cehrgpt 0.0.1__py3-none-any.whl → 0.0.2__py3-none-any.whl
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.
- cehrgpt/data/hf_cehrgpt_dataset_mapping.py +267 -1
- cehrgpt/data/hf_cehrgpt_dpo_collator.py +71 -0
- cehrgpt/data/hf_cehrgpt_dpo_dataset_mapping.py +61 -0
- cehrgpt/generation/generate_paired_cehrgpt_sequence.py +224 -0
- cehrgpt/generation/omop_converter_batch.py +3 -0
- cehrgpt/models/hf_cehrgpt.py +1 -0
- cehrgpt/models/tokenization_hf_cehrgpt.py +2 -2
- cehrgpt/rl_finetune/__init__.py +0 -0
- cehrgpt/rl_finetune/cehrgpt_dpo_trainer.py +586 -0
- cehrgpt/rl_finetune/cehrgpt_ppo_trainer.py +464 -0
- cehrgpt/rl_finetune/ppo_finetune.py +394 -0
- cehrgpt/rl_finetune/ppo_finetune_v2.py +373 -0
- cehrgpt/runners/hf_cehrgpt_dpo_runner.py +119 -0
- cehrgpt/runners/hf_cehrgpt_finetune_runner.py +24 -3
- cehrgpt/runners/hf_cehrgpt_pretrain_runner.py +44 -8
- cehrgpt/runners/hf_gpt_runner_argument_dataclass.py +4 -0
- cehrgpt/tools/generate_causal_patient_split_by_age.py +146 -0
- {cehrgpt-0.0.1.dist-info → cehrgpt-0.0.2.dist-info}/METADATA +52 -6
- {cehrgpt-0.0.1.dist-info → cehrgpt-0.0.2.dist-info}/RECORD +22 -12
- {cehrgpt-0.0.1.dist-info → cehrgpt-0.0.2.dist-info}/WHEEL +1 -1
- {cehrgpt-0.0.1.dist-info → cehrgpt-0.0.2.dist-info}/LICENSE +0 -0
- {cehrgpt-0.0.1.dist-info → cehrgpt-0.0.2.dist-info}/top_level.txt +0 -0
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import numpy as np
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import pandas as pd
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# Define race mapping
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race_mapping = {
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"38003613": "8557",
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"38003610": "8557",
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"38003579": "8515",
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"44814653": "0",
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}
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# Invalid age groups
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invalid_age_groups = [
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"age:100-110",
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"age:110-120",
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"age:120-130",
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"age:130-140",
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"age:140-150",
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"age:150-160",
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"age:160-170",
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"age:170-180",
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"age:180-190",
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"age:190-200",
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"age:640-650",
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"age:680-690",
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"age:730-740",
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"age:740-750",
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"age:890-900",
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"age:900-910",
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"age:-10-0",
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]
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def age_group_func(age_str):
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"""
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Categorize an age into a 10-year age group.
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Args:
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age_str (str): A string containing the age in the format "age:XX".
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Returns:
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str: A string representing the 10-year age group "age:XX-XX".
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"""
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age = int(age_str.split(":")[1])
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group_number = age // 10
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return f"age:{group_number * 10}-{(group_number + 1) * 10}"
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def map_race(race):
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return race_mapping.get(race, race)
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def main(args):
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# Load data
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patient_sequence = pd.read_parquet(args.patient_sequence)
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# Extract and preprocess demographics
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demographics = patient_sequence.concept_ids.apply(
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lambda concept_ids: concept_ids[:4]
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)
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patient_sequence["demographics"] = demographics
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year = demographics.apply(lambda concepts: concepts[0])
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age = demographics.apply(lambda concepts: concepts[1]).apply(age_group_func)
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gender = demographics.apply(lambda concepts: concepts[2])
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race = demographics.apply(lambda concepts: concepts[3])
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death = patient_sequence.concept_ids.apply(
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lambda concept_ids: int(concept_ids[-2] == "[DEATH]")
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)
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patient_sequence["year"] = year
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patient_sequence["age"] = age
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patient_sequence["gender"] = gender
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patient_sequence["race"] = race
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patient_sequence["death"] = death
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demographics = patient_sequence[
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["person_id", "death", "year", "age", "gender", "race", "split"]
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]
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demographics["race"] = demographics.race.apply(map_race)
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demographics_clean = demographics[
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(demographics.gender != "0") & (~demographics.age.isin(invalid_age_groups))
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]
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patient_sequence_clean = patient_sequence[
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patient_sequence.person_id.isin(demographics_clean.person_id)
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]
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# Calculate probabilities
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probs = (
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demographics_clean.groupby(["age"])["person_id"].count()
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/ len(demographics_clean)
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).reset_index()
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probs.rename(columns={"person_id": "prob"}, inplace=True)
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# Adjust probabilities
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np.random.seed(42)
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x = np.asarray(list(reversed(range(1, 11))))
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adjusted_probs = probs.prob * pd.Series(x)
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adjusted_probs = adjusted_probs / adjusted_probs.sum()
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probs["adjusted_prob"] = adjusted_probs
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demographics_for_sampling = patient_sequence_clean[
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["year", "age", "race", "gender", "person_id"]
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].merge(probs, on="age")
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demographics_for_sampling["adjusted_prob"] = (
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demographics_for_sampling.adjusted_prob
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/ demographics_for_sampling.adjusted_prob.sum()
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)
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# Train/Validation Split
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causal_train_split = demographics_for_sampling.sample(
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args.num_patients, replace=False, weights="adjusted_prob", random_state=1
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)
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causal_train_split["split"] = "train"
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causal_val_split = demographics_for_sampling[
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~demographics_for_sampling.person_id.isin(causal_train_split.person_id)
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]
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causal_val_split["split"] = "validation"
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causal_train_val_split = pd.concat([causal_train_split, causal_val_split])
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# Save outputs
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causal_train_val_split.to_parquet(args.output_folder, index=False)
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if __name__ == "__main__":
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import argparse
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parser = argparse.ArgumentParser(
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description="Arguments for a causal patient split by age groups"
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)
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parser.add_argument(
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"--patient_sequence",
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required=True,
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)
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parser.add_argument(
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"--num_patients",
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default=1_000_000,
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type=int,
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required=False,
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)
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parser.add_argument(
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"--output_folder",
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required=True,
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)
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# Call the main function with parsed arguments
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main(parser.parse_args())
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Metadata-Version: 2.2
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Name: cehrgpt
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Version: 0.0.
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Version: 0.0.2
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Summary: CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines
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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>
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License: MIT License
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@@ -12,11 +12,12 @@ Classifier: Programming Language :: Python :: 3
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Requires-Python: >=3.10.0
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: cehrbert==1.3.
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Requires-Dist: cehrbert==1.3.8
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Requires-Dist: openai==1.54.3
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Requires-Dist: optuna==4.0.0
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Requires-Dist: transformers==4.40.0
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Requires-Dist: tokenizers==0.19
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Requires-Dist: tokenizers==0.19.0
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Requires-Dist: peft==0.10.0
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Requires-Dist: trl==0.11.4
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Provides-Extra: dev
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Requires-Dist: pre-commit; extra == "dev"
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To install CEHRGPT, clone this repository and install the required dependencies.
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```bash
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git clone https://github.com/knatarajan-lab/cehrgpt
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cd cehrgpt
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git clone https://github.com/knatarajan-lab/cehrgpt.git
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cd cehrgpt
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pip install .
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```
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## Pretrain
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Pretrain cehrgpt using the Hugging Face trainer, the parameters can be found in the sample configuration yaml
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```bash
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mkdir test_results
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# This is NOT required when streaming is set to true
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mkdir test_dataset_prepared
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python -u -m cehrgpt.runners.hf_cehrgpt_pretrain_runner sample_configs/cehrgpt_pretrain_sample_config.yaml
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```
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## Generate synthetic sequences
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Generate synthetic sequences using the trained model
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```bash
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export TRANSFORMERS_VERBOSITY=info
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export CUDA_VISIBLE_DEVICES="0"
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python -u -m cehrgpt.generation.generate_batch_hf_gpt_sequence \
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--model_folder test_results \
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--tokenizer_folder test_results \
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--output_folder test_results \
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--num_of_patients 128 \
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--batch_size 32 \
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--buffer_size 128 \
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--context_window 1024 \
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--sampling_strategy TopPStrategy \
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--top_p 1.0 --temperature 1.0 --repetition_penalty 1.0 \
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--epsilon_cutoff 0.00 \
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--demographic_data_path sample_data/pretrain
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```
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## Convert synthetic sequences to OMOP
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```bash
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# omop converter requires the OHDSI vocabulary
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export OMOP_VOCAB_DIR = ""
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# the omop derived tables need to be built using pyspark
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export SPARK_WORKER_INSTANCES="1"
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export SPARK_WORKER_CORES="8"
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export SPARK_EXECUTOR_CORES="2"
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export SPARK_DRIVER_MEMORY="2g"
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export SPARK_EXECUTOR_MEMORY="2g"
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# Convert the sequences, create the omop derived tables
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sh scripts/omop_pipeline.sh \
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test_results/top_p10000/generated_sequences/ \
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test_results/top_p10000/restored_omop/ \
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$OMOP_VOCAB_DIR
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```
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## Citation
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```
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@article{cehrgpt2024,
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journal={arXiv preprint arXiv:2402.04400},
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year={2024}
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}
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```
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cehrgpt/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cehrgpt/data/hf_cehrgpt_dataset.py,sha256=7hvjjqE8WInVuRvAtNkFI_J-xluFBv1Ij4TPTdUxPM4,2570
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cehrgpt/data/hf_cehrgpt_dataset_collator.py,sha256=RYw5Isrwa4sdyQQ3Nf3cu7xPDA3m-c5ecCFf_y1TJKY,20497
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cehrgpt/data/hf_cehrgpt_dataset_mapping.py,sha256=
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cehrgpt/data/hf_cehrgpt_dataset_mapping.py,sha256=IjGwLKbEfNPxH3hsNmb8p48_imHnMWtslDK6f7R_1pc,16053
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cehrgpt/data/hf_cehrgpt_dpo_collator.py,sha256=cqDK0SUOt3yAqUHWKGuLVi3WmmUMZ6eyxTv9fC9idZA,2787
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cehrgpt/data/hf_cehrgpt_dpo_dataset_mapping.py,sha256=uCLF5VEsyZAG1aNwqEM6Jy5Lx7bI5ALku52Z6Anine0,2574
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cehrgpt/generation/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cehrgpt/generation/chatgpt_generation.py,sha256=SrnLwHLdNtnAOEg36gNjqfoT9yd12iyPgpZffL2AFJo,4428
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cehrgpt/generation/generate_batch_hf_gpt_sequence.py,sha256=-WLpKlulVVDJSdA2jXyp87gfLW4Q3aAtwULK8fDtn_E,11408
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cehrgpt/generation/
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cehrgpt/generation/generate_paired_cehrgpt_sequence.py,sha256=fLu3SHhRe_ZQfS09ebOktq2dekStgYfxmbrRawZQAO4,8280
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cehrgpt/generation/omop_converter_batch.py,sha256=-c0AlDVy5pJ5Afhr8ERiCHhoRrEk8ozJi3g0yFdWaMI,25348
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cehrgpt/generation/omop_entity.py,sha256=Q5Sr0AlyuPAm1FRPfnJO13q-u1fqRgYVHXruZ9g4xNE,19400
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cehrgpt/models/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cehrgpt/models/config.py,sha256=xek4W_siO7WtMAKE7zDsENotsIE70F8dcW-PTC0kBKk,9700
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cehrgpt/models/hf_cehrgpt.py,sha256=
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cehrgpt/models/hf_cehrgpt.py,sha256=CKseTvGkBFwXK40Z_uKD1_d84oSYCFqKmHI0qtdk72g,75757
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cehrgpt/models/hf_modeling_outputs.py,sha256=LaWa1jI6BRIKMEjWOy1QUeOfTur5y_p2c-JyuGVTdtw,10301
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cehrgpt/models/pretrained_embeddings.py,sha256=vLLVs17TLpXRqCVEWQxGGwPHkUJUO7laNTeBuyBK_yk,3238
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cehrgpt/models/special_tokens.py,sha256=-a7HPJBbdIH0qQ6B3CcRKqvpG6FZlm4nbVPTswGSJ4U,485
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cehrgpt/models/tokenization_hf_cehrgpt.py,sha256=
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31
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+
cehrgpt/models/tokenization_hf_cehrgpt.py,sha256=JAZjnmQq-JjUxZK7XIsqdZB07ZB7BC2WraCjpO_6AOM,42161
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32
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cehrgpt/omop/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cehrgpt/omop/condition_era.py,sha256=hPZALz2XaWnro_1bwIYNkI48foOJjueyg3CZ1BliCno,626
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31
34
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cehrgpt/omop/observation_period.py,sha256=TRMgv5Ya2RaS2im7oQ6BLC_5JL9EJYNYR62ApxIuHvg,1211
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@@ -35,11 +38,17 @@ cehrgpt/omop/sample_omop_tables.py,sha256=2JZ8BNSvssceinwFanvuCRh-YlKrKn25U9w1pL
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cehrgpt/omop/queries/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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cehrgpt/omop/queries/condition_era.py,sha256=LFB6vBAvshHJxtYIRkl7cfrF0kf7ay0piBKpmHBwrpE,2578
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cehrgpt/omop/queries/observation_period.py,sha256=fpzr5DMNw-QLoSwp2Iatfch88E3hyhZ75usiIdG3A0U,6410
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41
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+
cehrgpt/rl_finetune/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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42
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+
cehrgpt/rl_finetune/cehrgpt_dpo_trainer.py,sha256=VQHf5vy5i8K1imcqYakhitfAW-d2mnaEzkSoAYSW5kg,26062
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43
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+
cehrgpt/rl_finetune/cehrgpt_ppo_trainer.py,sha256=nYWYPCaWNjDGEwlo6UHOK1rvOZUx1vuJ8kYuAszI8Zg,17925
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44
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+
cehrgpt/rl_finetune/ppo_finetune.py,sha256=tSy-C0Kzgj5ffclBIDj-RTj78ZfrLmTESxVxd0n9yuE,13971
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45
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+
cehrgpt/rl_finetune/ppo_finetune_v2.py,sha256=7dChwKpq4zKmpkcxP4hryqBoIkcwmTJ44_BF8R2RghQ,13285
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46
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cehrgpt/runners/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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39
47
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cehrgpt/runners/gpt_runner_util.py,sha256=88HKSVj-ADGBCMo7C3znKSMPnAAALa1iU_6P6i9sD0M,3867
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40
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-
cehrgpt/runners/
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cehrgpt/runners/
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cehrgpt/runners/
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48
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+
cehrgpt/runners/hf_cehrgpt_dpo_runner.py,sha256=Z4qNl9CZFC5YvUBc9ZzdOV5wsBFvMTdxfTn4jjtJQ-Y,4583
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49
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+
cehrgpt/runners/hf_cehrgpt_finetune_runner.py,sha256=reflNRb6YB6f_3jAfzFAdwKtTl6hvdIp9Jc7DC-Sv-U,32580
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50
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+
cehrgpt/runners/hf_cehrgpt_pretrain_runner.py,sha256=L3UpjtzxuS8a_tshlqpZN_sXnJSs3yzry0GZNT__05A,18200
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51
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+
cehrgpt/runners/hf_gpt_runner_argument_dataclass.py,sha256=gKVf4BLzNCFiJR7nZVkf-QRcj8fAEVvIUTV-AVH0g_U,5312
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cehrgpt/runners/hyperparameter_search_util.py,sha256=i4qAb_22JO78l40MSyBPwDgAGuGc96efXmg_833cSSo,9044
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44
53
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cehrgpt/time_to_event/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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45
54
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cehrgpt/time_to_event/time_to_event_model.py,sha256=tfXa24l_0q1TBZ68BPRrHRC_3KRWYxrWGIv4myJlIb8,8497
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@@ -50,11 +59,12 @@ cehrgpt/time_to_event/config/next_visit_type_prediction.yaml,sha256=WMj2ZutEvHKI
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cehrgpt/time_to_event/config/t2dm_hf.yaml,sha256=_oMQzh2eJTYzEaMOpmhAzbX-qmdsKlkORELL6HxOxHo,202
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cehrgpt/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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61
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cehrgpt/tools/ehrshot_benchmark.py,sha256=E-m_5srlYEw7Y7i9twIJWDvrkwNlop-6yZB-80FZid0,2667
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62
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+
cehrgpt/tools/generate_causal_patient_split_by_age.py,sha256=dmHiPAL_kR1WrhRteIiHH9dwMtMi3PVl8jXm2O06_gI,4177
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cehrgpt/tools/generate_pretrained_embeddings.py,sha256=lhFSacGv8bMld6qigKZN8Op8eXpFi0DsJuQbWKOWXqI,4160
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54
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cehrgpt/tools/merge_synthetic_real_dataasets.py,sha256=O1dbQ32Le0t15fwymwAh9mfNVLEWuFwW53DNvESrWbY,7589
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65
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cehrgpt/tools/upload_omop_tables.py,sha256=vdBAbkeAsGPA4NsyhNjelPVj3gS8yzmS1sKNM1Qk96g,3791
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cehrgpt-0.0.
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cehrgpt-0.0.
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cehrgpt-0.0.
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cehrgpt-0.0.
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cehrgpt-0.0.
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+
cehrgpt-0.0.2.dist-info/LICENSE,sha256=LOfC32zkfUIdGm8e_098jPbt8OHKtNWymDzxn2pA9Zk,1093
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67
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+
cehrgpt-0.0.2.dist-info/METADATA,sha256=joUmDJWMEBvYphrkwYiK273FwSL9okY74D93ncrbvMU,4878
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68
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+
cehrgpt-0.0.2.dist-info/WHEEL,sha256=52BFRY2Up02UkjOa29eZOS2VxUrpPORXg1pkohGGUS8,91
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69
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+
cehrgpt-0.0.2.dist-info/top_level.txt,sha256=akNCJBbMSLV8nkOzdVzdy13hMJ5CIQURnAS_YYEDVwA,17
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70
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+
cehrgpt-0.0.2.dist-info/RECORD,,
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File without changes
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File without changes
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