Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs. Issue 2 (18th March 2020)

• Record Type: Journal Article
• Authors: Xiao, Qiu; Zhang, Ning; Luo, Jiawei; Dai, Jianhua; Tang, Xiwei
• Is Part Of: Briefings in bioinformatics. Volume 22:Issue 2(2021)
• Page Start: 2043
• Page End: 2057
• Publication Date: 2020-03-18
• Subjects: microRNAs -- disease miRNA inference -- multi-source learning -- feature extraction -- adaptive learning; Genetics -- Data processing -- Periodicals; Molecular biology -- Data processing -- Periodicals; Genomes -- Data processing -- Periodicals; 572.80285
• DOI: 10.1093/bib/bbaa028
• Languages: English
• ISSNs: 1467-5463

Abstract

Abstract: Accumulating evidence has shown that microRNAs (miRNAs) play crucial roles in different biological processes, and their mutations and dysregulations have been proved to contribute to tumorigenesis. In silico identification of disease-associated miRNAs is a cost-effective strategy to discover those most promising biomarkers for disease diagnosis and treatment. The increasing available omics data sources provide unprecedented opportunities to decipher the underlying relationships between miRNAs and diseases by computational models. However, most existing methods are biased towards a single representation of miRNAs or diseases and are also not capable of discovering unobserved associations for new miRNAs or diseases without association information. In this study, we present a novel computational method with adaptive multi-source multi-view latent feature learning (M2LFL) to infer potential disease-associated miRNAs. First, we adopt multiple data sources to obtain similarity profiles and capture different latent features according to the geometric characteristic of miRNA and disease spaces. Then, the multi-modal latent features are projected to a common subspace to discover unobserved miRNA-disease associations in both miRNA and disease views, and an adaptive joint graph regularization term is developed to preserve the intrinsic manifold structures of multiple similarity profiles. Meanwhile, the Lp, q -norms are imposed into the projection matrices to ensure the sparsity and improve interpretability. The experimental results confirm the superior performance of our proposed method in screening reliable candidate disease miRNAs, which suggests that M2LFL could be an efficient tool to discover diagnostic biomarkers for guiding laborious clinical trials.