cehrgpt 0.1.3__tar.gz → 0.1.4__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (132) hide show
  1. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/PKG-INFO +2 -2
  2. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/pyproject.toml +1 -1
  3. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/PKG-INFO +2 -2
  4. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/requires.txt +1 -1
  5. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/.github/workflows/build-python.yaml +0 -0
  6. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/.github/workflows/tests.yaml +0 -0
  7. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/.gitignore +0 -0
  8. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/.pre-commit-config.yaml +0 -0
  9. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/LICENSE +0 -0
  10. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/README.md +0 -0
  11. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/constraints.txt +0 -0
  12. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/data_generation.md +0 -0
  13. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/feature_representation.md +0 -0
  14. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_configs/cehrgpt_pretrain_sample_config.yaml +0 -0
  15. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_configs/credential_file_sample.ini +0 -0
  16. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_data/omop_vocab/concept/concept.parquet +0 -0
  17. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_data/pretrain/patient_sequence.parquet +0 -0
  18. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_data/pretrained_embeddings/pretrained_embedding_concepts.pkl +0 -0
  19. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/sample_data/pretrained_embeddings/pretrained_embedding_vectors.npy +0 -0
  20. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/create_cehrgpt_pretraining_data.sh +0 -0
  21. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/extract_features_gpt.sh +0 -0
  22. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/level_three_evaluation.sh +0 -0
  23. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/omop_pipeline.sh +0 -0
  24. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/pool_generated_sequences.sh +0 -0
  25. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/scripts/run_linear_prob.sh +0 -0
  26. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/setup.cfg +0 -0
  27. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/spark_setup.md +0 -0
  28. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/__init__.py +0 -0
  29. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/__init__.py +0 -0
  30. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/__init__.py +0 -0
  31. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/htn_treatment_pathway.py +0 -0
  32. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/irregularity.py +0 -0
  33. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/__init__.py +0 -0
  34. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/attribute_inference.py +0 -0
  35. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/attribute_inference_config.yml +0 -0
  36. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/member_inference.py +0 -0
  37. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/nearest_neighbor_inference.py +0 -0
  38. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/reid_inference.py +0 -0
  39. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/privacy/utils.py +0 -0
  40. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/treatment_pathway/__init__.py +0 -0
  41. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/treatment_pathway/depression_treatment_pathway.py +0 -0
  42. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/treatment_pathway/diabetes_treatment_pathway.py +0 -0
  43. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/treatment_pathway/htn_treatment_pathway.py +0 -0
  44. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/analysis/treatment_pathway/treatment_pathway.py +0 -0
  45. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/cehrgpt_args.py +0 -0
  46. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/__init__.py +0 -0
  47. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/cehrgpt_data_processor.py +0 -0
  48. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/hf_cehrgpt_dataset.py +0 -0
  49. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/hf_cehrgpt_dataset_collator.py +0 -0
  50. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/hf_cehrgpt_dataset_mapping.py +0 -0
  51. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/data/sample_packing_sampler.py +0 -0
  52. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/__init__.py +0 -0
  53. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/cehrgpt_conditional_generation.py +0 -0
  54. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/chatgpt_generation.py +0 -0
  55. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/generate_batch_hf_gpt_sequence.py +0 -0
  56. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/omop_converter_batch.py +0 -0
  57. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/generation/omop_entity.py +0 -0
  58. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/gpt_utils.py +0 -0
  59. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/__init__.py +0 -0
  60. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/activations.py +0 -0
  61. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/config.py +0 -0
  62. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/gpt2.py +0 -0
  63. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/hf_cehrgpt.py +0 -0
  64. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/hf_modeling_outputs.py +0 -0
  65. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/pretrained_embeddings.py +0 -0
  66. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/special_tokens.py +0 -0
  67. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/models/tokenization_hf_cehrgpt.py +0 -0
  68. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/__init__.py +0 -0
  69. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/condition_era.py +0 -0
  70. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/observation_period.py +0 -0
  71. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/omop_argparse.py +0 -0
  72. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/omop_table_builder.py +0 -0
  73. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/ontology.py +0 -0
  74. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/queries/__init__.py +0 -0
  75. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/queries/condition_era.py +0 -0
  76. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/queries/observation_period.py +0 -0
  77. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/omop/sample_omop_tables.py +0 -0
  78. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/__init__.py +0 -0
  79. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/data_utils.py +0 -0
  80. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/gpt_runner_util.py +0 -0
  81. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/hf_cehrgpt_finetune_runner.py +0 -0
  82. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/hf_cehrgpt_pretrain_runner.py +0 -0
  83. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/hf_gpt_runner_argument_dataclass.py +0 -0
  84. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/hyperparameter_search_util.py +0 -0
  85. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/runners/sample_packing_trainer.py +0 -0
  86. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/simulations/__init__.py +0 -0
  87. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/simulations/generate_plots.py +0 -0
  88. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/simulations/run_simulation.sh +0 -0
  89. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/simulations/time_embedding_simulation.py +0 -0
  90. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/simulations/time_token_simulation.py +0 -0
  91. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/__init__.py +0 -0
  92. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/config/1_year_cabg.yaml +0 -0
  93. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/config/30_day_readmission.yaml +0 -0
  94. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/config/next_visit_type_prediction.yaml +0 -0
  95. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/config/t2dm_hf.yaml +0 -0
  96. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/time_to_event_model.py +0 -0
  97. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/time_to_event_prediction.py +0 -0
  98. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/time_to_event/time_to_event_utils.py +0 -0
  99. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/__init__.py +0 -0
  100. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/ehrshot_benchmark.py +0 -0
  101. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/generate_causal_patient_split_by_age.py +0 -0
  102. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/generate_pretrained_embeddings.py +0 -0
  103. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/linear_prob/__init__.py +0 -0
  104. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/linear_prob/compute_cehrgpt_features.py +0 -0
  105. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/linear_prob/train_with_cehrgpt_features.py +0 -0
  106. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/merge_synthetic_real_datasets.py +0 -0
  107. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/tools/upload_omop_tables.py +0 -0
  108. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/SOURCES.txt +0 -0
  109. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/dependency_links.txt +0 -0
  110. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/top_level.txt +0 -0
  111. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/synthetic_data_generation.md +0 -0
  112. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/__init__.py +0 -0
  113. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/integration_tests/__init__.py +0 -0
  114. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/integration_tests/runners/__init__.py +0 -0
  115. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/integration_tests/runners/hf_cehrgpt_pretrain_runner_test.py +0 -0
  116. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/integration_tests/runners/hf_cehrgpt_pretrain_sample_packing_runner_test.py +0 -0
  117. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/integration_tests/runners/hf_cehrgpt_pretrain_sfm_runner_test.py +0 -0
  118. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/__init__.py +0 -0
  119. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/gpt_utils_test.py +0 -0
  120. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/__init__.py +0 -0
  121. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/model_utils_test.py +0 -0
  122. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/rotary_embedding_test.py +0 -0
  123. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/tokenization/__init__.py +0 -0
  124. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/tokenization/create_bins_with_spline_test.py +0 -0
  125. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/models/tokenization/create_sample_from_bins_test.py +0 -0
  126. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/numeric_concept_statistics_test.py +0 -0
  127. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/runners/__init__.py +0 -0
  128. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/runners/hf_cehrgpt_finetune_runner_test.py +0 -0
  129. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/tokenization_test.py +0 -0
  130. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/tools/__init__.py +0 -0
  131. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/unit_tests/tools/upload_omop_tables_test.py +0 -0
  132. {cehrgpt-0.1.3 → cehrgpt-0.1.4}/zero_shot_prediction.md +0 -0
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: cehrgpt
3
- Version: 0.1.3
3
+ Version: 0.1.4
4
4
  Summary: CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines
5
5
  Author-email: Chao Pang <chaopang229@gmail.com>, Xinzhuo Jiang <xj2193@cumc.columbia.edu>, Krishna Kalluri <kk3326@cumc.columbia.edu>, Elise Minto <em3697@cumc.columbia.edu>, Jason Patterson <jp3477@cumc.columbia.edu>, Nishanth Parameshwar Pavinkurve <np2689@cumc.columbia.edu>, Karthik Natarajan <kn2174@cumc.columbia.edu>
6
6
  License: MIT License
@@ -13,7 +13,7 @@ Requires-Python: >=3.10.0
13
13
  Description-Content-Type: text/markdown
14
14
  License-File: LICENSE
15
15
  Requires-Dist: cehrbert>=1.4.8
16
- Requires-Dist: cehrbert_data==0.0.11
16
+ Requires-Dist: cehrbert_data>=0.1.1
17
17
  Requires-Dist: openai==1.54.3
18
18
  Requires-Dist: optuna==4.0.0
19
19
  Requires-Dist: transformers==4.44.1
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/pyproject.toml RENAMED
@@ -29,7 +29,7 @@ classifiers = [
29
29
 
30
30
  dependencies = [
31
31
  "cehrbert>=1.4.8",
32
- "cehrbert_data==0.0.11",
32
+ "cehrbert_data>=0.1.1",
33
33
  "openai==1.54.3",
34
34
  "optuna==4.0.0",
35
35
  "transformers==4.44.1",
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: cehrgpt
3
- Version: 0.1.3
3
+ Version: 0.1.4
4
4
  Summary: CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines
5
5
  Author-email: Chao Pang <chaopang229@gmail.com>, Xinzhuo Jiang <xj2193@cumc.columbia.edu>, Krishna Kalluri <kk3326@cumc.columbia.edu>, Elise Minto <em3697@cumc.columbia.edu>, Jason Patterson <jp3477@cumc.columbia.edu>, Nishanth Parameshwar Pavinkurve <np2689@cumc.columbia.edu>, Karthik Natarajan <kn2174@cumc.columbia.edu>
6
6
  License: MIT License
@@ -13,7 +13,7 @@ Requires-Python: >=3.10.0
13
13
  Description-Content-Type: text/markdown
14
14
  License-File: LICENSE
15
15
  Requires-Dist: cehrbert>=1.4.8
16
- Requires-Dist: cehrbert_data==0.0.11
16
+ Requires-Dist: cehrbert_data>=0.1.1
17
17
  Requires-Dist: openai==1.54.3
18
18
  Requires-Dist: optuna==4.0.0
19
19
  Requires-Dist: transformers==4.44.1
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt.egg-info/requires.txt RENAMED
@@ -1,5 +1,5 @@
1
1
  cehrbert>=1.4.8
2
- cehrbert_data==0.0.11
2
+ cehrbert_data>=0.1.1
3
3
  openai==1.54.3
4
4
  optuna==4.0.0
5
5
  transformers==4.44.1
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/.gitignore RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/.pre-commit-config.yaml RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/LICENSE RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/README.md RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/constraints.txt RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/data_generation.md RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/setup.cfg RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/spark_setup.md RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/__init__.py RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/src/cehrgpt/__init__.py RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/tests/__init__.py RENAMED
File without changes
{cehrgpt-0.1.3 → cehrgpt-0.1.4}/zero_shot_prediction.md RENAMED
File without changes