ProtoCell4P: An Explainable Prototype-based Neural Network for Patient Classification Using Single-cell RNA-seq

This repo contains the source code for our manuscript to Bioinformatics.

Setup

lupus dataset

• Change directory to ./data/lupus
• Follow the instruction of ./data/lupus/download.txt

  cardio dataset

• Change directory to ./data/cardio
• Follow the instruction of ./data/cardio/download.txt

  covid dataset

• Change directory to ./data/covid
• Follow the instruction of ./data/covid/download.txt

Usage

• Change directory to ./src

  Run ProtoCell4P

• Run sh run.sh

  Run BaseModel

• Run sh run_base.sh

  Run Ablation Studies

• Run sh run_ablation.sh

Citation

If you find our research useful, please consider citing:

@article{xiong2023protocell4p,
  title={ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq},
  author={Xiong, Guangzhi and Bekiranov, Stefan and Zhang, Aidong},
  journal={Bioinformatics},
  volume={39},
  number={8},
  pages={btad493},
  year={2023},
  publisher={Oxford University Press}
}