Chen Y, Wen Y, Xie C, Chen X, He S, Bo X, Zhang Z. MOCSS: Multi-omics data clustering and cancer subtyping via shared and specific representation learning.
iScience 2023;
26:107378. [PMID:
37559907 PMCID:
PMC10407241 DOI:
10.1016/j.isci.2023.107378]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/23/2023] [Accepted: 07/07/2023] [Indexed: 08/11/2023] Open
Abstract
Cancer is an extremely complex disease and each type of cancer usually has several different subtypes. Multi-omics data can provide more comprehensive biological information for identifying and discovering cancer subtypes. However, existing unsupervised cancer subtyping methods cannot effectively learn comprehensive shared and specific information of multi-omics data. Therefore, a novel method is proposed based on shared and specific representation learning. For each omics data, two autoencoders are applied to extract shared and specific information, respectively. To reduce redundancy and mutual interference, orthogonality constraint is introduced to separate shared and specific information. In addition, contrastive learning is applied to align the shared information and strengthen their consistency. Finally, the obtained shared and specific information for all samples are used for clustering tasks to achieve cancer subtyping. Experimental results demonstrate that the proposed method can effectively capture shared and specific information of multi-omics data and outperform other state-of-the-art methods on cancer subtyping.
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