scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links
Gefei Wang, Jia Zhao, Yingxin Lin, Tianyu Liu, Yize Zhao, Hongyu Zhao
Abstract
Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our understanding of cell functions and disease mechanisms from various omics perspectives. As these technologies evolve rapidly and data resources expand, there is a growing need for computational methods that can integrate information from different modalities to facilitate joint analysis of single-cell multi-omics data. However, integrating single-cell omics datasets presents unique challenges due to varied feature correlations and technology-specific limitations. To address these challenges, we introduce scMODAL, a deep learning framework tailored for single-cell multi-omics data alignment using feature links. scMODAL integrates datasets with limited known positively correlated features, leveraging neural networks and generative adversarial networks to align cell embeddings and preserve feature topology. Our experiments demonstrate scMODAL’s effectiveness in removing unwanted variation, preserving biological information, and accurately identifying cell subpopulations across diverse datasets. scMODAL not only advances integration tasks but also supports downstream analyses such as feature imputation and feature relationship inference, offering a robust solution for advancing single-cell multi-omics research. Single-cell multi-omics integration is challenged by varied feature relationships and modality-specific limitations. Here, the authors present scMODAL, a deep learning framework that leverages known feature links to align single-cell omics, enabling accurate integration and downstream analyses.