update ans

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
+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
 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:
@@ -58,7 +58,28 @@ Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_c
   params:
     config_dict:
       label_channel: cell_type
-",0.4494999945163727,all_total_runs:210|all_finished_runs:148|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:70.48%,False
+",0.4494999945163727,all_total_runs:210|all_finished_runs:148|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:14|step3_2_total_runs:20|step3_2_finished_runs:1|finished_rate:70.48%,False,"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
 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:
@@ -123,7 +144,28 @@ f7c1c579-2dc0-47e2-ba19-8165c5a0e353(Intestine),"step2:https://wandb.ai/xzy11632
   params:
     config_dict:
       label_channel: cell_type
-",0.4900000095367432,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.05%,False
+",0.4900000095367432,all_total_runs:210|all_finished_runs:166|step2_total_runs:150|step2_finished_runs:113|step3_0_total_runs:20|step3_0_finished_runs:14|step3_1_total_runs:20|step3_1_finished_runs:19|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:79.05%,False,"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
 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: {}
@@ -184,7 +226,29 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/
   params:
     config_dict:
       label_channel: cell_type
-",0.3653995394706726,all_total_runs:196|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:86|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:20|finished_rate:63.78%,False
+",0.3653995394706726,all_total_runs:196|all_finished_runs:125|step2_total_runs:150|step2_finished_runs:86|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:20|finished_rate:63.78%,False,"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
 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: {}
@@ -246,7 +310,42 @@ e40c6272-af77-4a10-9385-62a398884f27,"step2:https://wandb.ai/xzy11632/dance-dev/
   params:
     config_dict:
       label_channel: cell_type
-",0.450367659330368,all_total_runs:196|all_finished_runs:157|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:20|step3_2_finished_runs:20|finished_rate:80.10%,False
+",0.450367659330368,all_total_runs:196|all_finished_runs:157|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:20|step3_2_finished_runs:20|finished_rate:80.10%,False,"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
 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:
@@ -309,7 +408,38 @@ fa27492b-82ff-4ab7-ac61-0e2b184eee67(Intestine),"step2:https://wandb.ai/xzy11632
   params:
     config_dict:
       label_channel: cell_type
-",0.512499988079071,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.00%,False
+",0.512499988079071,all_total_runs:196|all_finished_runs:147|step2_total_runs:150|step2_finished_runs:119|step3_0_total_runs:20|step3_0_finished_runs:13|step3_1_total_runs:20|step3_1_finished_runs:15|step3_2_total_runs:6|step3_2_finished_runs:0|finished_rate:75.00%,False,"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
 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:
@@ -368,4 +498,27 @@ d6dfdef1-406d-4efb-808c-3c5eddbfe0cb,"step2:https://wandb.ai/xzy11632/dance-dev/
   params:
     config_dict:
       label_channel: cell_type
-",0.5648086071014404,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False
+",0.5648086071014404,all_total_runs:210|all_finished_runs:133|step2_total_runs:150|step2_finished_runs:120|step3_0_total_runs:20|step3_0_finished_runs:11|step3_1_total_runs:20|step3_1_finished_runs:2|step3_2_total_runs:20|step3_2_finished_runs:0|finished_rate:63.33%,False,"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