genhpf 1.0.8__tar.gz → 1.0.9__tar.gz

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  1. {genhpf-1.0.8/src/genhpf.egg-info → genhpf-1.0.9}/PKG-INFO +1 -1
  2. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf.py +11 -0
  3. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/train.py +5 -1
  4. {genhpf-1.0.8 → genhpf-1.0.9/src/genhpf.egg-info}/PKG-INFO +1 -1
  5. {genhpf-1.0.8 → genhpf-1.0.9}/.gitignore +0 -0
  6. {genhpf-1.0.8 → genhpf-1.0.9}/.pre-commit-config.yaml +0 -0
  7. {genhpf-1.0.8 → genhpf-1.0.9}/LICENSE +0 -0
  8. {genhpf-1.0.8 → genhpf-1.0.9}/README.md +0 -0
  9. {genhpf-1.0.8 → genhpf-1.0.9}/examples/pretrain/mlm/genhpf/flattened_pt.yaml +0 -0
  10. {genhpf-1.0.8 → genhpf-1.0.9}/examples/pretrain/simclr/genhpf/genhpf_hierarchical_pt.yaml +0 -0
  11. {genhpf-1.0.8 → genhpf-1.0.9}/examples/pretrain/wav2vec2/genhpf/hierarchical_pt.yaml +0 -0
  12. {genhpf-1.0.8 → genhpf-1.0.9}/examples/test/genhpf/genhpf_flattened.yaml +0 -0
  13. {genhpf-1.0.8 → genhpf-1.0.9}/examples/test/genhpf/genhpf_hierarchical.yaml +0 -0
  14. {genhpf-1.0.8 → genhpf-1.0.9}/examples/test/genhpf/meds_hierarchical.yaml +0 -0
  15. {genhpf-1.0.8 → genhpf-1.0.9}/examples/train/genhpf/genhpf_flattened_ft.yaml +0 -0
  16. {genhpf-1.0.8 → genhpf-1.0.9}/examples/train/genhpf/genhpf_hierarchical_ft.yaml +0 -0
  17. {genhpf-1.0.8 → genhpf-1.0.9}/examples/train/genhpf/genhpf_hierarchical_scr.yaml +0 -0
  18. {genhpf-1.0.8 → genhpf-1.0.9}/examples/train/genhpf/meds_hierarchical_scr.yaml +0 -0
  19. {genhpf-1.0.8 → genhpf-1.0.9}/pyproject.toml +0 -0
  20. {genhpf-1.0.8 → genhpf-1.0.9}/setup.cfg +0 -0
  21. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/__init__.py +0 -0
  22. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/__init__.py +0 -0
  23. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/config.yaml +0 -0
  24. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/configs.py +0 -0
  25. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/constants.py +0 -0
  26. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/initialize.py +0 -0
  27. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/configs/utils.py +0 -0
  28. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/__init__.py +0 -0
  29. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/binary_cross_entropy.py +0 -0
  30. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/binary_cross_entropy_with_logits.py +0 -0
  31. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/criterion.py +0 -0
  32. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/cross_entropy.py +0 -0
  33. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/multi_task_criterion.py +0 -0
  34. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/simclr_criterion.py +0 -0
  35. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/criterions/wav2vec2_criterion.py +0 -0
  36. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/datasets/__init__.py +0 -0
  37. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/datasets/dataset.py +0 -0
  38. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/datasets/genhpf_dataset.py +0 -0
  39. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/datasets/meds_dataset.py +0 -0
  40. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/loggings/__init__.py +0 -0
  41. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/loggings/meters.py +0 -0
  42. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/loggings/metrics.py +0 -0
  43. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/loggings/progress_bar.py +0 -0
  44. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/__init__.py +0 -0
  45. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf_mlm.py +0 -0
  46. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf_predictor.py +0 -0
  47. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf_simclr.py +0 -0
  48. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf_wav2vec2.py +0 -0
  49. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/__init__.py +0 -0
  50. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/gather_layer.py +0 -0
  51. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/grad_multiply.py +0 -0
  52. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/gumbel_vector_quantizer.py +0 -0
  53. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/identity_layer.py +0 -0
  54. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/layer_norm.py +0 -0
  55. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/modules/positional_encoding.py +0 -0
  56. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/__init__.py +0 -0
  57. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/__init__.py +0 -0
  58. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/README.md +0 -0
  59. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/__init__.py +0 -0
  60. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/ehrs/__init__.py +0 -0
  61. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/ehrs/ehr.py +0 -0
  62. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/ehrs/eicu.py +0 -0
  63. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/ehrs/mimiciii.py +0 -0
  64. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/ehrs/mimiciv.py +0 -0
  65. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/main.py +0 -0
  66. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/manifest.py +0 -0
  67. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/sample_dataset.py +0 -0
  68. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/utils/__init__.py +0 -0
  69. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/genhpf/utils/utils.py +0 -0
  70. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/manifest.py +0 -0
  71. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/preprocess/preprocess_meds.py +0 -0
  72. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/test.py +0 -0
  73. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/trainer.py +0 -0
  74. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/checkpoint_utils.py +0 -0
  75. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/data_utils.py +0 -0
  76. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/distributed_utils.py +0 -0
  77. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/file_io.py +0 -0
  78. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/pdb.py +0 -0
  79. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/utils.py +0 -0
  80. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf.egg-info/SOURCES.txt +0 -0
  81. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf.egg-info/dependency_links.txt +0 -0
  82. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf.egg-info/entry_points.txt +0 -0
  83. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf.egg-info/requires.txt +0 -0
  84. {genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf.egg-info/top_level.txt +0 -0
{genhpf-1.0.8/src/genhpf.egg-info → genhpf-1.0.9}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.2
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  Name: genhpf
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- Version: 1.0.8
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+ Version: 1.0.9
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  Summary: GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning
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  Author-email: Jungwoo Oh <ojw0123@kaist.ac.kr>, Kyunghoon Hur <pacesun@kaist.ac.kr>
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  License: MIT license
{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/models/genhpf.py RENAMED
@@ -73,6 +73,7 @@ class GenHPFConfig(BaseConfig):
73
73
  )
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74
 
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  vocab_size: int = II("dataset.vocab_size")
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+ debug: bool = II("common.debug")
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  class GenHPF(nn.Module):
@@ -80,6 +81,16 @@ class GenHPF(nn.Module):
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  super().__init__()
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  self.cfg = cfg
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+ if cfg.debug:
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+ cfg.encoder_layers = 1
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+ cfg.encoder_embed_dim = 32
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+ cfg.encoder_ffn_embed_dim = 128
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+ cfg.encoder_attention_heads = 2
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+ cfg.agg_layers = 1
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+ cfg.agg_embed_dim = 32
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+ cfg.agg_ffn_embed_dim = 128
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+ cfg.agg_attention_heads = 2
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+
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  self.structure = cfg.structure
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  assert self.structure in GENHPF_MODEL_ARCH_CHOICES
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{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/scripts/train.py RENAMED
@@ -37,7 +37,11 @@ def main(cfg: Config) -> None:
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  logging.config.dictConfig(OmegaConf.to_container(cfg.job_logging_cfg))
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  if cfg.common.debug:
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- os.environ["OMP_NUM_THREADS"] = "1"
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+ os.environ["OMP_NUM_THREADS"] = "4"
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+ os.environ["MKL_NUM_THREADS"] = "4"
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+ torch.set_num_threads(4)
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+ torch.set_num_interop_threads(4)
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+ cfg.optimization.max_epoch = 1
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  assert cfg.dataset.batch_size is not None, "batch_size must be specified"
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  metrics.reset()
{genhpf-1.0.8 → genhpf-1.0.9/src/genhpf.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.2
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2
  Name: genhpf
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- Version: 1.0.8
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+ Version: 1.0.9
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  Summary: GenHPF: General Healthcare Predictive Framework with Multi-task Multi-source Learning
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  Author-email: Jungwoo Oh <ojw0123@kaist.ac.kr>, Kyunghoon Hur <pacesun@kaist.ac.kr>
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  License: MIT license
{genhpf-1.0.8 → genhpf-1.0.9}/.gitignore RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/.pre-commit-config.yaml RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/LICENSE RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/README.md RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/pyproject.toml RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/setup.cfg RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/__init__.py RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/trainer.py RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/pdb.py RENAMED
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{genhpf-1.0.8 → genhpf-1.0.9}/src/genhpf/utils/utils.py RENAMED
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