update ans

OmicsML · Jan 12, 2025 · c8c4e2b · c8c4e2b
1 parent 9846dee
commit c8c4e2b
Show file tree

Hide file tree

Showing 6 changed files with 2,596 additions and 0 deletions.
diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv
@@ -0,0 +1,136 @@
+Dataset_id,cta_celltypist,cta_celltypist_best_yaml,cta_celltypist_best_res,cta_celltypist_run_stats,cta_celltypist_check
+2adb1f8a-a6b1-4909-8ee8-484814e2d4bf,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/0rvmzkia|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/e9ndxdji,https://wandb.ai/xzy11632/dance-dev/sweeps/6lndzud2,https://wandb.ai/xzy11632/dance-dev/sweeps/kboc5b0g","- type: filter.gene
+  target: FilterGenesPercentile
+  params: {}
+- type: normalize
+  target: Log1P
+  params: {}
+- type: filter.gene
+  target: FilterGenesRegression
+  params:
+    num_genes: 3000
+- type: feature.cell
+  params:
+    out: feature.cell
+    log_level: INFO
+  target: FeatureCellPlaceHolder
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.24699999392032623,all_total_runs:493|all_finished_runs:376|step2_total_runs:450|step2_finished_runs:336|step3_0_total_runs:20|step3_0_finished_runs:20|step3_1_total_runs:3|step3_1_finished_runs:0|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:76.27%,False
+fe52003e-1460-4a65-a213-2bb1a508332f,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/lx05p3vr|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/iuazawqt,https://wandb.ai/xzy11632/dance-dev/sweeps/s9ckkiye,https://wandb.ai/xzy11632/dance-dev/sweeps/kval7p9y","- type: filter.gene
+  target: FilterGenesScanpyOrder
+  params:
+    order:
+    - min_counts
+    - min_cells
+    - max_counts
+    - max_cells
+    min_counts: 0.01
+    max_counts: 0.99
+    min_cells: 0.01
+    max_cells: 0.99
+- type: normalize
+  target: ScaleFeature
+  params: {}
+- type: filter.gene
+  target: FilterGenesRegression
+  params:
+    num_genes: 3000
+- type: feature.cell
+  params:
+    out: feature.cell
+    log_level: INFO
+  target: FeatureCellPlaceHolder
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.9113029837608336,all_total_runs:510|all_finished_runs:347|step2_total_runs:450|step2_finished_runs:329|step3_0_total_runs:20|step3_0_finished_runs:1|step3_1_total_runs:20|step3_1_finished_runs:1|step3_2_total_runs:20|step3_2_finished_runs:16|finished_rate:68.04%,False
+c2a461b1-0c15-4047-9fcb-1f966fe55100,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/igxg3cvm|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/0fxcrj2d,https://wandb.ai/xzy11632/dance-dev/sweeps/ldrt5co9,https://wandb.ai/xzy11632/dance-dev/sweeps/f375yojf","- type: filter.gene
+  target: FilterGenesPercentile
+  params:
+    min_val: 7
+    max_val: 98
+    mode: cv
+- type: normalize
+  target: ScaleFeature
+  params:
+    mode: minmax
+    eps: 0.5
+- type: filter.gene
+  target: FilterGenesTopK
+  params:
+    num_genes: 7024
+    top: true
+    mode: cv
+- type: feature.cell
+  target: FeatureCellPlaceHolder
+  params:
+    out: feature.cell
+    log_level: INFO
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.2565000057220459,all_total_runs:510|all_finished_runs:382|step2_total_runs:450|step2_finished_runs:322|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:74.90%,False
+b0e547f0-462b-4f81-b31b-5b0a5d96f537,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/mz273ff5|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/gm5ga5mm,https://wandb.ai/xzy11632/dance-dev/sweeps/gh2p49n8,https://wandb.ai/xzy11632/dance-dev/sweeps/2w6dihtz","- type: filter.gene
+  target: FilterGenesPercentile
+  params:
+    min_val: 5
+    max_val: 99
+    mode: cv
+- type: normalize
+  target: NormalizeTotal
+  params:
+    target_sum: 1000000
+    max_fraction: 0.05
+- type: filter.gene
+  target: FilterGenesTopK
+  params:
+    num_genes: 227
+    top: false
+    mode: rv
+- type: feature.cell
+  target: GaussRandProjFeature
+  params:
+    out: feature.cell
+    log_level: INFO
+    n_components: 872
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.1655000001192093,all_total_runs:493|all_finished_runs:400|step2_total_runs:450|step2_finished_runs:360|step3_0_total_runs:3|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:20|step3_2_total_runs:20|step3_2_finished_runs:20|finished_rate:81.14%,False
+d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/sweeps/bvgjtmzk|step3:https://wandb.ai/xzy11632/dance-dev/sweeps/4lc9v41j,https://wandb.ai/xzy11632/dance-dev/sweeps/qgpqm3rx,https://wandb.ai/xzy11632/dance-dev/sweeps/l6uoduzp","- type: filter.gene
+  target: FilterGenesPercentile
+  params: {}
+- type: normalize
+  target: ScTransform
+  params:
+    processes_num: 8
+- type: filter.gene
+  target: FilterGenesRegression
+  params:
+    num_genes: 3000
+- type: feature.cell
+  params:
+    out: feature.cell
+    log_level: INFO
+  target: FeatureCellPlaceHolder
+- type: misc
+  target: SetConfig
+  params:
+    config_dict:
+      feature_channel: feature.cell
+      label_channel: cell_type
+",0.16099999845027924,all_total_runs:493|all_finished_runs:331|step2_total_runs:450|step2_finished_runs:327|step3_0_total_runs:20|step3_0_finished_runs:0|step3_1_total_runs:20|step3_1_finished_runs:4|step3_2_total_runs:3|step3_2_finished_runs:0|finished_rate:67.14%,False