update ans

Author: xingzhongyu

examples/atlas/sweep_results/Blood_ans.csv

@@ -844,7 +844,38 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_c
     config_dict:
       feature_channel: SCNFeature
       label_channel: cell_type
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+  target: FilterGenesScanpyOrder
+  params:
+    order:
+    - min_counts
+    - min_cells
+    - max_counts
+    - max_cells
+    min_counts: 0.01
+    max_counts: 0.99
+    min_cells: 0.01
+    max_cells: 0.99
+- type: normalize
+  target: ScaleFeature
+  params: {}
+- type: filter.gene
+  target: HighlyVariableGenesRawCount
+  params:
+    n_top_genes: 3000
+- type: feature.cell
+  params:
+    out: feature.cell
+    log_level: INFO
+    split_name: train
+  target: WeightedFeatureSVD
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
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   target: FilterGenesScanpyOrder
   params:
@@ -1466,7 +1497,7 @@ Dataset_id,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_c
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesPercentile
   params: {}
@@ -2060,7 +2091,7 @@ e8681d74-ac9e-4be5-be14-1cf1bbd54dd7,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesPlaceHolder
   params: {}

examples/atlas/sweep_results/Brain_ans.csv

@@ -1,5 +1,5 @@
 Dataset_id,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_scdeepsort_run_stats,cta_actinn_run_stats,cta_singlecellnet_run_stats,cta_celltypist_run_stats,cta_scdeepsort_check,cta_celltypist_check,cta_actinn_check,cta_singlecellnet_check
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   target: FilterGenesPlaceHolder
   params: {}
 - type: normalize
@@ -103,7 +103,7 @@ Dataset_id,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_singlecellnet
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesPercentile
   params: {}
@@ -125,7 +125,26 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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+  target: FilterGenesPercentile
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: HighlyVariableGenesRawCount
+  params:
+    n_top_genes: 3000
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
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   target: FilterGenesScanpyOrder
   params:
     order:
@@ -182,7 +201,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesPercentile
   params:
@@ -401,7 +420,7 @@ c5d88abe-f23a-45fa-a534-788985e93dad,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
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 83b5e943-a1d5-4164-b3f2-f7a37f01b524,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/8jryp9lp|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/ukwfwav1,https://wandb.ai/xzy11632/dance-dev/sweeps/fufwxjwm,https://wandb.ai/xzy11632/dance-dev/sweeps/f601wnp4","- type: filter.gene
   target: FilterGenesScanpyOrder
   params:

examples/atlas/sweep_results/Heart_ans.csv

@@ -348,7 +348,7 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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+",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%,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kxkmzv41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/467ux2eq,https://wandb.ai/xzy11632/dance-dev/sweeps/213zwuix,https://wandb.ai/xzy11632/dance-dev/sweeps/qa7qjg5q","- type: filter.gene
   target: FilterGenesPlaceHolder
   params: {}
 - type: normalize