3535000085830688,,,,,,,,,,,,,, +",0.3465 f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/j4vz4ws5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tecc0rt6,https://wandb.ai/xzy11632/dance-dev/sweeps/jtni6g54,https://wandb.ai/xzy11632/dance-dev/sweeps/uu6v00z6","- type: filter.gene target: FilterGenesPercentile params: @@ -1629,7 +3751,96 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.6455000042915344,,,,,,,,,,,,,, +",0.6455000042915344,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5o741t7i|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/63x9jmta,https://wandb.ai/xzy11632/dance-dev/sweeps/rlwzwx5n,https://wandb.ai/xzy11632/dance-dev/sweeps/jvvacpgh","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6570000052452087,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:443|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:83.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6570000052452087,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hibrhoos|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2ljc12im,https://wandb.ai/xzy11632/dance-dev/sweeps/uokkhdx4,https://wandb.ai/xzy11632/dance-dev/sweeps/saiqel71","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 9652 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.6575,all_total_runs:150|all_finished_runs:114|step2_total_runs:90|step2_finished_runs:62|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:76.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.657 ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b47t3rbw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xf8y2bet,https://wandb.ai/xzy11632/dance-dev/sweeps/60mja5m8,https://wandb.ai/xzy11632/dance-dev/sweeps/y27ceukr","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1698,4 +3909,100 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.3409999907016754,,,,,,,,,,,,,, +",0.3409999907016754,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2r7es2cd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5ppq5ml0,https://wandb.ai/xzy11632/dance-dev/sweeps/2or6v893,https://wandb.ai/xzy11632/dance-dev/sweeps/490783q6","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3425000011920929,all_total_runs:600|all_finished_runs:498|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + 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 +",0.3425000011920929,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ogkykku8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i14mq3cb,https://wandb.ai/xzy11632/dance-dev/sweeps/3px9dsp3,https://wandb.ai/xzy11632/dance-dev/sweeps/iat7lp6o","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.329,all_total_runs:150|all_finished_runs:105|step2_total_runs:90|step2_finished_runs:66|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:70.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.329 diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv index ff57eb09..4be4dacc 100644 --- a/examples/atlas/sweep_results/Intestine_ans.csv +++ b/examples/atlas/sweep_results/Intestine_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mvhlvdxl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0zk0bilm,https://wandb.ai/xzy11632/dance-dev/sweeps/z9xnldun,https://wandb.ai/xzy11632/dance-dev/sweeps/xctbkm4s","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -91,7 +91,49 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4595 +",0.4595,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w85f0jr1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yvez2as1,https://wandb.ai/xzy11632/dance-dev/sweeps/3r5lt9pe,https://wandb.ai/xzy11632/dance-dev/sweeps/78288m6z","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4645000100135803,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4645000100135803 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/dedm26ib|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/765195mr,https://wandb.ai/xzy11632/dance-dev/sweeps/4f58apli,https://wandb.ai/xzy11632/dance-dev/sweeps/fvoqt6jw","- type: filter.gene target: FilterGenesPercentile params: @@ -195,7 +237,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.496 +",0.496,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1h4jwpys|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iz2i7d43,https://wandb.ai/xzy11632/dance-dev/sweeps/zcebhj28,https://wandb.ai/xzy11632/dance-dev/sweeps/p4bod1sy","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.48100000619888306,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.48100000619888306 e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2ygbd0g1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wa5xd2jo,https://wandb.ai/xzy11632/dance-dev/sweeps/njbvga25,https://wandb.ai/xzy11632/dance-dev/sweeps/1ueyprxc","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -307,7 +391,51 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3770364623739333 +",0.3770364623739333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8izf00fq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/60jnxyqe,https://wandb.ai/xzy11632/dance-dev/sweeps/oi5dwmnr,https://wandb.ai/xzy11632/dance-dev/sweeps/omvup8nd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3941039443016052,all_total_runs:600|all_finished_runs:491|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3941039443016052 6a270451-b4d9-43e0-aa89-e33aac1ac74b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hpjhyj9q|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wyv5vmis,https://wandb.ai/xzy11632/dance-dev/sweeps/8qobi3e5,https://wandb.ai/xzy11632/dance-dev/sweeps/jkwnilze","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -424,7 +552,73 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.44485294117647056 +",0.4448529411764705,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h9h46fsq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fh35mitj,https://wandb.ai/xzy11632/dance-dev/sweeps/lzx18s0e,https://wandb.ai/xzy11632/dance-dev/sweeps/tvi3f3a1","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_cells + - max_counts + min_counts: 431 + min_cells: 0.09906132245998966 + max_counts: 0.923950882549364 + max_cells: 0.981253017438922 +- type: normalize + target: ScaleFeature + params: + mode: l2 + eps: 0.7 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 2113 + n_bins: 15 + flavor: seurat +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 885 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4375,all_total_runs:600|all_finished_runs:509|step2_total_runs:540|step2_finished_runs:449|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:84.83%,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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4319852888584137 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n6knsnsf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6opqehxd,https://wandb.ai/xzy11632/dance-dev/sweeps/2xlryh6l,https://wandb.ai/xzy11632/dance-dev/sweeps/lz3o81dv","- type: filter.gene target: FilterGenesPercentile params: @@ -526,7 +720,69 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632 config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.506 +",0.506,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vg93532i|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/42fh6nzf,https://wandb.ai/xzy11632/dance-dev/sweeps/659h8tiv,https://wandb.ai/xzy11632/dance-dev/sweeps/asrfudv3","- 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5304999947547913,all_total_runs:600|all_finished_runs:510|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5304999947547913 d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vim4nmzr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tp4lwwq5,https://wandb.ai/xzy11632/dance-dev/sweeps/amhduqwq,https://wandb.ai/xzy11632/dance-dev/sweeps/fmj9uxc4","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -615,4 +871,50 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5601074546675622 +",0.5601074546675622,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w4ju135u|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8plcumyk,https://wandb.ai/xzy11632/dance-dev/sweeps/67bwy8sx,https://wandb.ai/xzy11632/dance-dev/sweeps/ltrjfmqu","- 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: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.580926775932312,all_total_runs:600|all_finished_runs:473|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.83%,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: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.580926775932312 diff --git a/examples/atlas/sweep_results/Kidney_ans.csv b/examples/atlas/sweep_results/Kidney_ans.csv index b44f4b7f..e1a15dfb 100644 --- a/examples/atlas/sweep_results/Kidney_ans.csv +++ b/examples/atlas/sweep_results/Kidney_ans.csv @@ -1,4 +1,4 @@ -Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/whvpjn2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rq2xo8wj,https://wandb.ai/xzy11632/dance-dev/sweeps/jwo7gft3,https://wandb.ai/xzy11632/dance-dev/sweeps/dbka8jop","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -87,7 +87,51 @@ a51c6ece-5731-4128-8c1e-5060e80c69e4,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2725 +",0.2725,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/80xdc1ba|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sny3930k,https://wandb.ai/xzy11632/dance-dev/sweeps/volqelag,https://wandb.ai/xzy11632/dance-dev/sweeps/5jxnqx6h","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2770000100135803,all_total_runs:600|all_finished_runs:447|step2_total_runs:540|step2_finished_runs:401|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:9|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:74.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2770000100135803 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/r1y7gnbt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8z8b7s39,https://wandb.ai/xzy11632/dance-dev/sweeps/xv3zpnqo,https://wandb.ai/xzy11632/dance-dev/sweeps/9rlhjyjr","- type: filter.gene target: FilterGenesPercentile params: {} @@ -174,7 +218,51 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5945 +",0.5945,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9toa84vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t5uul8vm,https://wandb.ai/xzy11632/dance-dev/sweeps/1mgc0dge,https://wandb.ai/xzy11632/dance-dev/sweeps/azn53fsv","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.578499972820282,all_total_runs:600|all_finished_runs:439|step2_total_runs:540|step2_finished_runs:387|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:12|finished_rate:73.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.578499972820282 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/a6rgr8w4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ssb28ejh,https://wandb.ai/xzy11632/dance-dev/sweeps/thvgw7zh,https://wandb.ai/xzy11632/dance-dev/sweeps/0a06jn63","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -279,7 +367,67 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.5705 +",0.5705,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/e43anxgn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3stmar8u,https://wandb.ai/xzy11632/dance-dev/sweeps/s2cpm80t,https://wandb.ai/xzy11632/dance-dev/sweeps/u3ugwnhn","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + 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 +",0.5914999842643738,all_total_runs:600|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:391|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:73.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + 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 +",0.5914999842643738 105c7dad-0468-4628-a5be-2bb42c6a8ae4,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/hbvj1oip|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xq06tu32,https://wandb.ai/xzy11632/dance-dev/sweeps/yiz263kv,https://wandb.ai/xzy11632/dance-dev/sweeps/b9zvve4u","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -400,7 +548,69 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.6975 +",0.6975,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/avkuxvpt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jdctlnyj,https://wandb.ai/xzy11632/dance-dev/sweeps/2i0dhz25,https://wandb.ai/xzy11632/dance-dev/sweeps/esaiggjt","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7124999761581421,all_total_runs:600|all_finished_runs:440|step2_total_runs:540|step2_finished_runs:392|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:73.33%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.7124999761581421 5af90777-6760-4003-9dba-8f945fec6fdf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ltca3oim|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9oulbho9,https://wandb.ai/xzy11632/dance-dev/sweeps/ko18r05s,https://wandb.ai/xzy11632/dance-dev/sweeps/zg1qkqy0","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -511,7 +721,51 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Kidney),"step2:https://wandb.ai/xzy11632/da config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2625 +",0.2625,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/x43ntzx4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/irntnkow,https://wandb.ai/xzy11632/dance-dev/sweeps/9tdspve1,https://wandb.ai/xzy11632/dance-dev/sweeps/5yvw6kpr","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2994999885559082,all_total_runs:586|all_finished_runs:420|step2_total_runs:540|step2_finished_runs:386|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:71.67%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2994999885559082 dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cdcv6mna|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ne54nu6k,https://wandb.ai/xzy11632/dance-dev/sweeps/0z8zj8do,https://wandb.ai/xzy11632/dance-dev/sweeps/bi91nl8w","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -620,7 +874,58 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.229 +",0.229,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/51phjfg4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rb2c4x3n,https://wandb.ai/xzy11632/dance-dev/sweeps/4m4fq5j5,https://wandb.ai/xzy11632/dance-dev/sweeps/pqqd7mez","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 6 + max_val: 99 + mode: rv +- type: normalize + target: Log1P + params: + base: 7.449177659482961 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 5312 + top: true + mode: var +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 375 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2224999964237213,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:400|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:20|finished_rate:76.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.22100000083446503 9df60c57-fdf3-4e93-828e-fe9303f20438,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/m28fu5e4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rd136al3,https://wandb.ai/xzy11632/dance-dev/sweeps/o1v4t50e,https://wandb.ai/xzy11632/dance-dev/sweeps/j5ef3unu","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -710,8 +1015,55 @@ dea717d4-7bc0-4e46-950f-fd7e1cc8df7d,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2735 -be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1a0xicia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wunz1pqq,https://wandb.ai/xzy11632/dance-dev/sweeps/0n5dswxy,https://wandb.ai/xzy11632/dance-dev/sweeps/13if0wtd","- type: filter.gene +",0.2735,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ku1n6b7v|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ng92wwrv,https://wandb.ai/xzy11632/dance-dev/sweeps/67oq9j9d,https://wandb.ai/xzy11632/dance-dev/sweeps/4holfqbm","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: Log1P + params: + base: 5.085645037530894 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 8932 + top: false + mode: rv +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 108 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27649998664855957,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:403|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:7|finished_rate:73.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.27549999952316284 +be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1a0xicia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h2asuybg,https://wandb.ai/xzy11632/dance-dev/sweeps/8uxvnhwl,https://wandb.ai/xzy11632/dance-dev/sweeps/ph5yhz9y","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -745,7 +1097,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4384999871253967,all_total_runs:183|all_finished_runs:139|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:75.96%,False,"- type: filter.gene +",0.43849998712539673,all_total_runs:212|all_finished_runs:167|step2_total_runs:151|step2_finished_runs:120|step3_0_total_runs:21|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:78.77%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -779,7 +1131,7 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.4384999871253967,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xl2nwacs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qhr4km04,https://wandb.ai/xzy11632/dance-dev/sweeps/7vqnpicq,https://wandb.ai/xzy11632/dance-dev/sweeps/t8ovlamf","- type: filter.gene +",0.43849998712539673,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xl2nwacs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qhr4km04,https://wandb.ai/xzy11632/dance-dev/sweeps/7vqnpicq,https://wandb.ai/xzy11632/dance-dev/sweeps/t8ovlamf","- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -815,7 +1167,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.451 +",0.451,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bueblvgh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/qxcu5gfb,https://wandb.ai/xzy11632/dance-dev/sweeps/dl2izc9t,https://wandb.ai/xzy11632/dance-dev/sweeps/11iznmvf","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4440000057220459,all_total_runs:600|all_finished_runs:445|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:8|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:74.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4440000057220459 32b9bdce-2481-4c85-ba1b-6ad5fcea844c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8arpp0bg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kutscmkt,https://wandb.ai/xzy11632/dance-dev/sweeps/d1iadk7m,https://wandb.ai/xzy11632/dance-dev/sweeps/87cnxjeb","- type: filter.gene target: FilterGenesPercentile params: {} @@ -910,7 +1306,49 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.247 +",0.247,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ch3i3tkk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/3ra9d12m,https://wandb.ai/xzy11632/dance-dev/sweeps/0yy5nksn,https://wandb.ai/xzy11632/dance-dev/sweeps/0dpb06b7","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + 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 +",0.2370000034570694,all_total_runs:600|all_finished_runs:501|step2_total_runs:540|step2_finished_runs:441|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:83.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + 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 +",0.2370000034570694 0b4a15a7-4e9e-4555-9733-2423e5c66469,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sk7ynfj9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/64bshk8k,https://wandb.ai/xzy11632/dance-dev/sweeps/y9l1vpb7,https://wandb.ai/xzy11632/dance-dev/sweeps/v6t2nb4k","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -1007,9 +1445,53 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: SCNFeature + label_channel: cell_type +",0.2355,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b17chya1|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2knyp5e6,https://wandb.ai/xzy11632/dance-dev/sweeps/fpvymfqu,https://wandb.ai/xzy11632/dance-dev/sweeps/7yvf6lid","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2485000044107437,all_total_runs:600|all_finished_runs:470|step2_total_runs:540|step2_finished_runs:416|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:14|finished_rate:78.33%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.2355 +",0.2485000044107437 53d208b0-2cfd-4366-9866-c3c6114081bc,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qc59eog9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/539khgz0,https://wandb.ai/xzy11632/dance-dev/sweeps/afbpb46d,https://wandb.ai/xzy11632/dance-dev/sweeps/mn356re7","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1134,7 +1616,69 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.8657335406946605 +",0.8657335406946605,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p6h1i8ws|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/fhzengv5,https://wandb.ai/xzy11632/dance-dev/sweeps/23unbp67,https://wandb.ai/xzy11632/dance-dev/sweeps/9j9n7dtn","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:400|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:20|step3_2_finished_runs:14|finished_rate:74.83%,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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708 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FilterGenesPlaceHolder params: {} - type: normalize @@ -1239,7 +1783,51 @@ be39785b-67cb-4177-be19-a40ee3747e45,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.16666666666666666 +",0.1666666666666666,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0vjmseqv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tjum1tpz,https://wandb.ai/xzy11632/dance-dev/sweeps/buc7ui45,https://wandb.ai/xzy11632/dance-dev/sweeps/dsbpgsg6","- 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 + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5,all_total_runs:572|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:441|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:77.45%,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 + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5 f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/6zzg3aev|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ti1w2l2i,https://wandb.ai/xzy11632/dance-dev/sweeps/en9xlysw,https://wandb.ai/xzy11632/dance-dev/sweeps/cbj2rjp1","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize @@ -1320,7 +1908,7 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.34491315136476425,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene +",0.3449131513647642,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1338,7 +1926,71 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.34491315136476425 +",0.3449131513647642,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0my62r0x|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2j2fewq5,https://wandb.ai/xzy11632/dance-dev/sweeps/cepp4w5d,https://wandb.ai/xzy11632/dance-dev/sweeps/6xvxfv4t","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + 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 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log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33247917890548706,all_total_runs:600|all_finished_runs:483|step2_total_runs:540|step2_finished_runs:423|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:80.50%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.33247917890548706 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+",0.3766423357664233,all_total_runs:150|all_finished_runs:96|step2_total_runs:90|step2_finished_runs:74|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:64.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1563,9 +2259,71 @@ f801b7a9-80a6-4d09-9161-71474deb58ae,"step2:https://wandb.ai/xzy11632/dance-dev/ target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: SCNFeature + label_channel: cell_type +",0.3759124087591241,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0vcqva6z|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/t219mhhy,https://wandb.ai/xzy11632/dance-dev/sweeps/o8k3c6lv,https://wandb.ai/xzy11632/dance-dev/sweeps/n54ib73r","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3620437979698181,all_total_runs:600|all_finished_runs:469|step2_total_runs:540|step2_finished_runs:411|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:78.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.3759124087591241 +",0.3620437979698181 fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fv5txyhd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gftuks1f,https://wandb.ai/xzy11632/dance-dev/sweeps/vhtoxock,https://wandb.ai/xzy11632/dance-dev/sweeps/1qsjz3ai","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1668,7 +2426,49 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2915 +",0.2915,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l6gb8igg|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/avpo32k2,https://wandb.ai/xzy11632/dance-dev/sweeps/8ga8qet1,https://wandb.ai/xzy11632/dance-dev/sweeps/0lz70ruz","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28049999475479126,all_total_runs:600|all_finished_runs:487|step2_total_runs:540|step2_finished_runs:427|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:81.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.28049999475479126 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Kidney),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/02te0za8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8narfff8,https://wandb.ai/xzy11632/dance-dev/sweeps/gt2dfvtp,https://wandb.ai/xzy11632/dance-dev/sweeps/1deo7tn9","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1791,7 +2591,51 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4125 +",0.4125,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/75eb8mu2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/m6j8n05u,https://wandb.ai/xzy11632/dance-dev/sweeps/hvbyary3,https://wandb.ai/xzy11632/dance-dev/sweeps/536wy46e","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4284999966621399,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:430|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:81.67%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4284999966621399 0b75c598-0893-4216-afe8-5414cab7739d,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/h267r9gw|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gsf3qy1c,https://wandb.ai/xzy11632/dance-dev/sweeps/dzembwwg,https://wandb.ai/xzy11632/dance-dev/sweeps/iygud7ig","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1880,7 +2724,69 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2465 +",0.2465,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zw08f3vc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zokwex9g,https://wandb.ai/xzy11632/dance-dev/sweeps/6w8eah70,https://wandb.ai/xzy11632/dance-dev/sweeps/rh47nlz0","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.244499996304512,all_total_runs:600|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:406|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:77.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: NormalizeTotal + params: {} +- type: filter.gene + target: 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 +",0.244499996304512 2aa1c93c-4ef3-4e9a-98e7-0bd37933953c,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cgm5lh8e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r6m7zdo1,https://wandb.ai/xzy11632/dance-dev/sweeps/rvpunccy,https://wandb.ai/xzy11632/dance-dev/sweeps/50vokx7l","- type: filter.gene target: FilterGenesPercentile params: @@ -1986,7 +2892,69 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.488034188034188 +",0.488034188034188,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zw2x3j2g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yayfm8nk,https://wandb.ai/xzy11632/dance-dev/sweeps/shh6b1z9,https://wandb.ai/xzy11632/dance-dev/sweeps/oyem3gtm","- 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: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.488034188747406,all_total_runs:599|all_finished_runs:466|step2_total_runs:540|step2_finished_runs:408|step3_0_total_runs:19|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:77.80%,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: ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.488034188747406 2423ce2c-3149-4cca-a2ff-cf682ea29b5f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z3v3k8xa|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rxf8w4kk,https://wandb.ai/xzy11632/dance-dev/sweeps/oq5yjvcy,https://wandb.ai/xzy11632/dance-dev/sweeps/g644vduv","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -2111,4 +3079,66 @@ fd072bc3-2dfb-46f8-b4e3-467cb3223182,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.8657335406946605 +",0.8657335406946605,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yvdvm8br|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tuecazpp,https://wandb.ai/xzy11632/dance-dev/sweeps/1axejlbz,https://wandb.ai/xzy11632/dance-dev/sweeps/zpq9n7oj","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708,all_total_runs:586|all_finished_runs:488|step2_total_runs:540|step2_finished_runs:450|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.28%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.8750647902488708 diff --git a/examples/atlas/sweep_results/Lung_ans.csv b/examples/atlas/sweep_results/Lung_ans.csv index ff167c9b..e87456fa 100644 --- a/examples/atlas/sweep_results/Lung_ans.csv +++ b/examples/atlas/sweep_results/Lung_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,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/31p1jl13|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/jv0qygxw,https://wandb.ai/xzy11632/dance-dev/sweeps/3k1x4ael,https://wandb.ai/xzy11632/dance-dev/sweeps/0drfyazl","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -85,7 +85,69 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.486 +",0.486,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/88sp4mxc|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uz23y4v1,https://wandb.ai/xzy11632/dance-dev/sweeps/4mlv8rqb,https://wandb.ai/xzy11632/dance-dev/sweeps/vc7o5nsc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4790000021457672,all_total_runs:600|all_finished_runs:479|step2_total_runs:540|step2_finished_runs:431|step3_0_total_runs:20|step3_0_finished_runs:10|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4790000021457672 f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/u66vt0zy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0e4fl2ig,https://wandb.ai/xzy11632/dance-dev/sweeps/26t9dcb3,https://wandb.ai/xzy11632/dance-dev/sweeps/6er1nf7y","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -111,7 +173,7 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.30799999833106995,all_total_runs:225|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:35|step3_0_finished_runs:26|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:80.00%,False,"- type: filter.gene +",0.3079999983310699,all_total_runs:225|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:35|step3_0_finished_runs:26|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:80.00%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -136,7 +198,7 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.30799999833106995,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sa0zrzyh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ddp05p3y,https://wandb.ai/xzy11632/dance-dev/sweeps/4n5kvy4f,https://wandb.ai/xzy11632/dance-dev/sweeps/4nw3qvss","- type: filter.gene +",0.3079999983310699,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/sa0zrzyh|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ddp05p3y,https://wandb.ai/xzy11632/dance-dev/sweeps/4n5kvy4f,https://wandb.ai/xzy11632/dance-dev/sweeps/4nw3qvss","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: NormalizeTotal @@ -170,7 +232,56 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3055 +",0.3055,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fbs68rd7|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xcit9qy8,https://wandb.ai/xzy11632/dance-dev/sweeps/4ftre5j8,https://wandb.ai/xzy11632/dance-dev/sweeps/f5uutcyi","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 4 + max_val: 96 + mode: cv +- type: normalize + target: Log1P + params: + base: 9.29338977585692 +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 4645 + top: false + mode: sum +- type: feature.cell + target: CellPCA + params: + out: feature.cell + log_level: INFO + n_components: 671 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.2939999997615814,all_total_runs:600|all_finished_runs:463|step2_total_runs:540|step2_finished_runs:411|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:77.17%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + target: CellPCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.29350000619888306 3de0ad6d-4378-4f62-b37b-ec0b75a50d94,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cztlwh8l|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xnekcm5a,https://wandb.ai/xzy11632/dance-dev/sweeps/92k8gjvn,https://wandb.ai/xzy11632/dance-dev/sweeps/ebwccpe0","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -277,7 +388,72 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.167 +",0.167,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gr6v110e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2af03zz4,https://wandb.ai/xzy11632/dance-dev/sweeps/q5e23azt,https://wandb.ai/xzy11632/dance-dev/sweeps/s3ytrjbv","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - max_counts + - max_cells + - min_cells + min_counts: 458 + min_cells: 0.011591892698839612 + max_counts: 0.9504786715733048 + max_cells: 0.968929807966842 +- type: normalize + target: Log1P + params: + base: 2.5831898659365935 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 1528 + span: 0.25048936376968134 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 757 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.17399999499320984,all_total_runs:600|all_finished_runs:472|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:78.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + 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 +",0.17299999296665192 1e5bd3b8-6a0e-4959-8d69-cafed30fe814,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/gvzf9hvu|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xn6gkyue,https://wandb.ai/xzy11632/dance-dev/sweeps/wohspkph,https://wandb.ai/xzy11632/dance-dev/sweeps/0es2sjqj","- type: filter.gene target: FilterGenesPercentile params: @@ -311,7 +487,7 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.35850000381469727,all_total_runs:210|all_finished_runs:168|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:80.00%,False,"- type: filter.gene +",0.3585000038146972,all_total_runs:210|all_finished_runs:168|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:80.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -383,7 +559,69 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.34 +",0.34,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q46hxsfq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6dkzww83,https://wandb.ai/xzy11632/dance-dev/sweeps/ctnmrdn1,https://wandb.ai/xzy11632/dance-dev/sweeps/6og1pgzb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3650000095367432,all_total_runs:600|all_finished_runs:449|step2_total_runs:540|step2_finished_runs:392|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:17|finished_rate:74.83%,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 + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.3650000095367432 4ed927e9-c099-49af-b8ce-a2652d069333(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/up1qmjf2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xlh552ry,https://wandb.ai/xzy11632/dance-dev/sweeps/w64bnq3j,https://wandb.ai/xzy11632/dance-dev/sweeps/t7nbjgz0","- type: filter.gene target: FilterGenesPercentile params: @@ -502,43 +740,51 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.6425 -01209dce-3575-4bed-b1df-129f57fbc031(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bhc72mqi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgh7gu1,https://wandb.ai/xzy11632/dance-dev/sweeps/oyrg3g50,https://wandb.ai/xzy11632/dance-dev/sweeps/yazhk2wh","- type: filter.gene - target: FilterGenesPercentile +",0.6425,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o3xgoa6y|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bqb8ige8,https://wandb.ai/xzy11632/dance-dev/sweeps/32xe959r,https://wandb.ai/xzy11632/dance-dev/sweeps/wajc9h8x","- type: filter.gene + target: FilterGenesScanpyOrder params: - min_val: 8 - max_val: 98 - mode: sum + 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: - base: 2.3999362085689735 + target: NormalizeTotal + params: {} - type: filter.gene - target: HighlyVariableGenesRawCount + target: FilterGenesRegression params: - n_top_genes: 2774 - span: 0.14012171784395563 + num_genes: 3000 - type: feature.cell - target: WeightedFeaturePCA params: out: feature.cell log_level: INFO - n_components: 143 - feat_norm_mode: l2 -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.30799999833106995,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.6570000052452087,all_total_runs:600|all_finished_runs:490|step2_total_runs:540|step2_finished_runs:432|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize - target: NormalizePlaceHolder + target: NormalizeTotal params: {} - type: filter.gene target: FilterGenesRegression @@ -550,7 +796,61 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6570000052452087 +01209dce-3575-4bed-b1df-129f57fbc031(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bhc72mqi|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgh7gu1,https://wandb.ai/xzy11632/dance-dev/sweeps/oyrg3g50,https://wandb.ai/xzy11632/dance-dev/sweeps/yazhk2wh","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 8 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 2.3999362085689735 +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 2774 + span: 0.14012171784395563 +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 143 + feat_norm_mode: l2 +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.3079999983310699,all_total_runs:210|all_finished_runs:180|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:85.71%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + 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 + split_name: train + target: WeightedFeatureSVD +- type: graph.cell target: CellFeatureGraph params: cell_feature_channel: feature.cell @@ -616,7 +916,69 @@ f72958f5-7f42-4ebb-98da-445b0c6de516,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2835 +",0.2835,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8072p0n9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eh05iegv,https://wandb.ai/xzy11632/dance-dev/sweeps/0hraadqb,https://wandb.ai/xzy11632/dance-dev/sweeps/pyj1uv1u","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type 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config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6744999885559082,all_total_runs:210|all_finished_runs:177|step2_total_runs:150|step2_finished_runs:120|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:84.29%,False,"- type: filter.gene +",0.703000009059906,all_total_runs:572|all_finished_runs:447|step2_total_runs:540|step2_finished_runs:427|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.15%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -771,10 +1130,11 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScaleFeature - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: HighlyVariableGenesRawCount + target: HighlyVariableGenesLogarithmizedByTopGenes params: n_top_genes: 3000 - type: feature.cell @@ -783,16 +1143,14 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc log_level: INFO split_name: train target: WeightedFeatureSVD -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: + feature_channel: feature.cell label_channel: cell_type -",0.6744999885559082,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/i6274vfx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7dcfwbih,https://wandb.ai/xzy11632/dance-dev/sweeps/teou6ic8,https://wandb.ai/xzy11632/dance-dev/sweeps/b0q7l3ro","- type: filter.gene +",0.703000009059906 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-",0.6945,all_total_runs:150|all_finished_runs:107|step2_total_runs:90|step2_finished_runs:68|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:0|finished_rate:71.33%,False,"- type: filter.gene +",0.6744999885559082,all_total_runs:210|all_finished_runs:177|step2_total_runs:150|step2_finished_runs:120|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:84.29%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -835,56 +1200,25 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - target: SCNFeature -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: SCNFeature - label_channel: cell_type 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target: FilterGenesPercentile - params: {} -- type: normalize - target: ScTransform + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph params: - processes_num: 8 -- type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} -- type: feature.cell - target: SCNFeature + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature label_channel: cell_type -",0.1545 -486486d4-9462-43e5-9249-eb43fa5a49a6,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/949fx7i2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/48o2a3bp,https://wandb.ai/xzy11632/dance-dev/sweeps/rz2qkusr,https://wandb.ai/xzy11632/dance-dev/sweeps/0pyosaoa","- type: filter.gene 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3000 - type: feature.cell target: SCNFeature - type: misc @@ -938,8 +1272,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.524 -7b3368a5-c1a0-4973-9e75-d95b4150c7da,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/llbot2wd|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7rwgizyg,https://wandb.ai/xzy11632/dance-dev/sweeps/f72tj8le,https://wandb.ai/xzy11632/dance-dev/sweeps/teurxxdt","- type: filter.gene +",0.6945,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zl582av4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zlh4j7ft,https://wandb.ai/xzy11632/dance-dev/sweeps/dxovufnv,https://wandb.ai/xzy11632/dance-dev/sweeps/ojvv4lhn","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -952,20 +1285,25 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Lung),"step2:https://wandb.ai/xzy11632/danc min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.15458937198067632,all_total_runs:150|all_finished_runs:111|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:74.00%,False,"- type: filter.gene 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n_components: 791 + feat_norm_mode: null +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.14900000393390656,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:82.38%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type 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params: + processes_num: 8 +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.1545,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/rxpz0717|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kwdb5hwh,https://wandb.ai/xzy11632/dance-dev/sweeps/8y8lxfu9,https://wandb.ai/xzy11632/dance-dev/sweeps/tc33wt4o","- type: filter.gene + target: FilterGenesPlaceHolder +- type: normalize + target: ScaleFeature + params: + mode: minmax + eps: 0.1 +- type: filter.gene + target: FilterGenesRegression + params: + method: scmap + num_genes: 4755 +- 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 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FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.5285000205039978 +7b3368a5-c1a0-4973-9e75-d95b4150c7da,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/xtfsfufy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lu662hzj,https://wandb.ai/xzy11632/dance-dev/sweeps/zsy2u3xl","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + values: + - - min_counts + - min_cells + - max_counts + - max_cells + - - min_counts + - min_cells + - max_cells + - max_counts + - - min_counts + - max_counts + - min_cells + - max_cells + - - min_counts + - max_counts + - max_cells + - min_cells + - - min_counts + - max_cells + - 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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 + target: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.1582125574350357 +e04daea4-4412-45b5-989e-76a9be070a89,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8zrdwmrx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/kukr7kps,https://wandb.ai/xzy11632/dance-dev/sweeps/er20styk,https://wandb.ai/xzy11632/dance-dev/sweeps/u54ch3g2","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.12990762293338776,all_total_runs:210|all_finished_runs:156|step2_total_runs:150|step2_finished_runs:108|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:74.29%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.12990762293338776,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0p7su6u6|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wglkhxfr,https://wandb.ai/xzy11632/dance-dev/sweeps/7wvua5jk,https://wandb.ai/xzy11632/dance-dev/sweeps/idsyyyng","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 99 + mode: sum +- type: normalize + target: ScaleFeature + params: + mode: standardize + eps: -1 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type 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ScTransform + params: + processes_num: 8 +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",0.4014388489208633,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d4ed7of2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4cqjlphf,https://wandb.ai/xzy11632/dance-dev/sweeps/wwtpqhff,https://wandb.ai/xzy11632/dance-dev/sweeps/2hsqujqo","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesLogarithmizedByTopGenes + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA 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filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.2515000104904175,all_total_runs:210|all_finished_runs:172|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:18|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.90%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature label_channel: cell_type -",0.12009237875288684,all_total_runs:149|all_finished_runs:122|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:19|step3_2_finished_runs:19|finished_rate:81.88%,False,"- type: filter.gene +",0.2515000104904175,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvhvfd0e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r8kvjad3,https://wandb.ai/xzy11632/dance-dev/sweeps/2gztfme0,https://wandb.ai/xzy11632/dance-dev/sweeps/moka4ir1","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1026,11 +2659,13 @@ e04daea4-4412-45b5-989e-76a9be070a89,,,,,,,,"step2:https://wandb.ai/xzy11632/dan min_cells: 0.01 max_cells: 0.99 - type: normalize - target: NormalizeTotal - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -1039,8 +2674,7 @@ e04daea4-4412-45b5-989e-76a9be070a89,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.11431870669745958 -e9175006-8978-4417-939f-819855eab80e,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4hf1e1zt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/17uqbg1j,https://wandb.ai/xzy11632/dance-dev/sweeps/w8z7bp2m,https://wandb.ai/xzy11632/dance-dev/sweeps/609y6mnf","- type: filter.gene 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SetConfig + params: + config_dict: + label_channel: cell_type +",0.22349999845027924,all_total_runs:210|all_finished_runs:173|step2_total_runs:150|step2_finished_runs:116|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:17|finished_rate:82.38%,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: 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 +",0.2214999943971634,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8wu00rrs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emkgdv7m,https://wandb.ai/xzy11632/dance-dev/sweeps/yz3ptmyb,https://wandb.ai/xzy11632/dance-dev/sweeps/8zpy4daf","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder params: {} - type: feature.cell target: SCNFeature @@ -1094,27 +2845,155 @@ e9175006-8978-4417-939f-819855eab80e,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.8252427184466019 -0ba16f4b-cb87-4fa3-9363-19fc51eec6e7,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nzqxkwr2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/dxp2byqu,https://wandb.ai/xzy11632/dance-dev/sweeps/lkiksixl,https://wandb.ai/xzy11632/dance-dev/sweeps/txxkqm04","- type: filter.gene - target: FilterGenesPlaceHolder 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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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:443|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:83.83%,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: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.226500004529953 +d8da613f-e681-4c69-b463-e94f5e66847f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/7n25es77|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/vslww26r,https://wandb.ai/xzy11632/dance-dev/sweeps/dnhruay0,https://wandb.ai/xzy11632/dance-dev/sweeps/213rny4x","- 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: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",0.1815000027418137,all_total_runs:210|all_finished_runs:169|step2_total_runs:150|step2_finished_runs:118|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:80.48%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} - type: filter.gene target: FilterGenesRegression params: num_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature label_channel: cell_type -",0.4014388489208633,all_total_runs:150|all_finished_runs:117|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:2|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.00%,False,"- type: filter.gene +",0.1815000027418137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qpyso58s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n9xhwciz,https://wandb.ai/xzy11632/dance-dev/sweeps/zb5fdqlj,https://wandb.ai/xzy11632/dance-dev/sweeps/gdl97dnb","- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1122,28 +3001,8 @@ e9175006-8978-4417-939f-819855eab80e,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression - params: - num_genes: 3000 -- type: feature.cell - target: SCNFeature -- type: misc - target: SetConfig - params: - config_dict: - feature_channel: SCNFeature - label_channel: cell_type -",0.4014388489208633 -a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ugznmank|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/2zv9lzme,https://wandb.ai/xzy11632/dance-dev/sweeps/8ptyl7c3","- type: filter.gene - target: FilterGenesPercentile - params: - min_val: 2 - max_val: 98 - mode: rv -- type: normalize - target: NormalizePlaceHolder -- type: filter.gene - target: FilterGenesNumberPlaceHolder + target: HighlyVariableGenesLogarithmizedByMeanAndDisp + params: {} - type: feature.cell target: SCNFeature - type: misc @@ -1152,14 +3011,15 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy116 config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.36123348017621143,all_total_runs:130|all_finished_runs:105|step2_total_runs:90|step2_finished_runs:67|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|finished_rate:80.77%,False,"- type: filter.gene +",0.1705,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize - target: NormalizePlaceHolder - params: {} + target: ScTransform + params: + processes_num: 8 - type: filter.gene - target: FilterGenesNumberPlaceHolder + target: HighlyVariableGenesLogarithmizedByMeanAndDisp params: {} - type: feature.cell target: SCNFeature @@ -1169,8 +3029,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy116 config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.3303964757709251 -8c42cfd0-0b0a-46d5-910c-fc833d83c45e,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvhvfd0e|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/r8kvjad3,https://wandb.ai/xzy11632/dance-dev/sweeps/2gztfme0,https://wandb.ai/xzy11632/dance-dev/sweeps/moka4ir1","- type: filter.gene +",0.1705,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1lf1dmfq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wmh2vp6l,https://wandb.ai/xzy11632/dance-dev/sweeps/9zkgyabm,https://wandb.ai/xzy11632/dance-dev/sweeps/eg7prnlf","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1183,22 +3042,25 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy116 min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.265,all_total_runs:149|all_finished_runs:113|step2_total_runs:90|step2_finished_runs:73|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:19|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.84%,False,"- type: filter.gene +",0.17249999940395355,all_total_runs:600|all_finished_runs:493|step2_total_runs:540|step2_finished_runs:439|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:14|finished_rate:82.17%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1211,67 +3073,101 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Lung),,,,,,,,"step2:https://wandb.ai/xzy116 min_cells: 0.01 max_cells: 0.99 - type: normalize - target: ScTransform - params: - processes_num: 8 + target: ScaleFeature + params: {} - type: filter.gene target: HighlyVariableGenesRawCount params: n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.265 -2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Lung),,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8wu00rrs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/emkgdv7m,https://wandb.ai/xzy11632/dance-dev/sweeps/yz3ptmyb,https://wandb.ai/xzy11632/dance-dev/sweeps/8zpy4daf","- type: filter.gene +",0.17249999940395355 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-",0.2355,all_total_runs:150|all_finished_runs:118|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:78.67%,False,"- type: filter.gene - target: FilterGenesPercentile +",0.648901104927063,all_total_runs:196|all_finished_runs:158|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:80.61%,False,"- type: filter.gene + target: FilterGenesPlaceHolder params: {} - type: normalize target: Log1P params: {} - type: filter.gene - target: FilterGenesNumberPlaceHolder - params: {} + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature label_channel: cell_type -",0.2355 -d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/qpyso58s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/n9xhwciz,https://wandb.ai/xzy11632/dance-dev/sweeps/zb5fdqlj,https://wandb.ai/xzy11632/dance-dev/sweeps/gdl97dnb","- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.6483516693115234,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s1tkaoyx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/48ud2zju,https://wandb.ai/xzy11632/dance-dev/sweeps/hvco0aoq,https://wandb.ai/xzy11632/dance-dev/sweeps/hab6rxge","- 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: {} + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -1280,16 +3176,26 @@ d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.1705,all_total_runs:150|all_finished_runs:86|step2_total_runs:90|step2_finished_runs:65|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:57.33%,True,"- type: filter.gene - target: FilterGenesPlaceHolder - params: {} +",0.65,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 - type: normalize target: ScTransform params: processes_num: 8 - type: filter.gene - target: HighlyVariableGenesLogarithmizedByMeanAndDisp - params: {} + target: FilterGenesRegression + params: + num_genes: 3000 - type: feature.cell target: SCNFeature - type: misc @@ -1298,8 +3204,7 @@ d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.1705 -4023a2bc-6325-47db-bfdf-9639e91042c2,,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s1tkaoyx|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/48ud2zju,https://wandb.ai/xzy11632/dance-dev/sweeps/hvco0aoq,https://wandb.ai/xzy11632/dance-dev/sweeps/hab6rxge","- type: filter.gene +",0.65,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/w6h9lrkf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/828yc8fb,https://wandb.ai/xzy11632/dance-dev/sweeps/xetdwps8,https://wandb.ai/xzy11632/dance-dev/sweeps/6mtvx8u2","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1316,18 +3221,22 @@ d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",0.65,all_total_runs:150|all_finished_runs:97|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:64.67%,False,"- type: filter.gene +",0.6615384817123413,all_total_runs:586|all_finished_runs:480|step2_total_runs:540|step2_finished_runs:440|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:20|finished_rate:81.91%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1344,19 +3253,75 @@ d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + 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 +",0.6615384817123413 +71be997d-ff75-41b9-8a9f-1288c865f921(Lung),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/v5hbb1ob|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/la5t6f69,https://wandb.ai/xzy11632/dance-dev/sweeps/6f1i7xhi,https://wandb.ai/xzy11632/dance-dev/sweeps/q7mkmn1w","- 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 + 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 +",0.5454545617103577,all_total_runs:168|all_finished_runs:119|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:6|step3_0_finished_runs:0|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:70.83%,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 + split_name: train + target: WeightedFeatureSVD +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature label_channel: cell_type -",0.65 -71be997d-ff75-41b9-8a9f-1288c865f921(Lung),,,,,,,,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tmb6nbhs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xwzuin,https://wandb.ai/xzy11632/dance-dev/sweeps/3xl8m5ai,https://wandb.ai/xzy11632/dance-dev/sweeps/a6q7uf5a","- type: filter.gene +",0.5454545617103577,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/tmb6nbhs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h0xwzuin,https://wandb.ai/xzy11632/dance-dev/sweeps/3xl8m5ai,https://wandb.ai/xzy11632/dance-dev/sweeps/a6q7uf5a","- type: filter.gene target: FilterGenesPercentile params: min_val: 7 @@ -1407,4 +3372,48 @@ d8da613f-e681-4c69-b463-e94f5e66847f,,,,,,,,"step2:https://wandb.ai/xzy11632/dan config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.42424242424242425 +",0.4242424242424242,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/4zpkroz8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/8ya78zvj,https://wandb.ai/xzy11632/dance-dev/sweeps/etsb2867,https://wandb.ai/xzy11632/dance-dev/sweeps/ul16ui5e","- 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 + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4848484992980957,all_total_runs:572|all_finished_runs:438|step2_total_runs:540|step2_finished_runs:435|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.57%,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 + target: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4848484992980957 diff --git a/examples/atlas/sweep_results/Pancreas_ans.csv b/examples/atlas/sweep_results/Pancreas_ans.csv index 870281cd..c15bd8ff 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,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res +Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_scdeepsort_step2_best_yaml,cta_scdeepsort_step2_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check,cta_singlecellnet_step2_best_yaml,cta_singlecellnet_step2_best_res,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_actinn_step2_best_yaml,cta_actinn_step2_best_res 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: @@ -113,7 +113,69 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.402 +",0.402,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/22ozz7li|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7af40uoa,https://wandb.ai/xzy11632/dance-dev/sweeps/go7b10ao,https://wandb.ai/xzy11632/dance-dev/sweeps/fogjho7h","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4149999916553498,all_total_runs:586|all_finished_runs:442|step2_total_runs:540|step2_finished_runs:402|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:6|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:75.43%,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: Log1P + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4149999916553498 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: @@ -234,6 +296,66 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_s config_dict: feature_channel: SCNFeature label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/t544qsq4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mdst6ozg,https://wandb.ai/xzy11632/dance-dev/sweeps/5wuust9u,https://wandb.ai/xzy11632/dance-dev/sweeps/0jz8lzw5","- 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 + target: GaussRandProjFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:600|all_finished_runs:455|step2_total_runs:540|step2_finished_runs:415|step3_0_total_runs:20|step3_0_finished_runs:17|step3_1_total_runs:20|step3_1_finished_runs:12|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:75.83%,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: ScaleFeature + 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 ",1.0 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/alp04n2p|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pncdq2k1,https://wandb.ai/xzy11632/dance-dev/sweeps/z1tnppgo,https://wandb.ai/xzy11632/dance-dev/sweeps/s4ka2u4s","- type: filter.gene target: FilterGenesPercentile @@ -260,7 +382,7 @@ 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:132|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:62.86%,False,"- type: filter.gene +",0.2599999904632568,all_total_runs:210|all_finished_runs:132|step2_total_runs:150|step2_finished_runs:104|step3_0_total_runs:20|step3_0_finished_runs:12|step3_1_total_runs:20|step3_1_finished_runs:11|step3_2_total_runs:20|step3_2_finished_runs:5|finished_rate:62.86%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -285,7 +407,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.25999999046325684,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/szccibek|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ncv8d9cl,https://wandb.ai/xzy11632/dance-dev/sweeps/9c2q16tc,https://wandb.ai/xzy11632/dance-dev/sweeps/t3jzvjsd","- type: filter.gene +",0.2599999904632568,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/szccibek|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ncv8d9cl,https://wandb.ai/xzy11632/dance-dev/sweeps/9c2q16tc,https://wandb.ai/xzy11632/dance-dev/sweeps/t3jzvjsd","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -332,7 +454,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2375 +",0.2375,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mb7tyn1a|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/tbsp1xsw,https://wandb.ai/xzy11632/dance-dev/sweeps/cx1inrux,https://wandb.ai/xzy11632/dance-dev/sweeps/ffjmt120","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:457|step2_total_runs:540|step2_finished_runs:410|step3_0_total_runs:20|step3_0_finished_runs:16|step3_1_total_runs:20|step3_1_finished_runs:16|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:76.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174 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: @@ -435,7 +599,49 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.313 +",0.313,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/nflips6b|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/k7q8z2pc,https://wandb.ai/xzy11632/dance-dev/sweeps/qcv9a0iw,https://wandb.ai/xzy11632/dance-dev/sweeps/252d5f2x","- 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 +",0.328000009059906,all_total_runs:600|all_finished_runs:436|step2_total_runs:540|step2_finished_runs:376|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:72.67%,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 +",0.328000009059906 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: @@ -560,6 +766,68 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/9wolfmyb|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/9mvl5sx5,https://wandb.ai/xzy11632/dance-dev/sweeps/9fpnmpj0,https://wandb.ai/xzy11632/dance-dev/sweeps/ryu2aorc","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",1.0,all_total_runs:586|all_finished_runs:451|step2_total_runs:540|step2_finished_runs:424|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:13|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:76.96%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: 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: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type ",1.0 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/fwdw9o1c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/30k56x2x,https://wandb.ai/xzy11632/dance-dev/sweeps/ic80cn5k,https://wandb.ai/xzy11632/dance-dev/sweeps/3nxuuyy6","- type: filter.gene target: FilterGenesPercentile @@ -592,7 +860,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.24650000035762787,all_total_runs:210|all_finished_runs:169|step2_total_runs:150|step2_finished_runs:116|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.48%,False,"- type: filter.gene +",0.2465000003576278,all_total_runs:210|all_finished_runs:169|step2_total_runs:150|step2_finished_runs:116|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:18|step3_2_total_runs:20|step3_2_finished_runs:15|finished_rate:80.48%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -617,7 +885,7 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.24549999833106995,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b7bg7l7f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i15ygwm0,https://wandb.ai/xzy11632/dance-dev/sweeps/sk1wej2m,https://wandb.ai/xzy11632/dance-dev/sweeps/kyoy45e1","- type: filter.gene +",0.2454999983310699,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/b7bg7l7f|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/i15ygwm0,https://wandb.ai/xzy11632/dance-dev/sweeps/sk1wej2m,https://wandb.ai/xzy11632/dance-dev/sweeps/kyoy45e1","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: ScaleFeature @@ -652,7 +920,69 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.252 +",0.252,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l86ls3ov|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/lnfv32gq,https://wandb.ai/xzy11632/dance-dev/sweeps/2q0nk04q,https://wandb.ai/xzy11632/dance-dev/sweeps/16gfa1y6","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:600|all_finished_runs:503|step2_total_runs:540|step2_finished_runs:448|step3_0_total_runs:20|step3_0_finished_runs:18|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:18|finished_rate:83.83%,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: 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 +",0.25850000977516174 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: {} @@ -678,7 +1008,7 @@ 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 @@ -703,7 +1033,7 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ params: config_dict: label_channel: cell_type -",0.38967135548591614,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y7k7yxnm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eokqtgdx,https://wandb.ai/xzy11632/dance-dev/sweeps/a6sdhtgr,https://wandb.ai/xzy11632/dance-dev/sweeps/1qwufafk","- type: filter.gene +",0.3896713554859161,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y7k7yxnm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/eokqtgdx,https://wandb.ai/xzy11632/dance-dev/sweeps/a6sdhtgr,https://wandb.ai/xzy11632/dance-dev/sweeps/1qwufafk","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -757,7 +1087,47 @@ b07e5164-baf6-43d2-bdba-5a249d0da879,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.392018779342723 +",0.392018779342723,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/n58tiwn8|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/uhkwcf89,https://wandb.ai/xzy11632/dance-dev/sweeps/ucmsvu93,https://wandb.ai/xzy11632/dance-dev/sweeps/ws9k52zd","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- 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 +",0.39201876521110535,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:440|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:83.17%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- 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 +",0.39201876521110535 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: @@ -882,7 +1252,69 @@ c5d88abe-f23a-45fa-a534-788985e93dad(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.7231329690346083 +",0.7231329690346083,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0vghv5c|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/v0trjp3v,https://wandb.ai/xzy11632/dance-dev/sweeps/ghm1g52e,https://wandb.ai/xzy11632/dance-dev/sweeps/w5ig97h5","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6502732038497925,all_total_runs:600|all_finished_runs:496|step2_total_runs:540|step2_finished_runs:437|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:82.67%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: 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 +",0.6502732038497925 a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8n01i0az|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0ub6c440,https://wandb.ai/xzy11632/dance-dev/sweeps/ia5uvd84,https://wandb.ai/xzy11632/dance-dev/sweeps/0ex0khdw","- type: filter.gene target: FilterGenesPlaceHolder params: {} @@ -989,7 +1421,51 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.9204545454545454 +",0.9204545454545454,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/swbuefez|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4rfpc6i6,https://wandb.ai/xzy11632/dance-dev/sweeps/zh0y5b7w,https://wandb.ai/xzy11632/dance-dev/sweeps/es9x4wkl","- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.931818187236786,all_total_runs:600|all_finished_runs:443|step2_total_runs:540|step2_finished_runs:383|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:73.83%,False,"- type: filter.gene + target: FilterGenesPlaceHolder + params: {} +- 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 +",0.931818187236786 5a11f879-d1ef-458a-910c-9b0bdfca5ebf(Pancreas),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/zqtpjc1h|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/1hyvxkgj,https://wandb.ai/xzy11632/dance-dev/sweeps/86i5rx8r,https://wandb.ai/xzy11632/dance-dev/sweeps/xz26h5pz","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1042,25 +1518,79 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: processes_num: 8 - type: filter.gene - target: FilterGenesRegression + target: FilterGenesRegression + params: + num_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeaturePCA +- type: graph.cell + target: CellFeatureGraph + params: + cell_feature_channel: feature.cell +- type: misc + target: SetConfig + params: + config_dict: + label_channel: cell_type +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p1kvq9l5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mj8qxe4y,https://wandb.ai/xzy11632/dance-dev/sweeps/o382i5n0,https://wandb.ai/xzy11632/dance-dev/sweeps/tl4iv383","- 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 + target: SCNFeature +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: SCNFeature + label_channel: cell_type +",1.0,all_total_runs:150|all_finished_runs:27|step2_total_runs:90|step2_finished_runs:15|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:18.00%,True,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: Log1P + params: {} +- type: filter.gene + target: FilterGenesTopK params: num_genes: 3000 - type: feature.cell - params: - out: feature.cell - log_level: INFO - split_name: train - target: WeightedFeaturePCA -- type: graph.cell - target: CellFeatureGraph - params: - cell_feature_channel: feature.cell + target: SCNFeature - type: misc target: SetConfig params: config_dict: + feature_channel: SCNFeature label_channel: cell_type -",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/p1kvq9l5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/mj8qxe4y,https://wandb.ai/xzy11632/dance-dev/sweeps/o382i5n0,https://wandb.ai/xzy11632/dance-dev/sweeps/tl4iv383","- type: filter.gene +",1.0,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/ldwyub15|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/wbohhp4w,https://wandb.ai/xzy11632/dance-dev/sweeps/4m9kquzw,https://wandb.ai/xzy11632/dance-dev/sweeps/dy3sel7f","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1073,21 +1603,25 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type -",1.0,all_total_runs:150|all_finished_runs:27|step2_total_runs:90|step2_finished_runs:15|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:5|step3_2_total_runs:20|step3_2_finished_runs:3|finished_rate:18.00%,True,"- type: filter.gene +",1.0,all_total_runs:600|all_finished_runs:432|step2_total_runs:540|step2_finished_runs:382|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:17|step3_2_total_runs:20|step3_2_finished_runs:13|finished_rate:72.00%,False,"- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1100,19 +1634,23 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ min_cells: 0.01 max_cells: 0.99 - type: normalize - target: Log1P + target: ScaleFeature params: {} - type: filter.gene - target: FilterGenesTopK + target: HighlyVariableGenesRawCount params: - num_genes: 3000 + n_top_genes: 3000 - type: feature.cell - target: SCNFeature + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD - type: misc target: SetConfig params: config_dict: - feature_channel: SCNFeature + feature_channel: feature.cell label_channel: cell_type ",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/00hfamxx,https://wandb.ai/xzy11632/dance-dev/sweeps/2l74ctr7","- type: filter.gene @@ -1140,7 +1678,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.47699999809265137,all_total_runs:210|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:59.52%,True,"- type: filter.gene +",0.4769999980926513,all_total_runs:210|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:103|step3_0_total_runs:20|step3_0_finished_runs:5|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:17|finished_rate:59.52%,True,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1165,7 +1703,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.47699999809265137,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3ch2l5s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pgj5t8lc,https://wandb.ai/xzy11632/dance-dev/sweeps/tmjfipc9,https://wandb.ai/xzy11632/dance-dev/sweeps/zudbm7ur","- type: filter.gene +",0.4769999980926513,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/l3ch2l5s|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/pgj5t8lc,https://wandb.ai/xzy11632/dance-dev/sweeps/tmjfipc9,https://wandb.ai/xzy11632/dance-dev/sweeps/zudbm7ur","- type: filter.gene target: FilterGenesPlaceHolder - type: normalize target: ScaleFeature @@ -1202,7 +1740,55 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4745 +",0.4745,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/s0e382wf|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/hemo1t7y,https://wandb.ai/xzy11632/dance-dev/sweeps/x2gofgl5,https://wandb.ai/xzy11632/dance-dev/sweeps/9cwz7pvl","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 8 + max_val: 98 + mode: sum +- type: normalize + target: Log1P + params: + base: 6.12335875625052 +- type: filter.gene + target: FilterGenesRegression + params: + method: seurat3 + num_genes: 8561 +- type: feature.cell + target: GaussRandProjFeature + params: + out: feature.cell + log_level: INFO + n_components: 909 +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4634999930858612,all_total_runs:599|all_finished_runs:425|step2_total_runs:539|step2_finished_runs:367|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:19|finished_rate:70.95%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- 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: CellSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.4589999914169311 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/1g4wscpu","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1228,7 +1814,7 @@ 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:152|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:16|finished_rate:72.38%,False,"- type: filter.gene +",0.2739999890327453,all_total_runs:210|all_finished_runs:152|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:16|finished_rate:72.38%,False,"- type: filter.gene target: FilterGenesPercentile params: {} - type: normalize @@ -1253,7 +1839,7 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ params: config_dict: label_channel: cell_type -",0.27399998903274536,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d1q0greq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxfkabxr,https://wandb.ai/xzy11632/dance-dev/sweeps/br7tiz9e,https://wandb.ai/xzy11632/dance-dev/sweeps/rarxceli","- type: filter.gene +",0.2739999890327453,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/d1q0greq|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/xxfkabxr,https://wandb.ai/xzy11632/dance-dev/sweeps/br7tiz9e,https://wandb.ai/xzy11632/dance-dev/sweeps/rarxceli","- type: filter.gene target: FilterGenesScanpyOrder params: order: @@ -1306,7 +1892,49 @@ a68b64d8-aee3-4947-81b7-36b8fe5a44d2(Pancreas),"step2:https://wandb.ai/xzy11632/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.2605 +",0.2605,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/vqaxcou0|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7vnuzemx,https://wandb.ai/xzy11632/dance-dev/sweeps/hlo0w2iq,https://wandb.ai/xzy11632/dance-dev/sweeps/693fk2tv","- 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: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174,all_total_runs:601|all_finished_runs:487|step2_total_runs:541|step2_finished_runs:427|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:81.03%,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: FeatureCellPlaceHolder +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.25850000977516174 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/qaf8aynk,https://wandb.ai/xzy11632/dance-dev/sweeps/3hef99ol","- type: filter.gene target: FilterGenesScanpyOrder params: @@ -1423,7 +2051,69 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.4095 +",0.4095,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lzckrtvs|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/h108k8vo,https://wandb.ai/xzy11632/dance-dev/sweeps/yglgx70h,https://wandb.ai/xzy11632/dance-dev/sweeps/19oi9utb","- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.41350001096725464,all_total_runs:600|all_finished_runs:499|step2_total_runs:540|step2_finished_runs:442|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:83.17%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.41350001096725464 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: @@ -1510,7 +2200,7 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.35952848722986247,all_total_runs:150|all_finished_runs:115|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.67%,False,"- type: filter.gene +",0.3595284872298624,all_total_runs:150|all_finished_runs:115|step2_total_runs:90|step2_finished_runs:60|step3_0_total_runs:20|step3_0_finished_runs:15|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.67%,False,"- type: filter.gene target: FilterGenesPlaceHolder params: {} - type: normalize @@ -1528,7 +2218,47 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.35952848722986247 +",0.3595284872298624,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/5i2bqatn|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/f3fnnke6,https://wandb.ai/xzy11632/dance-dev/sweeps/0nyyt1k7,https://wandb.ai/xzy11632/dance-dev/sweeps/oaa1e4hg","- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- 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 +",0.4420432150363922,all_total_runs:600|all_finished_runs:494|step2_total_runs:540|step2_finished_runs:434|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:82.33%,False,"- type: filter.gene + target: FilterGenesPercentile + params: {} +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: FilterGenesNumberPlaceHolder + params: {} +- 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 +",0.4420432150363922 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/geh4eyae","- type: filter.gene target: FilterGenesPercentile params: {} @@ -1627,4 +2357,60 @@ ff45e623-7f5f-46e3-b47d-56be0341f66b,"step2:https://wandb.ai/xzy11632/dance-dev/ config_dict: feature_channel: SCNFeature label_channel: cell_type -",0.6378575776019476 +",0.6378575776019476,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/q75qr9j4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/sk8ji4mk,https://wandb.ai/xzy11632/dance-dev/sweeps/bjg9ihgt,https://wandb.ai/xzy11632/dance-dev/sweeps/w24yl7xi","- type: filter.gene + target: FilterGenesPercentile + params: + min_val: 9 + max_val: 98 + mode: rv +- type: normalize + target: Log1P + params: + base: 9.215313360927013 +- type: filter.gene + target: FilterGenesNumberPlaceHolder +- type: feature.cell + target: WeightedFeaturePCA + params: + out: feature.cell + log_level: INFO + n_components: 323 + feat_norm_mode: standardize +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6792452931404114,all_total_runs:600|all_finished_runs:486|step2_total_runs:540|step2_finished_runs:426|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:81.00%,False,"- type: filter.gene + target: FilterGenesScanpyOrder + params: + order: + - min_counts + - min_cells + - max_counts + - max_cells + min_counts: 0.01 + max_counts: 0.99 + min_cells: 0.01 + max_cells: 0.99 +- type: normalize + target: ScaleFeature + params: {} +- type: filter.gene + target: HighlyVariableGenesRawCount + params: + n_top_genes: 3000 +- type: feature.cell + params: + out: feature.cell + log_level: INFO + split_name: train + target: WeightedFeatureSVD +- type: misc + target: SetConfig + params: + config_dict: + feature_channel: feature.cell + label_channel: cell_type +",0.6786366105079651