This is the official repository for the paper titled "FedMedICL: Towards Holistic Evaluation of Distribution Shifts in Federated Medical Imaging" accepted at MICCAI24. FedMedICL is a unified framework designed to address federated medical imaging challenges across various dimensions including label, demographic, and temporal distribution shifts. Unlike traditional benchmarks that assess performance under a single type of distribution shift, FedMedICL offers a more holistic evaluation across dynamic healthcare settings.
This project requires Python 3.8 or higher and PyTorch 1.8 or later. Follow these steps to set up the Conda environment:
conda create -n fedmedicl1 python=3.9.19
conda activate fedmedicl1
pip install -r requirements.txt --extra-index-url https://download.pytorch.org/whl/cu116To get started, clone our repository:
git clone https://github.com/m1k2zoo/FedMedICL.git
cd FedMedICLFor complete details on downloading and preprocessing the datasets, please refer to the datasets documentation.
To get started with running experiments on our FedMedICL framework, we provide example scripts for each dataset using the FedAvg baseline located in the scripts directory:
- For main experiments, the scripts are named
FedAvg_<dataset>.sh, where <dataset> is the dataset name. - For novel disease outbreaks, use the script
novel_FedAvg_CheXCOVID.sh.
Below is an example script for training with the HAM10000 dataset using the FedAvg baseline:
bash scripts/FedAvg_HAM10000.shThe training results will be logged in the specified output_dir directory.
For advanced usage scenarios, such as experiments involving multiple datasets across clients, we provide an example under scripts/additional_examples.
The hyperparameters used in the FedAvg_.sh and novel_FedAvg_CheXCOVID.sh scripts match those we used in our experiments described in the paper. All main experiment datasets share the same hyperparameters, except for CheXpert, which has slightly different ones to accommodate its large-scale size.
We also provide the Weights & Biases sweeps used to re-run our experiments, which include the hyperparameters used. These can be found in the scripts/sweeps directory.
For information on supported algorithms, please refer to the supported algorithms documentation.
For details on how results are stored and organized, and for instructions on generating plots, please refer to the reporting documentation.
- Kumail Alhamoud: [email protected]
- Yasir Ghunaim: [email protected]
- Motasem Alfarra: [email protected]