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FedCVD

The First Real-World Federated Learning Benchmark on Cardiovascular Disease Data

Framework

Installation

Directory Structure

We recommend the user to use FedCVD following the directory structure below:

data:  store the raw data and preprocessed data for each client;
code:  use `FedCVD` in this directory;
output: store results and log files。

The directory structure is shown below:

├── workspace  
│   └── data
│   │   ├── ECG  
│   │   │   ├── raw
│   │   │   │   ├── SPH
│   │   │   │   ├── PTB
│   │   │   │   ├── SXPH
│   │   │   │   ├── G12EC
│   │   │   ├── preprocessed
│   │   │   │   ├── client1
│   │   │   │   ├── client2
│   │   │   │   ├── client3
│   │   │   │   ├── client4
│   │   ├── ECHO    
│   │   │   ├── raw
│   │   │   │   ├── CAMUS
│   │   │   │   ├── ECHONET
│   │   │   │   ├── HMCQU
│   │   │   ├── preprocessed
│   │   │   │   ├── client1
│   │   │   │   ├── client2
│   │   │   │   ├── client3
│   ├── output  
│   └── code  
│       └── FedCVD

You can run scripts below to create the directory structure:

mkdir workspace  
cd workspace  
mkdir data code output
cd data
mkdir -p ECG/raw ECG/preprocessed ECHO/raw ECHO/preprocessed
cd ECG/raw
mkdir SPH PTB SXPH G12EC
cd ../../ECHO/raw
mkdir CAMUS ECHONET HMCQU
cd ../../../
cd code

Data Downloading

Datasets for Fed-ECG can be downloaded from the URLs below:

Datasets for Fed-ECHO can be downloaded from the URLs below:

Note that a Stanford AIMI account is required to access the ECHONET-DYNAMIC dataset and a Kaggle account is required to access the HMC-QU dataset.

Data Preprocessing

Make sure the data is stored in the correct directory structure. The reference structure is shown below:

  • SPH directory must contain the following files or directories:
├── SPH
│   ├── ...
│   ├── metadata.csv
│   ├── records
│   │   ├── A00001.h5
│   │   ├── ...
│   │   └── A25770.h5
  • PTB directory must contain the following files or directories:
├── PTB
│   ├── ...
│   ├── ptbxl_database.csv
│   ├── records500
│   │   ├── 00000
│   │   │   ├── 00001_hr.dat
│   │   │   ├── 00001_hr.hea
│   │   │   └── ...
│   │   ├── ...
│   │   └── 21000
  • SXPH directory must contain the following files or directories:
├── SXPH
│   ├── ...
│   ├── WFDBRecords
│   │   ├── 01
│   │   │   ├── 010
│   │   │   │   ├── JS00001.hea
│   │   │   │   ├── JS00001.mat
│   │   │   │   └── ...
│   │   │   ├── ...
│   │   ├── ...
│   │   └── 46
  • G12EC directory must contain the following files or directories:
├── G12EC
│   ├── g1
│   │   ├── E00001.hea
│   │   ├── E00001.mat
│   │   └── ...
│   ├── ...
│   └── g11
  • CAMUS directory must contain the following files or directories:
├── CAMUS
│   ├── training
│   │   ├── patient0001
│   │   ├── ...
│   │   └── patient0450
│   ├── testing
│   │   ├── patient0001
│   │   ├── ...
│   │   └── patient0050
  • ECHONET directory must contain the following files or directories:
├── ECHONET
│   ├── ...
│   ├── FileList.csv
│   ├── VolumeTracings.csv
│   ├── Videos
│   │   ├── 0X1A0A263B22CCD966.avi
│   │   └── ...
  • HMCQU directory must contain the following files or directories:
├── HMCQU
│   ├── ...
│   ├── A4C.xlsx
│   ├── HMC-QU
│   │   ├── A4C
│   │   │   ├── ES0001 _4CH_1.avi
│   │   │   └── ...
│   ├── LV Ground-truth Segmentation Masks
│   │   ├── Mask_ES0001 _4CH_1.mat
│   │   └── ...

After downloading the data, you can run the following scripts to preprocess and split the data:

cd code/FedCVD/
bash scripts/preprocess/preprocess.sh
bash scripts/preprocess/split.sh

Environment Setup

You can use the following scripts to set up the environment:

cd code/FedCVD/
conda create -n fedcvd_env python=3.11 -y
conda activate fedcvd_env
pip install -r requirements.txt

Usage

You can run the scripts in the code/FedCVD/scripts directory to reproduce our experiments.