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DL techniques are being applied to assist medical professionals and researchers in improving clinical diagnosis, disease prediction and drug discovery. It is expected that DL will help to provide actionable knowledge from a variety of \u2018big data\u2019, including metabolomics data. In this review, we discuss the applicability of DL to metabolomics, while presenting and discussing several examples from recent research. We emphasize the use of DL in tackling bottlenecks in metabolomics data acquisition, processing, metabolite identification, as well as in metabolic phenotyping and biomarker discovery. Finally, we discuss how DL is used in genome-scale metabolic modelling and in interpretation of metabolomics data. The DL-based approaches discussed here may assist computational biologists with the integration, prediction and drawing of statistical inference about biological outcomes, based on metabolomics data.<\/jats:p>","DOI":"10.1093\/bib\/bbaa204","type":"journal-article","created":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T12:11:16Z","timestamp":1597147876000},"page":"1531-1542","source":"Crossref","is-referenced-by-count":99,"title":["Deep learning meets metabolomics: a methodological perspective"],"prefix":"10.1093","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0475-2763","authenticated-orcid":false,"given":"Partho","family":"Sen","sequence":"first","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, 20520 Turku, Finland"},{"name":"School of Medical Sciences, \u00d6rebro University, 702 81 \u00d6rebro, Sweden"}]},{"given":"Santosh","family":"Lamichhane","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, 20520 Turku, Finland"}]},{"given":"Vivek B","family":"Mathema","sequence":"additional","affiliation":[{"name":"Metabolomics and Systems Biology, Department of Biochemistry, and Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand"}]},{"given":"Aidan","family":"McGlinchey","sequence":"additional","affiliation":[{"name":"School of Medical Sciences, \u00d6rebro University, 702 81 \u00d6rebro, Sweden"}]},{"given":"Alex M","family":"Dickens","sequence":"additional","affiliation":[{"name":"Turku Bioscience Centre, University of Turku and \u00c5bo Akademi University, 20520 Turku, Finland"}]},{"given":"Sakda","family":"Khoomrung","sequence":"additional","affiliation":[{"name":"Metabolomics and Systems Biology, Department of Biochemistry, and Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 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