README.md

FedDM

Code for our paper: "FedDM: Federated Weakly Supervised Segmentation via Annotation Calibration and Gradient De-conflicting, TMI 2023."

In this work, we represent the first effort to formulate federated weakly supervised segmentation (FedWSS) and propose a novel Federated Drift Mitigation (FedDM) framework to learn segmentation models across multiple sites without sharing their raw data. FedDM is devoted to solving two main challenges (i.e., local drift on client-side optimization and global drift on server- side aggregation) caused by weak supervision signals in FL setting via Collaborative Annotation Calibration (CAC) and Hierarchical Gradient De-conflicting (HGD).

Running

Dependencies

pip install -r requirements.txt

Scripts

• download the prostate dataset promise, unzip and put it into the dir './data'
• preprocess the data

python python slice_promise.py 
    --source_dir='./data/promise' \
    --dest_dir='./data/promise_WSS' \
    --n_augment=0

• generate bounding-box annotations

python gen_weak.py 
    --base_folder='./data/promise_WSS/train' \
    --save_subfolder='box20' \
    --strategy='box_strat' \
    --selected_class=1 \
    --filling 1 \
    --seed=0 \
    --margin=20 \

python gen_weak.py 
    --base_folder='./data/promise_WSS/val' \
    --save_subfolder='box20' \
    --strategy='box_strat' \
    --selected_class=1 \
    --filling 1 \
    --seed=0 \
    --margin=0 \

• train the FedDM framework

python main.py 
    --dataset='./data/promise_WSS'\
    --workdir='results/prostate/'\
    --losses="[('CrossEntropy', {'idc': [0, 1]}, None, None, None, 1)]"\
    --folders="[('img', png_transform, False), ('gt', gt_transform, True)]+[('box20', gt_transform, True)]"\
    --network='ResidualUNet'\
    --n_class=2\
    --group=False\
    --n_epoch=200\
    --l_rate=5e-4\
    --batch_size=4\
    --client_num=4\
    --worker_steps=1 \
    --peer_learning=True \
    --ratio=0.6\
    --stop_epoch=50 \
    --seed=1

Citation

@ARTICLE{3235757,
  author={Zhu, Meilu and Chen, Zhen and Yuan, Yixuan},
  journal={IEEE Transactions on Medical Imaging}, 
  title={FedDM: Federated Weakly Supervised Segmentation via Annotation Calibration and Gradient De-conflicting}, 
  year={2023},
  doi={10.1109/TMI.2023.3235757}}