genhpf 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

genhpf/scripts/preprocess/preprocess_meds.py

@@ -148,11 +148,11 @@ def main():
         data_paths = [root_path]
 
     if not output_dir.exists():
-        output_dir.mkdir()
+        output_dir.mkdir(parents=True)
     else:
         if args.rebase:
             shutil.rmtree(output_dir)
-            output_dir.mkdir()
+            output_dir.mkdir(parents=True)
         elif output_dir.exists():
             if args.skip_if_exists:
                 ls = glob.glob(str(output_dir / "**/*"), recursive=True)

genhpf/scripts/test.py

@@ -208,6 +208,9 @@ def main(cfg: Config) -> None:
             meds_pred_output = meds_pred_output.with_columns(
                 pl.col("subject_id").map_elements(lambda x: x.split("_")[0], return_dtype=pl.String).cast(int)
             )
+            meds_pred_output = (
+                meds_pred_output.with_columns(pl.col("predicted_boolean_value").cast(bool))
+            )
             if not os.path.exists(cfg.meds.output_dir):
                 os.makedirs(cfg.meds.output_dir)
             meds_pred_output.write_parquet(os.path.join(cfg.meds.output_dir, f"{subset}.parquet"))

genhpf/scripts/train.py

@@ -281,6 +281,14 @@ def validate(
 
         progress.print(stats, tag=subset, step=trainer.get_num_updates())
 
+        if np.isnan(stats[cfg.checkpoint.best_checkpoint_metric]):
+            logger.info(
+                f"validation value for {cfg.checkpoint.best_checkpoint_metric} is NaN. "
+                "Changed the best checkpoint metric to loss."
+            )
+            cfg.checkpoint.best_checkpoint_metric = "loss"
+            cfg.checkpoint.maximize_best_checkpoint_metric = False
+
         valid_losses.append(stats[cfg.checkpoint.best_checkpoint_metric])
 
     return valid_losses

{genhpf-1.0.4.dist-info → genhpf-1.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: genhpf
-Version: 1.0.4
+Version: 1.0.6
 Summary: GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning
 Author-email: Jungwoo Oh <ojw0123@kaist.ac.kr>, Kyunghoon Hur <pacesun@kaist.ac.kr>
 License: MIT license

{genhpf-1.0.4.dist-info → genhpf-1.0.6.dist-info}/RECORD

@@ -36,11 +36,11 @@ genhpf/modules/identity_layer.py,sha256=uGRqfRBNhc-ha5wNrqawh5E1pw5Lm9GDGi1stju-
 genhpf/modules/layer_norm.py,sha256=-aVKThi1pWvVMbMAzyQG1co6MHPBCUZgxWJKYzIqsPQ,902
 genhpf/modules/positional_encoding.py,sha256=Rf_qHdQArljEggRO4EHufc_JHq9-i44Oog1w9Bh51DQ,754
 genhpf/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-genhpf/scripts/test.py,sha256=wWi7OLqxsW9blj21m3RTirvziQ5UpkjkngOkgkE3Vb4,10149
-genhpf/scripts/train.py,sha256=5f5PYOkiW7BahbFArvdOguAzUdDnY4Urw7Nx3aJ4kjs,12488
+genhpf/scripts/test.py,sha256=DZPiZa-Tm6kKLcK3R1EH82gjq4Hbl098IAY4kA3fQxg,10288
+genhpf/scripts/train.py,sha256=V4abCZ0r6qWxeJZdXyk4uXSVFXscqH_dhzk7CZuWrBA,12872
 genhpf/scripts/preprocess/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 genhpf/scripts/preprocess/manifest.py,sha256=ZIK16e4vs_cS2K_tM1GaT38hc1nBHk6JB9Uga6OjgU4,2711
-genhpf/scripts/preprocess/preprocess_meds.py,sha256=x5R4KDzzB-21IUHjfkyo4-Be1t9U4oaurjm5VhxZ5Rw,25050
+genhpf/scripts/preprocess/preprocess_meds.py,sha256=4GIK-_sQwB5A11FSbr_VnABY2MHxxNbFVmzSo71KpgQ,25074
 genhpf/scripts/preprocess/genhpf/README.md,sha256=qtpM_ABJk5yI8xbsUj1sZ71yX5bybx9ZvAymo0Lh5Vc,2877
 genhpf/scripts/preprocess/genhpf/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 genhpf/scripts/preprocess/genhpf/main.py,sha256=EF3sce0ltowMHIGK7zLEQEOnzOWQ_WJxoBowknHV3mQ,6161
@@ -59,9 +59,9 @@ genhpf/utils/distributed_utils.py,sha256=000xKlw8SLoSH16o6n2bB3eueGR0aVD_DufPYES
 genhpf/utils/file_io.py,sha256=hnZXdMtAibfFDoIfn-SDusl-v7ZImeUEh0eD2MIxbG4,4919
 genhpf/utils/pdb.py,sha256=400rk1pVfOpVpzKIFHnTRlZ2VCtBqRh9G-pRRwu2Oqo,930
 genhpf/utils/utils.py,sha256=BoC_7Gz8uCHbUBCpcXGBMD-5irApi_6xM7nU-2ac4aA,6176
-genhpf-1.0.4.dist-info/LICENSE,sha256=VK_rvhY2Xi_DAIZHtauni5O9-1_do5SNWjrskv4amg8,1065
-genhpf-1.0.4.dist-info/METADATA,sha256=Mgs4WysCKfBf4E2Jik2BgMdZPM8w1-rL5NoqgeqM5Zo,10589
-genhpf-1.0.4.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
-genhpf-1.0.4.dist-info/entry_points.txt,sha256=Wp94VV2w9KasBDLaluLM5EnjLgjNOAQVu44wKRDAwmQ,288
-genhpf-1.0.4.dist-info/top_level.txt,sha256=lk846Vmnvydb6UZn8xmowj60nkrZYexNOGGnPM-IbhA,7
-genhpf-1.0.4.dist-info/RECORD,,
+genhpf-1.0.6.dist-info/LICENSE,sha256=VK_rvhY2Xi_DAIZHtauni5O9-1_do5SNWjrskv4amg8,1065
+genhpf-1.0.6.dist-info/METADATA,sha256=jNN97lqcfOLt3fbpmwd643IcTT-PlVof7IlkCur9zQs,10589
+genhpf-1.0.6.dist-info/WHEEL,sha256=jB7zZ3N9hIM9adW7qlTAyycLYW9npaWKLRzaoVcLKcM,91
+genhpf-1.0.6.dist-info/entry_points.txt,sha256=Wp94VV2w9KasBDLaluLM5EnjLgjNOAQVu44wKRDAwmQ,288
+genhpf-1.0.6.dist-info/top_level.txt,sha256=lk846Vmnvydb6UZn8xmowj60nkrZYexNOGGnPM-IbhA,7
+genhpf-1.0.6.dist-info/RECORD,,