genhpf 1.0.8__py3-none-any.whl → 1.0.9__py3-none-any.whl

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Files changed (8) hide show
  1. genhpf/models/genhpf.py +11 -0
  2. genhpf/scripts/train.py +5 -1
  3. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/METADATA +1 -1
  4. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/RECORD +8 -8
  5. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/LICENSE +0 -0
  6. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/WHEEL +0 -0
  7. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/entry_points.txt +0 -0
  8. {genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/top_level.txt +0 -0
genhpf/models/genhpf.py CHANGED
@@ -73,6 +73,7 @@ class GenHPFConfig(BaseConfig):
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  )
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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/scripts/train.py CHANGED
@@ -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.dist-info → genhpf-1.0.9.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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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.dist-info → genhpf-1.0.9.dist-info}/RECORD RENAMED
@@ -23,7 +23,7 @@ genhpf/loggings/meters.py,sha256=ECdJTwFHx_4D22iNbv9VRxlh9iibX8aU9QeHPkqNmXQ,107
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  genhpf/loggings/metrics.py,sha256=3CSBA5C3bd-G-zNer7BeOqSZj-tn6twbpLqAlt-FQ_A,3935
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  genhpf/loggings/progress_bar.py,sha256=9-24WAFDsp6WSS-JncnQtQMwo7DnNEYakAt7a8pkhF0,14140
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  genhpf/models/__init__.py,sha256=EG4YnL8Uiem8iUNm72euHJlim0IZj3inzFVFCFOvPCE,2223
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- genhpf/models/genhpf.py,sha256=vqyJn9wv3eXLaxi0RTkqwuYTVzH3vTAVR1e5LOGUlhc,9344
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+ genhpf/models/genhpf.py,sha256=Y9f8H3fgUm1H-QWTnRzcQMu1Pkl6i0ZNNRuSmZZ6Zh0,9712
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  genhpf/models/genhpf_mlm.py,sha256=rExPpm1HDjljAjgFbYx2bgS6VSaIKF6-P7VJcq6YLB0,1882
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  genhpf/models/genhpf_predictor.py,sha256=i-XIh7S3ozpB_r4JZI27sfdnbANyQYpBIOrDDgsiWvc,2163
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  genhpf/models/genhpf_simclr.py,sha256=Iuqx0fy0AQurkTk0e5hEv12eJyeGGGiQJiRKXGgOTnI,1629
@@ -37,7 +37,7 @@ genhpf/modules/layer_norm.py,sha256=-aVKThi1pWvVMbMAzyQG1co6MHPBCUZgxWJKYzIqsPQ,
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  genhpf/modules/positional_encoding.py,sha256=Rf_qHdQArljEggRO4EHufc_JHq9-i44Oog1w9Bh51DQ,754
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  genhpf/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  genhpf/scripts/test.py,sha256=DZPiZa-Tm6kKLcK3R1EH82gjq4Hbl098IAY4kA3fQxg,10288
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- genhpf/scripts/train.py,sha256=-CY_OLRAX3wbthmH3fzkzSuZEEjHGKg0J4jzbbr9HoU,12942
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+ genhpf/scripts/train.py,sha256=juUgfSVLAXhtBPzIEG09W5lkLlKIv2GHIbMn7IgBJjc,13099
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  genhpf/scripts/preprocess/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  genhpf/scripts/preprocess/manifest.py,sha256=ZIK16e4vs_cS2K_tM1GaT38hc1nBHk6JB9Uga6OjgU4,2711
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  genhpf/scripts/preprocess/preprocess_meds.py,sha256=mch8Zl9Ht28fx7nsYfuFb0sc_PN6l1kBQ5iCeEEcrFw,25856
@@ -59,9 +59,9 @@ genhpf/utils/distributed_utils.py,sha256=000xKlw8SLoSH16o6n2bB3eueGR0aVD_DufPYES
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  genhpf/utils/file_io.py,sha256=hnZXdMtAibfFDoIfn-SDusl-v7ZImeUEh0eD2MIxbG4,4919
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  genhpf/utils/pdb.py,sha256=400rk1pVfOpVpzKIFHnTRlZ2VCtBqRh9G-pRRwu2Oqo,930
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  genhpf/utils/utils.py,sha256=BoC_7Gz8uCHbUBCpcXGBMD-5irApi_6xM7nU-2ac4aA,6176
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- genhpf-1.0.8.dist-info/LICENSE,sha256=VK_rvhY2Xi_DAIZHtauni5O9-1_do5SNWjrskv4amg8,1065
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- genhpf-1.0.8.dist-info/METADATA,sha256=k5-iE6UYfJ0rx_NJTuHVM4uw5IdhuJvztoORAtpc_6Q,10589
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- genhpf-1.0.8.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
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- genhpf-1.0.8.dist-info/entry_points.txt,sha256=Wp94VV2w9KasBDLaluLM5EnjLgjNOAQVu44wKRDAwmQ,288
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- genhpf-1.0.8.dist-info/top_level.txt,sha256=lk846Vmnvydb6UZn8xmowj60nkrZYexNOGGnPM-IbhA,7
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- genhpf-1.0.8.dist-info/RECORD,,
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+ genhpf-1.0.9.dist-info/LICENSE,sha256=VK_rvhY2Xi_DAIZHtauni5O9-1_do5SNWjrskv4amg8,1065
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+ genhpf-1.0.9.dist-info/METADATA,sha256=0YRTk9CjFLdEVayQOm7mvdDUi1oBVTLv-v-GANBbuaY,10589
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+ genhpf-1.0.9.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
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+ genhpf-1.0.9.dist-info/entry_points.txt,sha256=Wp94VV2w9KasBDLaluLM5EnjLgjNOAQVu44wKRDAwmQ,288
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+ genhpf-1.0.9.dist-info/top_level.txt,sha256=lk846Vmnvydb6UZn8xmowj60nkrZYexNOGGnPM-IbhA,7
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+ genhpf-1.0.9.dist-info/RECORD,,
{genhpf-1.0.8.dist-info → genhpf-1.0.9.dist-info}/WHEEL RENAMED
File without changes