Robust integrative biclustering for multi-view data

• Published in: Statistical methods in medical research Vol. 31; no. 11; pp. 2201 - 2216
• Main Authors: Zhang, Weijie, Wendt, Christine, Bowler, Russel, Hersh, Craig P, Safo, Sandra E
• Format: Journal Article
• Language: English
• Published: London, England SAGE Publications 01.11.2022; Sage Publications Ltd
• Subjects: Algorithms; Biomedical data; Cluster Analysis; Clusters; Decomposition; Gene Expression Profiling - methods; Genomics; Medical research; Oligonucleotide Array Sequence Analysis - methods; Proteomics; Regularization; Singular value decomposition; Subgroups; Variables; co-clustering; integrative biclustering; multiomics; stability selection; Multi-view biclustering; biclustering
• ISSN: 0962-2802; 1477-0334; 1477-0334
• DOI: 10.1177/09622802221122427

In many biomedical research, multiple views of data (e.g. genomics, proteomics) are available, and a particular interest might be the detection of sample subgroups characterized by specific groups of variables. Biclustering methods are well-suited for this problem as they assume that specific groups of variables might be relevant only to specific groups of samples. Many biclustering methods exist for detecting row–column clusters in a view but few methods exist for data from multiple views. The few existing algorithms are heavily dependent on regularization parameters for getting row–column clusters, and they impose unnecessary burden on users thus limiting their use in practice. We extend an existing biclustering method based on sparse singular value decomposition for single-view data to data from multiple views. Our method, integrative sparse singular value decomposition (iSSVD), incorporates stability selection to control Type I error rates, estimates the probability of samples and variables to belong to a bicluster, finds stable biclusters, and results in interpretable row–column associations. Simulations and real data analyses show that integrative sparse singular value decomposition outperforms several other single- and multi-view biclustering methods and is able to detect meaningful biclusters. iSSVD is a user-friendly, computationally efficient algorithm that will be useful in many disease subtyping applications.