fix exists filter on unverified paths, add chexpert fallback merge

Author: wa5rx3

scripts/run_data_pipeline.sh

@@ -71,7 +71,8 @@ $PYTHON -m src.data.build_triage_model_table
 
 echo "[9/19] build_pneumonia_labels_from_chexpert"
 $PYTHON -m src.data.build_pneumonia_labels_from_chexpert \
-    --metadata-root "$CXR_ROOT"
+    --metadata-root "$CXR_ROOT" \
+    --allow-fallback-study-merge
 
 echo "[10/19] build_pneumonia_training_table (u_ignore)"
 $PYTHON -m src.data.build_pneumonia_training_table \
@@ -120,7 +121,8 @@ $PYTHON -m src.data.build_image_pretraining_split
 
 echo "[18/19] build_image_multilabel_pretrain_table"
 $PYTHON -m src.data.build_image_multilabel_pretrain_table \
-    --metadata-root "$CXR_ROOT"
+    --metadata-root "$CXR_ROOT" \
+    --allow-fallback-study-merge
 
 echo "[19/19] build_nonED_image_eval_table"
 $PYTHON -m src.data.build_nonED_image_eval_table \

src/data/build_primary_imaging_cohort.py

@@ -28,8 +28,11 @@ def main() -> None:
 
     df = pd.read_parquet(args.input_manifest).copy()
 
-    # Keep only rows with valid paths
-    if "exists" in df.columns:
+    # Keep only rows with valid paths.
+    # exists=True  → verified present, keep.
+    # exists=False → verified missing, drop.
+    # exists=NA   → not checked, assume present.
+    if "exists" in df.columns and not df["exists"].isna().all():
         df = df[df["exists"] == True].copy()
 
     # Keep only frontal rows