An Empirical Framework for Domain Generalization In Clinical Settings

Paper

If you use this code in your research, please cite the following publication:

@inproceedings{zhang2021empirical,
  title={An empirical framework for domain generalization in clinical settings},
  author={Zhang, Haoran and Dullerud, Natalie and Seyyed-Kalantari, Laleh and Morris, Quaid and Joshi, Shalmali and Ghassemi, Marzyeh},
  booktitle={Proceedings of the Conference on Health, Inference, and Learning},
  pages={279--290},
  year={2021}
}

This paper can also be found on arxiv: https://arxiv.org/abs/2103.11163

Acknowledgements

Our implementation is a modified version of the excellent DomainBed framework (from commit a10458a). We also make use of some code from eICU Benchmarks.

To replicate the experiments in the paper:

Step 0: Environment and Prerequisites

Run the following commands to clone this repo and create the Conda environment:

git clone https://github.com/MLforHealth/ClinicalDG.git
cd ClinicalDG/
conda env create -f environment.yml
conda activate clinicaldg

Step 1: Obtaining the Data

See DataSources.md for detailed instructions.

Step 2: Running Experiments

Experiments can be ran using the same procedure as for the DomainBed framework, with a few additional adjustable data hyperparameters which should be passed in as a JSON formatted dictionary.

For example, to train a single model:

python -m clinicaldg.scripts.train\
       --algorithm ERM\
       --dataset eICUSubsampleUnobs\
       --es_method val\
       --hparams  '{"eicu_architecture": "GRU", "eicu_subsample_g1_mean": 0.5, "eicu_subsample_g2_mean": 0.05}'\
       --output_dir /path/to/output

To sweep a range of datasets, algorithms, and hyperparameters:

python -m clinicaldg.scripts.sweep launch\
       --output_dir=/my/sweep/output/path\
       --command_launcher slurm\
       --algorithms ERMID ERM IRM VREx RVP IGA CORAL MLDG GroupDRO \
       --datasets CXR CXRBinary\
       --n_hparams 10\
       --n_trials 5\
       --es_method train\
       --hparams '{"cxr_augment": 1}'

A detailed list of hparams available for each dataset can be found here.

We provide the bash scripts used for our main experiments in the bash_scripts directory. You will likely need to customize them, along with the launcher, to your compute environment.

Step 3: Aggregating Results

We provide sample code for creating aggregate results for an experiment in notebooks/AggResults.ipynb.

License

This source code is released under the MIT license, included here.

prockenschaub/ClinicalDG