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POPDx: An Automated Framework for Patient Phenotyping across 392,246 Individuals in the UK Biobank Study

POPDx (Population-based Objective Phenotyping by Deep Extrapolation) is a bilinear machine learning framework for simultaneous multi-phenotype recognition. For additional information, please refer to our manuscript, available at https://academic.oup.com/jamia/advance-article/doi/10.1093/jamia/ocac226/6873915.

License

The contents of this repository are released under the Stanford University academic license. For commercial use or other licensing inquiries, please contact Stanford's Office of Technology Licensing. Please refer to the license file in the folder for detailed information about the license.

To cite:
Yang, Lu, Sheng Wang, and Russ B. Altman. "POPDx: an automated framework for patient phenotyping across 392 246 individuals in the UK Biobank study." Journal of the American Medical Informatics Association 30.2 (2023): 245-255.

Tools for UK Biobank

Please stay tuned.

Installation

Please clone our github repository as follows:

git clone https://github.com/luyang-ai4med/POPDx.git

Dependencies

POPDx is developed in Python 3. We provide the conda environment containing the necessary dependencies. For your experiments, we suggest using a single GPU (e.g. NVIDIA Tesla V100 SXM2 16 GB).

conda env create -f popdx.yml
conda activate popdx

Label embeddings

Please refer to the sample notebook for generating the ICD-10/Phecode embeddings.

POPDx/code/create_label_embeddings.ipynb

Lines 1 to 6 in 2035055

{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "d58208cb",

POPDx training

POPDx can be explored and run through the command lines as follows:

python code/POPDx_train.py -h
python code/POPDx_train.py -d './save/POPDx_train'

Additional parameters can be defined by the user.

The script to train POPDx. 
Please specify the train/val datasets path in the python script.

optional arguments:
  -h, --help            show this help message and exit
  -d SAVE_DIR, --save_dir SAVE_DIR
                        The folder to save the trained POPDx model e.g.
                        "./save/POPDx_train"
  -s HIDDEN_SIZE, --hidden_size HIDDEN_SIZE
                        Default hidden size is 150.
  --use_gpu USE_GPU     Default setup is to use GPU.
  -lr LEARNING_RATE, --learning_rate LEARNING_RATE
                        Default learning rate is 0.0001
  -wd WEIGHT_DECAY, --weight_decay WEIGHT_DECAY
                        Default weight decay is 0

POPDx testing

POPDx can be tested through the command lines as follows:

python code/POPDx_test.py -h 
python code/POPDx_test.py -m "./save/POPDx_train/best_classifier.pth.tar" -o "./save/POPDx_train/test/"

Additional parameters can be defined by the user.

usage: POPDx_test.py [-h] -m MODEL_PATH -o OUTPUT_PATH [-s HIDDEN_SIZE]
                     [-b BATCH_SIZE] [--use_gpu USE_GPU]

The script to test POPDx. 
Please specify the path to the test datasets in the python script.

optional arguments:
  -h, --help            show this help message and exit
  -m MODEL_PATH, --model_path MODEL_PATH
                        The path to POPDx model e.g.
                        "./save/POPDx_train/best_classifier.pth.tar"
  -o OUTPUT_PATH, --output_path OUTPUT_PATH
                        The output directory e.g. "./save/POPDx_train/test/"
  -s HIDDEN_SIZE, --hidden_size HIDDEN_SIZE
                        Default hidden size is 150. Consistent with training.
  -b BATCH_SIZE, --batch_size BATCH_SIZE
                        Default batch size is 512.
  --use_gpu USE_GPU     Default setup is to not use GPU for test.