Con-AAE: Contrastive Cycle Adversarial Autoencoders for Single-cell Multi-omics Alignment and Integration.

Abstract

We have entered the multi-omics era and can measure cells from different aspects. Hence, we can get a more comprehensive view by integrating or matching data from different spaces corresponding to the same object. However, it is particularly challenging in the single-cell multi-omics scenario because such data are very sparse with extremely high dimensions. Though some techniques can be used to measure scATAC-seq and scRNA-seq simultaneously, the data are usually highly noisy due to the limitations of the experimental environment. To promote single-cell multi-omics research, we overcome the above challenges, proposing a novel framework, contrastive cycle adversarial autoencoders, which can align and integrate single-cell RNA-seq data and single-cell ATAC-seq data. Con-AAE can efficiently map the above data with high sparsity and noise from different spaces to a coordinated subspace, where alignment and integration tasks can be easier. We demonstrate its advantages on several datasets. Zenodo link: https://zenodo.org/badge/latestdoi/368779433 github: https://github.com/kakarotcq/Con-AAE. Supplementary data are available at Bioinformatics online.