Wheelodex » Projects » cehrbert

cehrbert

View on PyPI — Reverse Dependencies (0)

1.2.2 cehrbert-1.2.2-py3-none-any.whl

Wheel Details

Project: cehrbert
Version: 1.2.2
Filename: cehrbert-1.2.2-py3-none-any.whl
Download: [link]
Size: 137403
MD5: c1f2294c755782436296cf82329506a2
SHA256: 258483a935f864d09967a5f631babd59aabe80e94e937b5accc8f3d82f21c460
Uploaded: 2024-10-14 18:01:42 +0000

dist-info

METADATA · WHEEL · RECORD · top_level.txt · entry_points.txt

METADATA

Metadata-Version: 2.1
Name: cehrbert
Version: 1.2.2
Summary: CEHR-BERT: Incorporating temporal information from structured EHR data to improve prediction tasks
Author-Email: Chao Pang <chaopang229[at]gmail.com>, Xinzhuo Jiang <xj2193[at]cumc.columbia.edu>, Krishna Kalluri <kk3326[at]cumc.columbia.edu>, Nishanth Parameshwar Pavinkurve <np2689[at]cumc.columbia.edu>, Karthik Natarajan <kn2174[at]cumc.columbia.edu>
Project-Url: Homepage, https://github.com/cumc-dbmi/cehr-bert
License: MIT License
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.10.0
Requires-Dist: dask (==2024.1.1)
Requires-Dist: dask[dataframe] (==2024.1.1)
Requires-Dist: datasets (==2.16.1)
Requires-Dist: evaluate (==0.4.1)
Requires-Dist: fast-ml (==3.68)
Requires-Dist: femr (==0.2.0)
Requires-Dist: Jinja2 (==3.1.3)
Requires-Dist: meds (==0.3.3)
Requires-Dist: meds-reader (==0.1.9)
Requires-Dist: networkx (==3.2.1)
Requires-Dist: numpy (==1.24.3)
Requires-Dist: packaging (==23.2)
Requires-Dist: pandas (==2.2.0)
Requires-Dist: peft (==0.10.0)
Requires-Dist: Pillow (==10.3.0)
Requires-Dist: pyarrow (==15.0.0)
Requires-Dist: pydantic (==2.6.0)
Requires-Dist: python-dateutil (==2.8.2)
Requires-Dist: PyYAML (==6.0.1)
Requires-Dist: scikit-learn (==1.4.0)
Requires-Dist: scipy (==1.12.0)
Requires-Dist: tensorflow (==2.15.0)
Requires-Dist: tensorflow-datasets (==4.5.2)
Requires-Dist: tqdm (==4.66.1)
Requires-Dist: torch (==2.4.0)
Requires-Dist: tokenizers (==0.15.2)
Requires-Dist: transformers (==4.39.3)
Requires-Dist: accelerate (==0.31.0)
Requires-Dist: Werkzeug (==3.0.1)
Requires-Dist: wandb (==0.17.8)
Requires-Dist: xgboost (==2.0.3)
Requires-Dist: cehrbert-data (==0.0.4)
Requires-Dist: tensorflow-metal (==1.1.0); sys_platform == "darwin"
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pytest-cov; extra == "dev"
Requires-Dist: pytest-subtests; extra == "dev"
Requires-Dist: rootutils; extra == "dev"
Requires-Dist: hypothesis; extra == "dev"
Requires-Dist: black; extra == "dev"
Provides-Extra: dev
Description-Content-Type: text/markdown
License-File: LICENSE
[Description omitted; length: 7736 characters]

WHEEL

Wheel-Version: 1.0
Generator: setuptools (75.1.0)
Root-Is-Purelib: true
Tag: py3-none-any

RECORD

Path Digest Size
cehrbert/__init__.py sha256=SeN20vi3fzBN7ABLROuAqrI_Uwtf14Qpu8gQtByezTk 322
cehrbert/config/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/config/grid_search_config.py sha256=ubut7cNXEQ9HVC3ILikrPYtqby8xLI2Wt_QG4XR9RJs 387
cehrbert/data_generators/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/data_generators/data_classes.py sha256=Vz1fxPCNCkUq77dngjOfYskGelUJ5Fzyed1bWEMAhUk 1136
cehrbert/data_generators/data_generator_base.py sha256=j-4DDafrFHezIrdHDid2udiinxIAzL3FQAwt_Lw8GBk 16643
cehrbert/data_generators/graph_sample_method.py sha256=VE0OAZe1VDWthylbD1u8ZIbapGPxguoSQKqVbVrJ4ak 2916
cehrbert/data_generators/learning_objective.py sha256=btz_MS_NoPGEEn0mk8pqAIZi5M__3tU_EjhGIgMiPo4 40923
cehrbert/data_generators/tokenizer.py sha256=TrJcNxom5JLCsx9ZM9rGClPi8p_lMF3y4bxYrx3ZE84 4878
cehrbert/data_generators/hf_data_generator/__init__.py sha256=4or7EsI66g0vf4r0HpuVCQuKInkZ-pmSTMCsh70W96E 146
cehrbert/data_generators/hf_data_generator/hf_dataset.py sha256=NQZB_qdRA4Gyu-rf8Oq5pgoe7rDog6Dvz4Af-j0sWvg 5391
cehrbert/data_generators/hf_data_generator/hf_dataset_collator.py sha256=652b_O7oktC2QXwv7ih2PAFF_O2liH9Kd1V00wEK9VA 12667
cehrbert/data_generators/hf_data_generator/hf_dataset_mapping.py sha256=bfVouI26iyekpCO-Gto52s-6q9RjhzNLOmRtYO51H_Y 19283
cehrbert/data_generators/hf_data_generator/meds_utils.py sha256=BuE8dKODWWkk_nTfunwP_7Qj3vHmyY7y5xWEhQkxyU0 11512
cehrbert/data_generators/hf_data_generator/patient_block.py sha256=pREWOQv46aIttE9lMoZ54tnwAPz3jgMjFdlK1HuKNxw 16552
cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/__init__.py sha256=Dvr6nrBZLe98QjzYWzEtizya3kTNcj3DhVHzmokDslw 169
cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_base.py sha256=o1xC3K_sPjSP_g7P-vHxJM4gkV61AiTkRsBsOHzIpgU 5915
cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_micmic4.py sha256=NixOuiWmufVZ1Jr3whtOyprKg0YMG5okaWCo5zi_E3w 2045
cehrbert/data_generators/hf_data_generator/meds_to_cehrbert_conversion_rules/meds_to_cehrbert_omop.py sha256=1XNsJx8Z5sfYbEyUEoqiDNemRwGBBXcWBscB1m3rTug 1503
cehrbert/evaluations/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/evaluations/evaluation.py sha256=3Nj-zwltSoy2WLML74e9YhDL4jkUueZfH3gy_SQBETI 15544
cehrbert/evaluations/evaluation_parameters.py sha256=ZExYmxMM7_xhYKvclGIr2fb55iOjD30rfY_eTdTRbVg 987
cehrbert/evaluations/evaluation_parse_args.py sha256=_N9wYD8SN28J8LgzINh6NecThLPSzKAz6jrzQIbjDcQ 6711
cehrbert/evaluations/transfer_learning_evaluation.py sha256=4AJ5G_aqCmxKmgS9_ARTCBCz1euP1gkRoFsI59tLSl4 479
cehrbert/evaluations/model_evaluators/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/evaluations/model_evaluators/bert_model_evaluators.py sha256=fNI5e2TiHnt-c37NjAUmLNzYBX9jxag8iP_gabxZoFM 10123
cehrbert/evaluations/model_evaluators/frequency_model_evaluators.py sha256=gFqyvXkEpFoDGRvbXJs4S_j9XR7B5xNlVR_toXWVSUw 5893
cehrbert/evaluations/model_evaluators/hierarchical_bert_evaluators.py sha256=CfNyTcpRQdJRRmmh3urdfurcikQii93i5SZXUIgv6sA 11224
cehrbert/evaluations/model_evaluators/model_evaluators.py sha256=N8b1owd5NVZKv7g8Dw2YRBVHCSWlkhqryTkmjkZ1JPY 3104
cehrbert/evaluations/model_evaluators/sequence_model_evaluators.py sha256=5HSAaFbyqxuAET1n-vi1F9k5HPALbrtb0q8ctamBWxo 17942
cehrbert/keras_transformer/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/keras_transformer/bert.py sha256=MJOx4d9wk8SylIP_iNeBMSYdc8KKVpSCOUUnsrhIWLo 4261
cehrbert/keras_transformer/extras.py sha256=LF9J9ItpcuWOpghg5zgIkTmDN2xn9RoNZw_ly0tHrvs 5165
cehrbert/keras_transformer/position.py sha256=Vb-eqUk24_oWsmgINItV1dShxWrKxEVcNRNk7CSoZpo 1852
cehrbert/med_extension/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/med_extension/schema_extension.py sha256=weMnf9OBU9XLrtKMweNGzmQA10Q4bL8Sm6rIbUDRc9Q 975
cehrbert/models/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/models/bert_models.py sha256=UZPwaT1A0cUCqPzsmmwkPUG6PhFUYnHeV7wHxUEyckg 6876
cehrbert/models/bert_models_visit_prediction.py sha256=HAYvnUCUsYjvEmWdnZv8qJA4sHqqYln5uRA45Tz_GAs 8243
cehrbert/models/evaluation_models.py sha256=MPO_5rwcEO2ka6XsS2uhgzKFKqx3MH7_ueUSXrl5ssA 23677
cehrbert/models/hierachical_bert_model_v2.py sha256=nA7YQW1DQD_pIQlONfza-83sCBNV9Hf821cJZojZWEc 13888
cehrbert/models/hierachical_phenotype_model_new.py sha256=OF-UuYnQrCm_pw_hNhKDA-YeVlTYyrF0ul3SxL-admg 18243
cehrbert/models/loss_schedulers.py sha256=8RFxv8zto8WdkNn5b16cldUnpG8EWqlI1kEDHETV5R4 1801
cehrbert/models/parse_args.py sha256=lt3QxIfwfEzIiOWnBTiySCL0vypVGOWu74J5D_9kWbM 12198
cehrbert/models/hf_models/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/models/hf_models/config.py sha256=Cei4wBU--PDHSdwgQn2qn-Cw3_ZAqTYFS50EJdSVfWY 10464
cehrbert/models/hf_models/hf_cehrbert.py sha256=7UNO4OU4e4INgIqBMT1D8RRwFzOiSZ858teShw9Z5w4 19782
cehrbert/models/hf_models/hf_modeling_outputs.py sha256=YyyW05yQBf6K4GX-fhJJDzmZ6taz-ZvGt-rgqlaPVZE 13711
cehrbert/models/hf_models/tokenization_hf_cehrbert.py sha256=4xOc41dnCrw_aiIyjmdXe_c_Ptn4xXpHkP69s3mnWOo 16707
cehrbert/models/hf_models/tokenization_utils.py sha256=CJQNjGoQNXAG9-ym1fOsaMnMtHywDRhljbm4yh0YzpM 1853
cehrbert/models/layers/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/models/layers/custom_layers.py sha256=uxocWabOlSOL_NDSVJTu1hDwze5proHhJYVDF1hKRfY 37846
cehrbert/models/layers/hierarchical_custom_layers.py sha256=FO59lidKv-N4LYnYZDC-rfDSiTIyH-vta3LM31hSYWk 7511
cehrbert/runners/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/runners/hf_cehrbert_finetune_runner.py sha256=h9lyP_5VuytnZrKLU4zMtHoMfPu_HmYQiTZshRJo1sU 18132
cehrbert/runners/hf_cehrbert_pretrain_runner.py sha256=r5UlLzRGNk9uJJYfqzsNzw58Ub70Lf01B1ewfIf4oe0 13671
cehrbert/runners/hf_runner_argument_dataclass.py sha256=ZNzzzV6alnyN_5zD4ro2v432PUhomnNQCaUC7gZJfug 12967
cehrbert/runners/runner_util.py sha256=9vg5I3omgy55ppE2XH9cL2bDovhV170ObV6gsoCFz7A 19269
cehrbert/tools/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/tools/download_omop_tables.py sha256=-OUTeqHxZb7vjd3oIvuT2IpxLaFkkIjDWFCln8XZ3Vk 4697
cehrbert/trainers/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/trainers/model_trainer.py sha256=2-FbJmeADqI4mFsuePxZZLDESKofjOFt2_Y2fLRjxrg 11314
cehrbert/trainers/train_cehr_bert.py sha256=Cq8MQ15IVE7DWeeaVBiOOUSXRXWJKWnF_FX9N8broTc 7457
cehrbert/utils/__init__.py sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU 0
cehrbert/utils/checkpoint_utils.py sha256=lSUY8PGGJ1vz9dDWhxniXPWONfFn0UnUwAFSntsVYcY 7289
cehrbert/utils/logging_utils.py sha256=mWu0N07t1YuJsQjxmZFXsQfwT5FofPxuOuiLQ99R-tE 382
cehrbert/utils/model_utils.py sha256=dwzPQq1QYMO42-Z6XOMX7C9xMuqkiYaV7Kb9L3CuheY 12260
cehrbert/utils/stat_utils.py sha256=7eOpnypZRU0peC__OXgomUiwmaxk6rPyW3SkyK5I52c 9128
cehrbert-1.2.2.dist-info/LICENSE sha256=LOfC32zkfUIdGm8e_098jPbt8OHKtNWymDzxn2pA9Zk 1093
cehrbert-1.2.2.dist-info/METADATA sha256=XbtpH2sOd3PL5kqHyjcGm5HiC_qliraDQDTIuit_ckQ 9948
cehrbert-1.2.2.dist-info/WHEEL sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ 91
cehrbert-1.2.2.dist-info/entry_points.txt sha256=IG-Eieaj9aFk4Cu9SRU5-98E3Zsel6XRn4NqzkQCDd0 165
cehrbert-1.2.2.dist-info/top_level.txt sha256=U1GROPpcQJpLdKrZBNJhgypK1cBVMHi6n13zne3KU8o 9
cehrbert-1.2.2.dist-info/RECORD — —

top_level.txt

cehrbert

entry_points.txt

[console_scripts]
cehrbert-finetuning = cehrbert.runners.hf_cehrbert_finetuning_runner:main
cehrbert-pretraining = cehrbert.runners.hf_cehrbert_pretrain_runner:main