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Ma Z, Lu YY, Wang Y, Lin R, Yang Z, Zhang F, Wang Y. Metric learning for comparing genomic data with triplet network. Brief Bioinform 2022; 23:6679451. [DOI: 10.1093/bib/bbac345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Many biological applications are essentially pairwise comparison problems, such as evolutionary relationships on genomic sequences, contigs binning on metagenomic data, cell type identification on gene expression profiles of single-cells, etc. To make pair-wise comparison, it is necessary to adopt suitable dissimilarity metric. However, not all the metrics can be fully adapted to all possible biological applications. It is necessary to employ metric learning based on data adaptive to the application of interest. Therefore, in this study, we proposed MEtric Learning with Triplet network (MELT), which learns a nonlinear mapping from original space to the embedding space in order to keep similar data closer and dissimilar data far apart. MELT is a weakly supervised and data-driven comparison framework that offers more adaptive and accurate dissimilarity learned in the absence of the label information when the supervised methods are not applicable. We applied MELT in three typical applications of genomic data comparison, including hierarchical genomic sequences, longitudinal microbiome samples and longitudinal single-cell gene expression profiles, which have no distinctive grouping information. In the experiments, MELT demonstrated its empirical utility in comparison to many widely used dissimilarity metrics. And MELT is expected to accommodate a more extensive set of applications in large-scale genomic comparisons. MELT is available at https://github.com/Ying-Lab/MELT.
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Affiliation(s)
- Zhi Ma
- Department of Automation, Xiamen University , China
- National Institute for Data Science in Health and Medicine, Xiamen University
| | - Yang Young Lu
- Cheriton School of Computer Science, University of Waterloo , Waterloo, Ontario , Canada
| | - Yiwen Wang
- Department of Automation, Xiamen University , China
| | - Renhao Lin
- Department of Automation, Xiamen University , China
| | - Zizi Yang
- Department of Automation, Xiamen University , China
| | - Fang Zhang
- Cheriton School of Computer Science, University of Waterloo , Waterloo, Ontario , Canada
| | - Ying Wang
- Department of Automation, Xiamen University , China
- National Institute for Data Science in Health and Medicine, Xiamen University
- Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision , Xiamen, Fujian 361005 , China
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms , Xiamen, 361100 , China
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