genhpf 1.0.4__tar.gz → 1.0.6__tar.gz

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  1. {genhpf-1.0.4/src/genhpf.egg-info → genhpf-1.0.6}/PKG-INFO +1 -1
  2. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/preprocess_meds.py +2 -2
  3. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/test.py +3 -0
  4. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/train.py +8 -0
  5. {genhpf-1.0.4 → genhpf-1.0.6/src/genhpf.egg-info}/PKG-INFO +1 -1
  6. {genhpf-1.0.4 → genhpf-1.0.6}/.gitignore +0 -0
  7. {genhpf-1.0.4 → genhpf-1.0.6}/.pre-commit-config.yaml +0 -0
  8. {genhpf-1.0.4 → genhpf-1.0.6}/LICENSE +0 -0
  9. {genhpf-1.0.4 → genhpf-1.0.6}/README.md +0 -0
  10. {genhpf-1.0.4 → genhpf-1.0.6}/examples/pretrain/mlm/genhpf/flattened_pt.yaml +0 -0
  11. {genhpf-1.0.4 → genhpf-1.0.6}/examples/pretrain/simclr/genhpf/genhpf_hierarchical_pt.yaml +0 -0
  12. {genhpf-1.0.4 → genhpf-1.0.6}/examples/pretrain/wav2vec2/genhpf/hierarchical_pt.yaml +0 -0
  13. {genhpf-1.0.4 → genhpf-1.0.6}/examples/test/genhpf/genhpf_flattened.yaml +0 -0
  14. {genhpf-1.0.4 → genhpf-1.0.6}/examples/test/genhpf/genhpf_hierarchical.yaml +0 -0
  15. {genhpf-1.0.4 → genhpf-1.0.6}/examples/test/genhpf/meds_hierarchical.yaml +0 -0
  16. {genhpf-1.0.4 → genhpf-1.0.6}/examples/train/genhpf/genhpf_flattened_ft.yaml +0 -0
  17. {genhpf-1.0.4 → genhpf-1.0.6}/examples/train/genhpf/genhpf_hierarchical_ft.yaml +0 -0
  18. {genhpf-1.0.4 → genhpf-1.0.6}/examples/train/genhpf/genhpf_hierarchical_scr.yaml +0 -0
  19. {genhpf-1.0.4 → genhpf-1.0.6}/examples/train/genhpf/meds_hierarchical_scr.yaml +0 -0
  20. {genhpf-1.0.4 → genhpf-1.0.6}/pyproject.toml +0 -0
  21. {genhpf-1.0.4 → genhpf-1.0.6}/setup.cfg +0 -0
  22. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/__init__.py +0 -0
  23. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/__init__.py +0 -0
  24. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/config.yaml +0 -0
  25. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/configs.py +0 -0
  26. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/constants.py +0 -0
  27. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/initialize.py +0 -0
  28. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/configs/utils.py +0 -0
  29. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/__init__.py +0 -0
  30. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/binary_cross_entropy.py +0 -0
  31. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/binary_cross_entropy_with_logits.py +0 -0
  32. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/criterion.py +0 -0
  33. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/cross_entropy.py +0 -0
  34. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/multi_task_criterion.py +0 -0
  35. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/simclr_criterion.py +0 -0
  36. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/criterions/wav2vec2_criterion.py +0 -0
  37. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/datasets/__init__.py +0 -0
  38. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/datasets/dataset.py +0 -0
  39. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/datasets/genhpf_dataset.py +0 -0
  40. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/datasets/meds_dataset.py +0 -0
  41. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/loggings/__init__.py +0 -0
  42. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/loggings/meters.py +0 -0
  43. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/loggings/metrics.py +0 -0
  44. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/loggings/progress_bar.py +0 -0
  45. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/__init__.py +0 -0
  46. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/genhpf.py +0 -0
  47. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/genhpf_mlm.py +0 -0
  48. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/genhpf_predictor.py +0 -0
  49. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/genhpf_simclr.py +0 -0
  50. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/models/genhpf_wav2vec2.py +0 -0
  51. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/__init__.py +0 -0
  52. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/gather_layer.py +0 -0
  53. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/grad_multiply.py +0 -0
  54. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/gumbel_vector_quantizer.py +0 -0
  55. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/identity_layer.py +0 -0
  56. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/layer_norm.py +0 -0
  57. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/modules/positional_encoding.py +0 -0
  58. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/__init__.py +0 -0
  59. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/__init__.py +0 -0
  60. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/README.md +0 -0
  61. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/__init__.py +0 -0
  62. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/ehrs/__init__.py +0 -0
  63. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/ehrs/ehr.py +0 -0
  64. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/ehrs/eicu.py +0 -0
  65. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/ehrs/mimiciii.py +0 -0
  66. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/ehrs/mimiciv.py +0 -0
  67. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/main.py +0 -0
  68. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/manifest.py +0 -0
  69. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/sample_dataset.py +0 -0
  70. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/utils/__init__.py +0 -0
  71. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/genhpf/utils/utils.py +0 -0
  72. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/manifest.py +0 -0
  73. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/trainer.py +0 -0
  74. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/checkpoint_utils.py +0 -0
  75. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/data_utils.py +0 -0
  76. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/distributed_utils.py +0 -0
  77. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/file_io.py +0 -0
  78. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/pdb.py +0 -0
  79. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/utils.py +0 -0
  80. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf.egg-info/SOURCES.txt +0 -0
  81. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf.egg-info/dependency_links.txt +0 -0
  82. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf.egg-info/entry_points.txt +0 -0
  83. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf.egg-info/requires.txt +0 -0
  84. {genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf.egg-info/top_level.txt +0 -0
{genhpf-1.0.4/src/genhpf.egg-info → genhpf-1.0.6}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
2
2
  Name: genhpf
3
- Version: 1.0.4
3
+ Version: 1.0.6
4
4
  Summary: GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning
5
5
  Author-email: Jungwoo Oh <ojw0123@kaist.ac.kr>, Kyunghoon Hur <pacesun@kaist.ac.kr>
6
6
  License: MIT license
{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/preprocess/preprocess_meds.py RENAMED
@@ -148,11 +148,11 @@ def main():
148
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  data_paths = [root_path]
149
149
 
150
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  if not output_dir.exists():
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- output_dir.mkdir()
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+ output_dir.mkdir(parents=True)
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  else:
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  if args.rebase:
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  shutil.rmtree(output_dir)
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- output_dir.mkdir()
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+ output_dir.mkdir(parents=True)
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  elif output_dir.exists():
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  if args.skip_if_exists:
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  ls = glob.glob(str(output_dir / "**/*"), recursive=True)
{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/test.py RENAMED
@@ -208,6 +208,9 @@ def main(cfg: Config) -> None:
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  meds_pred_output = meds_pred_output.with_columns(
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  pl.col("subject_id").map_elements(lambda x: x.split("_")[0], return_dtype=pl.String).cast(int)
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  )
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+ meds_pred_output = (
212
+ meds_pred_output.with_columns(pl.col("predicted_boolean_value").cast(bool))
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+ )
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  if not os.path.exists(cfg.meds.output_dir):
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  os.makedirs(cfg.meds.output_dir)
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  meds_pred_output.write_parquet(os.path.join(cfg.meds.output_dir, f"{subset}.parquet"))
{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/scripts/train.py RENAMED
@@ -281,6 +281,14 @@ def validate(
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281
 
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  progress.print(stats, tag=subset, step=trainer.get_num_updates())
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283
 
284
+ if np.isnan(stats[cfg.checkpoint.best_checkpoint_metric]):
285
+ logger.info(
286
+ f"validation value for {cfg.checkpoint.best_checkpoint_metric} is NaN. "
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+ "Changed the best checkpoint metric to loss."
288
+ )
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+ cfg.checkpoint.best_checkpoint_metric = "loss"
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+ cfg.checkpoint.maximize_best_checkpoint_metric = False
291
+
284
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  valid_losses.append(stats[cfg.checkpoint.best_checkpoint_metric])
285
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  return valid_losses
{genhpf-1.0.4 → genhpf-1.0.6/src/genhpf.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.2
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2
  Name: genhpf
3
- Version: 1.0.4
3
+ Version: 1.0.6
4
4
  Summary: GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning
5
5
  Author-email: Jungwoo Oh <ojw0123@kaist.ac.kr>, Kyunghoon Hur <pacesun@kaist.ac.kr>
6
6
  License: MIT license
{genhpf-1.0.4 → genhpf-1.0.6}/.gitignore RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/.pre-commit-config.yaml RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/LICENSE RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/README.md RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/pyproject.toml RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/setup.cfg RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/__init__.py RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/trainer.py RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/pdb.py RENAMED
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{genhpf-1.0.4 → genhpf-1.0.6}/src/genhpf/utils/utils.py RENAMED
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