MEDFAIR: Benchmarking Fairness for Medical Imaging

Note: This is a fork from the original repository

MEDFAIR is a fairness benchmarking suite for medical imaging (paper). We are actively updating this repo and will incorporate more datasets and algorithms in the future. Contributions are warmly welcomed! Check our website for a brief summary of the paper.

😀 MEDFAIR is accepted to ICLR'23 as Spotlight!

Documentation

A detailed documentation can be found here.

Quick Start

Installation

Python >= 3.8+ and Pytorch >=1.10 are required for running the code. Other necessary packages are listed in environment.yml.

Installation via conda:

cd MEDFAIR/
conda env create -n fair_benchmark -f environment.yml
conda activate fair_benchmark

Dataset

Due to the data use agreements, we cannot directly share the download link. Please register and download datasets using the links from the table below:

Dataset	Access
CheXpert	Original data: https://stanfordmlgroup.github.io/competitions/chexpert/
	Demographic data: https://stanfordaimi.azurewebsites.net/datasets/192ada7c-4d43-466e-b8bb-b81992bb80cf
MIMIC-CXR	https://physionet.org/content/mimic-cxr-jpg/2.0.0/
PAPILA	https://www.nature.com/articles/s41597-022-01388-1#Sec6
HAM10000	https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/DBW86T
OCT	https://people.duke.edu/~sf59/RPEDC_Ophth_2013_dataset.htm
Fitzpatrick17k	https://github.com/mattgroh/fitzpatrick17k
COVID-CT-MD	https://doi.org/10.6084/m9.figshare.12991592
ADNI 1.5T/3T	https://ida.loni.usc.edu/login.jsp?project=ADNI

Data Preprocessing

See notebooks/HAM10000.ipynb for an simple example of how to preprocess the data into desired format. You can also find other preprocessing scripts for corresponding datasets. Basically, it contains 3 steps:

1. Preprocess metadata.
2. Split to train/val/test set
3. Save images into pickle files (optional -- we usually do this for 2D images instead of 3D images, as data IO is not the bottleneck for training 3D images).

After preprocessing, specify the paths of the metadata and pickle files in configs/datasets.json.

Run a single experiment

python main.py --experiment [experiment] --experiment_name [experiment_name] --dataset_name [dataset_name] \
     --backbone [backbone] --total_epochs [total_epochs] --sensitive_name [sensitive_name] \
     --batch_size [batch_size] --lr [lr] --sens_classes [sens_classes]  --val_strategy [val_strategy] \
     --output_dim [output_dim] --num_classes [num_classes]

For example, for running ERM in HAM10000 dataset with Sex as the sensitive attribute:

python main.py --experiment baseline --dataset_name HAM10000 \
     --total_epochs 20 --sensitive_name Sex --batch_size 1024 \
     --sens_classes 2 --output_dim 1 --num_classes 1

See parse_args.py for more options.

Run a grid search on a Slurm cluster/Regular Machine

python sweep/train-sweep/sweep_batch.py --is_slurm True/False

Set the other arguments as needed.

Model selection and Results analysis

See notebooks/results_analysis.ipynb for a step by step example.

Citation

Please consider citing our paper if you find this repo useful.

@inproceedings{zong2023medfair,
    title={MEDFAIR: Benchmarking Fairness for Medical Imaging},
    author={Yongshuo Zong and Yongxin Yang and Timothy Hospedales},
    booktitle={International Conference on Learning Representations (ICLR)},
    year={2023},
}

Acknowledgement

MEDFAIR adapts implementations from many repos (check here for the original implementation of the algorithms), as well as many other codes. Many thanks!