This repository contains an implementation of the sparse VAE framework applied to single-cell perturbation data, as descibed in "Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling".

Download or clone this repository. Then from inside the folder simply run:

pip install -e . 

An example script for the sandbox can be found in entry_points/demo.py. The code for reproducing the real data analysis can be found in entry_points/run_real_data_replogle_wandb.py.

@article{svae+,
  title={Learning Causal Representations of Single Cells via Sparse Mechanism Shift Modeling},
  author={Lopez, Romain and Tagasovska, Natasa and Ra, Stephen and Cho, Kyunghyun and Pritchard, Jonathan K. and Regev, Aviv },
  journal={Conference on Causal Learning and Reasoning},
  year={2023},
}