update ans

OmicsML · Jan 12, 2025 · 0a33784 · 0a33784
1 parent d97a92f
commit 0a33784
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Showing 4 changed files with 87 additions and 48 deletions.
diff --git a/examples/atlas/get_result_web.py b/examples/atlas/get_result_web.py
@@ -12,7 +12,7 @@
 from tqdm import tqdm
 
 from dance import logger
-from dance.settings import METADIR
+from dance.settings import DANCEDIR, METADIR
 from dance.utils import try_import
 
 # get yaml of best method
@@ -73,8 +73,18 @@ def get_sweep_url(step_csv: pd.DataFrame, single=True):
     """
     ids = step_csv["id"]
     sweep_urls = []
-    for run_id in tqdm(reversed(ids),
-                       leave=False):  #The reversal of order is related to additional_sweep_ids.append(sweep_id)
+    test_accs_exists = False
+    if "test_acc" in step_csv.columns:
+        test_accs = reversed(step_csv["test_acc"])
+        test_accs_exists = True
+    else:
+        test_accs = [np.nan] * len(ids)
+
+    for run_id, test_acc in tqdm(
+            zip(reversed(ids),
+                test_accs), leave=False):  #The reversal of order is related to additional_sweep_ids.append(sweep_id)
+        if test_accs_exists and pd.isna(test_acc):
+            continue
         api = wandb.Api(timeout=1000)
         run = api.run(f"/{entity}/{project}/runs/{run_id}")
         sweep_urls.append(run.sweep.url)
@@ -291,9 +301,9 @@ def get_new_ans(tissue):
 
     for method_folder in tqdm(methods):
         for dataset_id in collect_datasets:
-            if dataset_id == "f72958f5-7f42-4ebb-98da-445b0c6de516":  #f72958f5-7f42-4ebb-98da-445b0c6de516
+            if dataset_id == "0b4a15a7-4e9e-4555-9733-2423e5c66469":  #f72958f5-7f42-4ebb-98da-445b0c6de516
                 pass
-            file_path = f"../tuning/{method_folder}/{dataset_id}"
+            file_path = DANCEDIR / f"examples/tuning/{method_folder}/{dataset_id}"
             if not check_exist(file_path):
                 continue
             step2_url = get_sweep_url(pd.read_csv(f"{file_path}/results/pipeline/best_test_acc.csv"))

diff --git a/examples/atlas/sweep_results/Blood_ans.csv b/examples/atlas/sweep_results/Blood_ans.csv
@@ -889,7 +889,7 @@ 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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+",0.1969999969005584,"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
   target: FilterGenesPlaceHolder
 - type: normalize
   target: Log1P
@@ -993,7 +993,7 @@ 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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   target: FilterGenesPercentile
   params: {}
 - type: normalize
@@ -1077,7 +1077,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/
       feature_channel: feature.cell
       label_channel: cell_type
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-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
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   target: FilterGenesPercentile
   params: {}
 - type: normalize
@@ -1173,7 +1173,7 @@ 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
   target: FilterGenesScanpyOrder
   params:
@@ -1204,7 +1204,7 @@ c7775e88-49bf-4ba2-a03b-93f00447c958,"step2:https://wandb.ai/xzy11632/dance-dev/
     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
+",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
@@ -1296,7 +1296,7 @@ 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
@@ -1369,7 +1369,7 @@ 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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   target: FilterGenesScanpyOrder
   params:
@@ -1403,7 +1403,7 @@ ae29ebd0-1973-40a4-a6af-d15a5f77a80f,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesScanpyOrder
   params:
     order:
@@ -1517,7 +1517,7 @@ 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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   target: FilterGenesPlaceHolder
   params: {}
 - type: normalize
@@ -1602,7 +1602,7 @@ 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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   target: FilterGenesPlaceHolder
   params: {}
@@ -1625,7 +1625,7 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
       feature_channel: feature.cell
       label_channel: cell_type
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   target: FilterGenesPlaceHolder
 - type: normalize
   target: ScaleFeature
@@ -1701,7 +1701,7 @@ bc2a7b3d-f04e-477e-96c9-9d5367d5425c,"step2:https://wandb.ai/xzy11632/dance-dev/
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   target: FilterGenesScanpyOrder
   params:
@@ -2146,7 +2146,7 @@ d7d7e89c-c93a-422d-8958-9b4a90b69558,"step2:https://wandb.ai/xzy11632/dance-dev/
     config_dict:
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   target: FilterGenesPercentile
   params:
     min_val: 10