CPA - Compositional Perturbation Autoencoder#

The architecture of CPA

What is CPA?#

CPA is a framework to learn effects of perturbations at the single-cell level. CPA encodes and learns phenotypic drug response across different cell types, doses and drug combinations. CPA allows:

  • Out-of-distribution predictions of unseen drug and gene combinations at various doses and among different cell types.

  • Learn interpretable drug and cell-type latent spaces.

  • Estimate the dose-response curve for each perturbation and their combinations.

  • Transfer pertubration effects from on cell-type to an unseen cell-type.

  • Enable batch effect removal on a latent space and also gene expression space.

Getting started#

To get started with CPA, please follow the installation instructions in the Installation section.

Support and contribute#

If you have a question or new architecture or a model that could be integrated into our pipeline, you can post an issue.