boxiangliu / enformer-pytorch

Pytorch implementation of DeepMind's enformer.

This implementation is inspired by a previous pytorch implementation of enformer. This implementation has more careful weight initialization, and comes with a dataloader and training scripts.

Setup

This package has the following dependencies:

python==3.8.6
einops
torch==1.10
numpy
tensorflow==2.4.1
tqdm
pandas

see requirements.txt

Download toy data

python data/download.py

Train model with toy data

python bin/train.py

Citation

@article{avsec2021nmeth,
  title={Effective gene expression prediction from sequence by integrating long-range interactions},
  author={Avsec, Ziga and Agarwal, Vikram and Visentin, Daniel and Ledsam, Joseph R and Grabska-Barwinska, Agnieszka and Taylor, Kyle R and Assael, Yannis and Jumper, John and Kohli, Pushmeet and Kelley, David R},
  journal={Nature Methods},
  year={2021}
}