scFed: Federated learning for cell type classification with scRNA-seq

This repo contains the source code of the Python package federatedSinglecell. See our paper for a detailed description of federatedSinglecell.

Overview

Four major modules are included:

• FedSVM

• FedACTINN

• FedXGBoost

• FedGeneformer

Prerequisite

NVIDIA GPU + CUDA CuDNN (CPU may be possible with some modifications, but is not inherently supported)

We recommend running this repository using Anaconda. All dependencies for defining the environment are provided in requirements.txt

Use tokenizing_scRNAseq_data.ipynb to prepare FedGeneformer data.

Run

• FedSVM

      cd FedSVM
      python main_federatedSVM.py

• FedACTINN

      cd FedACTINN
      python main_federatedACTINN.py

• FedXGBoost

      cd FedXGBoost
      python main_xgb.py

• FedGeneformer

      cd FedGeneformer
      python fl-server.py
      python fl-gene.py {clientId}