cehrgpt 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

cehrgpt-0.1.3.dist-info/METADATA

@@ -0,0 +1,238 @@
+Metadata-Version: 2.4
+Name: cehrgpt
+Version: 0.1.3
+Summary: CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines
+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>
+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
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cehrbert>=1.4.8
+Requires-Dist: cehrbert_data==0.0.11
+Requires-Dist: openai==1.54.3
+Requires-Dist: optuna==4.0.0
+Requires-Dist: transformers==4.44.1
+Requires-Dist: tokenizers==0.19.0
+Requires-Dist: peft==0.10.0
+Requires-Dist: lightgbm
+Requires-Dist: polars
+Provides-Extra: dev
+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: flash-attn
+Requires-Dist: flash_attn; extra == "flash-attn"
+Dynamic: license-file
+
+# CEHRGPT
+
+[![PyPI - Version](https://img.shields.io/pypi/v/cehrgpt)](https://pypi.org/project/cehrgpt/)
+![Python](https://img.shields.io/badge/-Python_3.11-blue?logo=python&logoColor=white)
+[![tests](https://github.com/knatarajan-lab/cehrgpt/actions/workflows/tests.yaml/badge.svg)](https://github.com/knatarajan-lab/cehrgpt/actions/workflows/tests.yaml)
+[![license](https://img.shields.io/badge/License-MIT-green.svg?labelColor=gray)](https://github.com/knatarajan-lab/cehrgpt/blob/main/LICENSE)
+[![contributors](https://img.shields.io/github/contributors/knatarajan-lab/cehrgpt.svg)](https://github.com/knatarajan-lab/cehrgpt/graphs/contributors)
+
+CEHRGPT is a multi-task foundation model for structured electronic health records (EHR) data that supports three capabilities: feature representation, zero-shot prediction, and synthetic data generation.
+
+## 🎯 Key Capabilities
+
+### Feature Representation
+Extract meaningful patient embeddings from sequences of medical events using **linear probing** techniques for downstream tasks such as disease prediction, patient clustering, and risk stratification.
+
+### Zero-Shot Prediction
+Generate outcome predictions directly from prompts without requiring task-specific training, enabling rapid evaluation in low-label clinical settings.
+
+### Synthetic Data Generation
+Generate comprehensive patient profiles including demographics, medical history, treatment courses, and outcomes while implementing advanced privacy-preserving techniques to ensure generated data contains no identifiable information.
+The platform is fully compatible with the OMOP Common Data Model for seamless integration with existing healthcare systems.
+## 🚀 Installation
+
+Clone the repository and install dependencies:
+
+```bash
+git clone https://github.com/knatarajan-lab/cehrgpt.git
+cd cehrgpt
+pip install .
+```
+
+## 📋 Prerequisites
+
+Before getting started, set up the required environment variables:
+
+```bash
+export CEHRGPT_HOME=$(git rev-parse --show-toplevel)
+export OMOP_DIR=""                    # Path to your OMOP data
+export CEHR_GPT_DATA_DIR=""          # Path for processed data storage
+export CEHR_GPT_MODEL_DIR=""         # Path for model storage
+```
+
+Create the dataset cache directory:
+```bash
+mkdir $CEHR_GPT_DATA_DIR/dataset_prepared
+```
+
+## 🏗️ Model Training
+
+### Step 1: Generate Pre-training Data from OMOP
+
+Generate the training data following the [Data Generation Instruction](./data_generation.md).
+
+### Step 2: Pre-train CEHR-GPT
+
+Train the foundation model:
+
+```bash
+python -u -m cehrgpt.runners.hf_cehrgpt_pretrain_runner \
+  --model_name_or_path $CEHR_GPT_MODEL_DIR \
+  --tokenizer_name_or_path $CEHR_GPT_MODEL_DIR \
+  --output_dir $CEHR_GPT_MODEL_DIR \
+  --data_folder "$CEHR_GPT_DATA_DIR/patient_sequence/train" \
+  --dataset_prepared_path "$CEHR_GPT_DATA_DIR/dataset_prepared" \
+  --do_train true --seed 42 \
+  --dataloader_num_workers 16 --dataloader_prefetch_factor 8 \
+  --hidden_size 768 --num_hidden_layers 14 --max_position_embeddings 4096 \
+  --evaluation_strategy epoch --save_strategy epoch \
+  --sample_packing --max_tokens_per_batch 16384 \
+  --warmup_ratio 0.01 --weight_decay 0.01 \
+  --num_train_epochs 50 --learning_rate 0.0002 \
+  --use_early_stopping --early_stopping_threshold 0.001
+```
+
+> **Tip**: Increase `max_position_embeddings` for longer context windows based on your use case.
+
+## 🎯 Feature Representation
+
+CEHR-GPT enables extraction of meaningful patient embeddings from medical event sequences using **linear probing** techniques for downstream prediction tasks. The feature representation pipeline includes label generation, patient sequence extraction, and linear regression model training on the extracted representations.
+
+For detailed instructions including cohort creation, patient feature extraction, and linear probing evaluation, please follow the [Feature Representation Guide](./feature_representation.md).
+
+## 🔮 Zero-Shot Prediction
+
+CEHR-GPT can generate outcome predictions directly from clinical prompts without requiring task-specific training, making it ideal for rapid evaluation in low-label clinical settings. The zero-shot prediction capability performs time-to-event analysis by processing patient sequences and generating risk predictions based on learned medical patterns.
+
+For complete setup instructions including label generation, sequence preparation, and prediction execution, please follow the [Zero-Shot Prediction Guide](./zero_shot_prediction.md).
+
+## 🧬 Synthetic Data Generation
+
+CEHR-GPT generates comprehensive synthetic patient profiles including demographics, medical history, treatment courses, and outcomes while implementing advanced privacy-preserving techniques. The synthetic data maintains statistical fidelity to real patient populations without containing identifiable information, and outputs are fully compatible with the OMOP Common Data Model.
+
+For step-by-step instructions on generating synthetic sequences and converting them to OMOP format, please follow the [Synthetic Data Generation Guide](./synthetic_data_generation.md).
+
+## 📊 MEDS Support
+
+CEHR-GPT supports the Medical Event Data Standard (MEDS) format for enhanced interoperability.
+
+### Prerequisites
+
+Configure MEDS-specific environment variables:
+
+```bash
+export CEHR_GPT_MODEL_DIR=""    # CEHR-GPT model directory
+export MEDS_DIR=""              # MEDS data directory
+export MEDS_READER_DIR=""       # MEDS reader output directory
+```
+
+### Step 1: Create MIMIC MEDS Data
+
+Transform MIMIC files to MEDS format following the [MEDS_transforms](https://github.com/mmcdermott/MEDS_transforms/) repository instructions.
+
+### Step 2: Prepare MEDS Reader
+
+Convert MEDS data for CEHR-GPT compatibility:
+
+```bash
+meds_reader_convert $MEDS_DIR $MEDS_READER_DIR --num_threads 10
+```
+
+### Step 3: Pre-train with MEDS Data
+
+Execute pre-training using MEDS format:
+
+```bash
+python -u -m cehrgpt.runners.hf_cehrgpt_pretrain_runner \
+  --model_name_or_path $CEHR_GPT_MODEL_DIR \
+  --tokenizer_name_or_path $CEHR_GPT_MODEL_DIR \
+  --output_dir $CEHR_GPT_MODEL_DIR \
+  --data_folder $MEDS_READER_DIR \
+  --dataset_prepared_path "$CEHR_GPT_MODEL_DIR/dataset_prepared" \
+  --do_train true --seed 42 \
+  --dataloader_num_workers 16 --dataloader_prefetch_factor 8 \
+  --hidden_size 768 --num_hidden_layers 14 --max_position_embeddings 8192 \
+  --evaluation_strategy epoch --save_strategy epoch \
+  --sample_packing --max_tokens_per_batch 16384 \
+  --warmup_steps 500 --weight_decay 0.01 \
+  --num_train_epochs 50 --learning_rate 0.0002 \
+  --use_early_stopping --early_stopping_threshold 0.001 \
+  --is_data_in_meds --inpatient_att_function_type day \
+  --att_function_type day --include_inpatient_hour_token \
+  --include_auxiliary_token --include_demographic_prompt \
+  --meds_to_cehrbert_conversion_type "MedsToBertMimic4"
+```
+
+### Step 4: Generate MEDS Trajectories
+
+#### Environment Setup
+
+Configure trajectory generation environment:
+
+```bash
+export MEDS_LABEL_COHORT_DIR=""     # Cohort labels directory (parquet files)
+export MEDS_TRAJECTORY_DIR=""       # Trajectory output directory
+```
+
+#### Generate Synthetic Trajectories
+
+Create patient trajectories with the trained model:
+
+```bash
+python -u -m cehrgpt.generation.cehrgpt_conditional_generation \
+  --cohort_folder $MEDS_LABEL_COHORT_DIR \
+  --data_folder $MEDS_READER_DIR \
+  --dataset_prepared_path "$CEHR_GPT_MODEL_DIR/dataset_prepared" \
+  --model_name_or_path $CEHR_GPT_MODEL_DIR \
+  --tokenizer_name_or_path $CEHR_GPT_MODEL_DIR \
+  --output_dir $MEDS_TRAJECTORY_DIR \
+  --per_device_eval_batch_size 16 \
+  --num_of_trajectories_per_sample 2 \
+  --generation_input_length 4096 \
+  --generation_max_new_tokens 4096 \
+  --is_data_in_meds \
+  --att_function_type day --inpatient_att_function_type day \
+  --meds_to_cehrbert_conversion_type MedsToBertMimic4 \
+  --include_auxiliary_token --include_demographic_prompt \
+  --include_inpatient_hour_token
+```
+
+> **Important**: Ensure `generation_input_length` + `generation_max_new_tokens` ≤ `max_position_embeddings` (8192).
+
+#### Parameter Reference
+
+- `generation_input_length`: Input context length for generation
+- `generation_max_new_tokens`: Maximum new tokens to generate
+- `num_of_trajectories_per_sample`: Number of trajectories per patient sample
+
+## 📖 Citation
+
+If you use CEHRGPT in your research, please cite:
+
+```bibtex
+@article{cehrgpt2024,
+  title={CEHRGPT: Synthetic Data Generation for Electronic Health Records},
+  author={Natarajan, K and others},
+  journal={arXiv preprint arXiv:2402.04400},
+  year={2024}
+}
+```
+
+## 📄 License
+
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

{cehrgpt-0.1.1.dist-info → cehrgpt-0.1.3.dist-info}/RECORD

@@ -1,8 +1,9 @@
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@@ -62,13 +73,13 @@ cehrgpt/tools/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 cehrgpt/tools/generate_causal_patient_split_by_age.py,sha256=dmHiPAL_kR1WrhRteIiHH9dwMtMi3PVl8jXm2O06_gI,4177
 cehrgpt/tools/generate_pretrained_embeddings.py,sha256=lhFSacGv8bMld6qigKZN8Op8eXpFi0DsJuQbWKOWXqI,4160
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 cehrgpt/tools/upload_omop_tables.py,sha256=vdBAbkeAsGPA4NsyhNjelPVj3gS8yzmS1sKNM1Qk96g,3791
 cehrgpt/tools/linear_prob/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cehrgpt/tools/linear_prob/compute_cehrgpt_features.py,sha256=q0rmlBWDDEkjHjwcTouGUhCYa32a1vRicaDOAMsdW0I,20741
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 cehrgpt/tools/linear_prob/train_with_cehrgpt_features.py,sha256=w0UvzMKYGenN_KDVnbzutmy8IPLUxW5hPvpKKxDSL5U,5820
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cehrgpt-0.1.1.dist-info/METADATA

@@ -1,115 +0,0 @@
-Metadata-Version: 2.4
-Name: cehrgpt
-Version: 0.1.1
-Summary: CEHR-GPT: Generating Electronic Health Records with Chronological Patient Timelines
-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>
-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
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: cehrbert==1.4.5
-Requires-Dist: cehrbert_data==0.0.11
-Requires-Dist: openai==1.54.3
-Requires-Dist: optuna==4.0.0
-Requires-Dist: transformers==4.44.1
-Requires-Dist: tokenizers==0.19.0
-Requires-Dist: peft==0.10.0
-Requires-Dist: lightgbm
-Requires-Dist: polars
-Provides-Extra: dev
-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: flash-attn
-Requires-Dist: flash_attn; extra == "flash-attn"
-Dynamic: license-file
-
-# CEHRGPT
-
-[![PyPI - Version](https://img.shields.io/pypi/v/cehrgpt)](https://pypi.org/project/cehrgpt/)
-![Python](https://img.shields.io/badge/-Python_3.11-blue?logo=python&logoColor=white)
-[![tests](https://github.com/knatarajan-lab/cehrgpt/actions/workflows/tests.yaml/badge.svg)](https://github.com/knatarajan-lab/cehrgpt/actions/workflows/tests.yaml)
-[![license](https://img.shields.io/badge/License-MIT-green.svg?labelColor=gray)](https://github.com/knatarajan-lab/cehrgpt/blob/main/LICENSE)
-[![contributors](https://img.shields.io/github/contributors/knatarajan-lab/cehrgpt.svg)](https://github.com/knatarajan-lab/cehrgpt/graphs/contributors)
-
-## Description
-CEHRGPT is a synthetic data generation model developed to handle structured electronic health records (EHR) with enhanced privacy and reliability. It leverages state-of-the-art natural language processing techniques to create realistic, anonymized patient data that can be used for research and development without compromising patient privacy.
-
-## Features
-- **Synthetic Patient Data Generation**: Generates comprehensive patient profiles including demographics, medical history, treatment courses, and outcomes.
-- **Privacy-Preserving**: Implements techniques to ensure the generated data does not reveal identifiable information.
-- **Compatibility with OMOP**: Fully compatible with the OMOP common data model, allowing seamless integration with existing healthcare data systems.
-- **Extensible**: Designed to be adaptable to new datasets and different EHR systems.
-
-## Installation
-To install CEHRGPT, clone this repository and install the required dependencies.
-
-```bash
-git clone https://github.com/knatarajan-lab/cehrgpt.git
-cd cehrgpt
-pip install .
-```
-
-## Pretrain
-Pretrain cehrgpt using the Hugging Face trainer, the parameters can be found in the sample configuration yaml
-```bash
-mkdir test_results
-# This is NOT required when streaming is set to true
-mkdir test_dataset_prepared
-python -u -m cehrgpt.runners.hf_cehrgpt_pretrain_runner sample_configs/cehrgpt_pretrain_sample_config.yaml
-```
-
-## Generate synthetic sequences
-Generate synthetic sequences using the trained model
-```bash
-export TRANSFORMERS_VERBOSITY=info
-export CUDA_VISIBLE_DEVICES="0"
-python -u -m cehrgpt.generation.generate_batch_hf_gpt_sequence \
-  --model_folder test_results \
-  --tokenizer_folder test_results \
-  --output_folder test_results \
-  --num_of_patients 128 \
-  --batch_size 32 \
-  --buffer_size 128 \
-  --context_window 1024 \
-  --sampling_strategy TopPStrategy \
-  --top_p 1.0 --temperature 1.0 --repetition_penalty 1.0 \
-  --epsilon_cutoff 0.00 \
-  --demographic_data_path sample_data/pretrain
-```
-
-## Convert synthetic sequences to OMOP
-```bash
-# omop converter requires the OHDSI vocabulary
-export OMOP_VOCAB_DIR = ""
-# the omop derived tables need to be built using pyspark
-export SPARK_WORKER_INSTANCES="1"
-export SPARK_WORKER_CORES="8"
-export SPARK_EXECUTOR_CORES="2"
-export SPARK_DRIVER_MEMORY="2g"
-export SPARK_EXECUTOR_MEMORY="2g"
-
-# Convert the sequences, create the omop derived tables
-sh scripts/omop_pipeline.sh \
-  test_results/top_p10000/generated_sequences/ \
-  test_results/top_p10000/restored_omop/ \
-  $OMOP_VOCAB_DIR
-```
-
-## Citation
-```
-@article{cehrgpt2024,
-  title={CEHRGPT: Synthetic Data Generation for Electronic Health Records},
-  author={Natarajan, K and others},
-  journal={arXiv preprint arXiv:2402.04400},
-  year={2024}
-}