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OmicsML · Jan 12, 2025 · 7cb9810 · 7cb9810
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diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv
diff --git a/examples/atlas/sweep_results/Brain_ans.csv b/examples/atlas/sweep_results/Brain_ans.csv
diff --git a/examples/atlas/sweep_results/Heart_ans.csv b/examples/atlas/sweep_results/Heart_ans.csv
@@ -1532,7 +1532,45 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/
       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
-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
+1c739a3e-c3f5-49d5-98e0-73975e751201,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/z2v6lwrl|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zebalczl,https://wandb.ai/xzy11632/dance-dev/sweeps/av6xm0h7,https://wandb.ai/xzy11632/dance-dev/sweeps/lx1ky4rl","- type: filter.gene
+  target: FilterGenesScanpyOrder
+  params:
+    order:
+    - min_counts
+    - max_cells
+    - max_counts
+    - min_cells
+    min_counts: 226
+    min_cells: 0.047663500071270286
+    max_counts: 0.9287568186013924
+    max_cells: 0.991629947014312
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+    min_cells: 10
+    gmean_eps: 1
+    n_genes: 1261
+    n_cells: 100
+    bin_size: 528
+    bw_adjust: 1.8575579429886373
+- type: filter.gene
+  target: FilterGenesRegression
+  params:
+    method: enclasc
+    num_genes: 7844
+- type: feature.cell
+  target: FeatureCellPlaceHolder
+  params:
+    out: feature.cell
+    log_level: INFO
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.304500013589859,all_total_runs:510|all_finished_runs:397|step2_total_runs:450|step2_finished_runs:356|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:77.84%,False,"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
   target: ScaleFeature
@@ -1607,7 +1645,29 @@ ed852810-a003-4386-9846-1638362cee39,"step2:https://wandb.ai/xzy11632/dance-dev/
       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
-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
+4ed927e9-c099-49af-b8ce-a2652d069333,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lxi0z80g|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/spk2mp9z,https://wandb.ai/xzy11632/dance-dev/sweeps/xwvu3aat,https://wandb.ai/xzy11632/dance-dev/sweeps/ssfi4ars","- type: filter.gene
+  target: FilterGenesPlaceHolder
+- type: normalize
+  target: Log1P
+  params:
+    base: 6.02274143830023
+- type: filter.gene
+  target: FilterGenesRegression
+  params:
+    method: enclasc
+    num_genes: 8532
+- type: feature.cell
+  target: FeatureCellPlaceHolder
+  params:
+    out: feature.cell
+    log_level: INFO
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.24899999797344208,all_total_runs:510|all_finished_runs:369|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:19|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:72.35%,False,"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:
     min_val: 4

diff --git a/examples/atlas/sweep_results/Intestine_ans.csv b/examples/atlas/sweep_results/Intestine_ans.csv
@@ -1,4 +1,4 @@
-Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check
+Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check,cta_scdeepsort,cta_scdeepsort_best_yaml,cta_scdeepsort_best_res,cta_scdeepsort_run_stats,cta_scdeepsort_check,cta_actinn,cta_actinn_best_yaml,cta_actinn_best_res,cta_actinn_run_stats,cta_actinn_check,cta_singlecellnet,cta_singlecellnet_best_yaml,cta_singlecellnet_best_res,cta_singlecellnet_run_stats,cta_singlecellnet_check
 2adb1f8a-a6b1-4909-8ee8-484814e2d4bf(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/cal53l43|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6qn8k6fz,https://wandb.ai/xzy11632/dance-dev/sweeps/bk4iumv7,https://wandb.ai/xzy11632/dance-dev/sweeps/ogwnnypr","- type: filter.gene
   target: FilterGenesScanpyOrder
   params:
@@ -79,7 +79,26 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c
     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
+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/yjg75eb2|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/6n6m09lu,https://wandb.ai/xzy11632/dance-dev/sweeps/5o2qlh8l,https://wandb.ai/xzy11632/dance-dev/sweeps/is374gfu","- type: filter.gene
+  target: FilterGenesPlaceHolder
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: HighlyVariableGenesLogarithmizedByTopGenes
+  params:
+    n_top_genes: 3000
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
+",0.4595,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:58.00%,True
 f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/968ejhzy|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4mpkufxm,https://wandb.ai/xzy11632/dance-dev/sweeps/68q8gvfj,https://wandb.ai/xzy11632/dance-dev/sweeps/f094n1hy","- type: filter.gene
   target: FilterGenesScanpyOrder
   params:
@@ -165,7 +184,25 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632
     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
+",0.481000006198883,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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/kxkmzv41|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/rwswn0ja,https://wandb.ai/xzy11632/dance-dev/sweeps/cayifo99,https://wandb.ai/xzy11632/dance-dev/sweeps/y40of4uy","- type: filter.gene
+  target: FilterGenesPlaceHolder
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: HighlyVariableGenesLogarithmizedByMeanAndDisp
+  params: {}
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
+",0.496,all_total_runs:150|all_finished_runs:87|step2_total_runs:90|step2_finished_runs:64|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:58.00%,True
 e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/o6y5gglv|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/7g1mezgk,https://wandb.ai/xzy11632/dance-dev/sweeps/rqw2mq80,https://wandb.ai/xzy11632/dance-dev/sweeps/h31q7gkk","- type: filter.gene
   target: FilterGenesPercentile
   params: {}
@@ -248,7 +285,28 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/
     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
+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lydev3fk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/q4cn3mtb,https://wandb.ai/xzy11632/dance-dev/sweeps/3rx39oxw,https://wandb.ai/xzy11632/dance-dev/sweeps/xhgs2c15","- type: filter.gene
+  target: FilterGenesPercentile
+  params:
+    min_val: 10
+    max_val: 99
+    mode: cv
+- type: normalize
+  target: ScaleFeature
+  params:
+    mode: l2
+    eps: 0.7
+- type: filter.gene
+  target: FilterGenesNumberPlaceHolder
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
+",0.3840186190845617,all_total_runs:150|all_finished_runs:92|step2_total_runs:90|step2_finished_runs:58|step3_0_total_runs:20|step3_0_finished_runs:4|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:11|finished_rate:61.33%,False
 6a270451-b4d9-43e0-aa89-e33aac1ac74b,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/y7qskew9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/w5f3puka,https://wandb.ai/xzy11632/dance-dev/sweeps/ys90com4,https://wandb.ai/xzy11632/dance-dev/sweeps/xpfyrv5k","- type: filter.gene
   target: FilterGenesPlaceHolder
   params: {}
@@ -345,7 +403,33 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/
     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
+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2w7qh6m9|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/orery7et,https://wandb.ai/xzy11632/dance-dev/sweeps/w60mlkdg,https://wandb.ai/xzy11632/dance-dev/sweeps/gmdyzho8","- type: filter.gene
+  target: FilterGenesPlaceHolder
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+    min_cells: 3
+    gmean_eps: 1
+    n_genes: 2584
+    n_cells: null
+    bin_size: 380
+    bw_adjust: 4.122403001571971
+- type: filter.gene
+  target: HighlyVariableGenesLogarithmizedByTopGenes
+  params:
+    n_top_genes: 9393
+    n_bins: 15
+    flavor: cell_ranger
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
+",0.4522058823529412,all_total_runs:150|all_finished_runs:98|step2_total_runs:90|step2_finished_runs:75|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:3|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:65.33%,False
 fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/1gc9d2ad|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/yq6minkn,https://wandb.ai/xzy11632/dance-dev/sweeps/tjw6o4v5,https://wandb.ai/xzy11632/dance-dev/sweeps/0bads4k9","- type: filter.gene
   target: FilterGenesScanpyOrder
   params:
@@ -439,7 +523,25 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632
     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
+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/jocmyjw4|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/zo3i9mg9,https://wandb.ai/xzy11632/dance-dev/sweeps/cx6569af,https://wandb.ai/xzy11632/dance-dev/sweeps/o8jyq6rr","- type: filter.gene
+  target: FilterGenesPlaceHolder
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: HighlyVariableGenesLogarithmizedByMeanAndDisp
+  params: {}
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
+",0.506,all_total_runs:150|all_finished_runs:95|step2_total_runs:90|step2_finished_runs:72|step3_0_total_runs:20|step3_0_finished_runs:3|step3_1_total_runs:20|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:63.33%,False
 d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/2efkko22|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/5tshgz51,https://wandb.ai/xzy11632/dance-dev/sweeps/xj7266k8,https://wandb.ai/xzy11632/dance-dev/sweeps/hyob32ut","- type: filter.gene
   target: FilterGenesPercentile
   params:
@@ -521,4 +623,23 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/
     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
+",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,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/f0izdcdt|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/cp84ljtg,https://wandb.ai/xzy11632/dance-dev/sweeps/6tb70g8g,https://wandb.ai/xzy11632/dance-dev/sweeps/oa5ayktp","- type: filter.gene
+  target: FilterGenesPlaceHolder
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: HighlyVariableGenesRawCount
+  params:
+    n_top_genes: 3000
+- type: feature.cell
+  target: SCNFeature
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: SCNFeature
+      label_channel: cell_type
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