scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis

PLoS Comput Biol. 2024 Dec 18;20(12):e1012679. doi: 10.1371/journal.pcbi.1012679. eCollection 2024 Dec.

Abstract

With the rapidly development of biotechnology, it is now possible to obtain single-cell multi-omics data in the same cell. However, how to integrate and analyze these single-cell multi-omics data remains a great challenge. Herein, we introduce an interpretable multitask framework (scMoMtF) for comprehensively analyzing single-cell multi-omics data. The scMoMtF can simultaneously solve multiple key tasks of single-cell multi-omics data including dimension reduction, cell classification and data simulation. The experimental results shows that scMoMtF outperforms current state-of-the-art algorithms on these tasks. In addition, scMoMtF has interpretability which allowing researchers to gain a reliable understanding of potential biological features and mechanisms in single-cell multi-omics data.

MeSH terms

  • Algorithms*
  • Computational Biology* / methods
  • Genomics / methods
  • Humans
  • Machine Learning
  • Multiomics
  • Single-Cell Analysis* / methods

Grants and funding

This work was partially supported by the National Natural Science Foundation of China (No. 62472108 to W.L.; No. U24A20256 to W.L.; No. 62072122 to W.L.), the Natural Science Foundation of Guangxi (No. 2023JJG170006 to W.L.), the Guangxi BaGui Top Youth Talent Program to W.L, the Project of Guangxi Key Laboratory of Eye Health (No. GXYJK-202407 to W.L.), the Project of Guangxi Health Commission eye and related diseases artificial intelligence screen technology key laboratory (No. GXYAI-202402 to W.L.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.