RT Journal Article
SR Electronic
T1 MultiCPA: Multimodal Compositional Perturbation Autoencoder
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.07.08.499049
DO 10.1101/2022.07.08.499049
A1 Inecik, Kemal
A1 Uhlmann, Andreas
A1 Lotfollahi, Mohammad
A1 Theis, Fabian
YR 2022
UL http://biorxiv.org/content/early/2022/07/10/2022.07.08.499049.abstract
AB Single-cell multimodal profiling provides a high-resolution view of cellular information. Recently, multimodal profiling approaches have been coupled with CRISPR technologies to perform pooled screens of single or combinatorial perturbations. This opens the possibility of exploring the massive space of combinatorial perturbations and their regulatory effects computationally from the extrapolation of a few experimentally feasible combinations. Here, we propose MultiCPA, an end-to-end generative architecture to predict multimodal perturbation response at single cell level. Two mixing strategies to integrate multiple modalities are introduced and compared with existing methods. MultiCPA was also shown to accurately predict unseen combinatorial perturbation responses for multiple modalities. The code to reproduce the results is available on GitHub, theislab/multicpa.Competing Interest StatementF.J.T. consults for Immunai Inc., Singularity Bio B.V., CytoReason Ltd, and Omniscope Ltd, and has ownership interest in Dermagnostix GmbH and Cellarity.