Dealing with dimensionality: the application of machine learning to multi-omics data

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Motivation Machine learning (ML) methods are motivated by the need to automate information extraction from large datasets in order to support human users in data-driven tasks. This is an attractive approach for integrative joint analysis of vast amounts of omics data produced in next generation sequencing and other -omics assays. A systematic assessment of the current literature can help to identify key trends and potential gaps in methodology and applications. We surveyed the literature on ML multi-omic data integration and quantitatively explored the goals, techniques and data involved in this field. We were particularly interested in examining how researchers use ML to deal with the volume and complexity of these datasets.Results Our main finding is that the methods used are those that address the challenges of datasets with few samples and many features. Dimensionality reduction methods are used to reduce the feature count alongside models that can also appropriately handle relatively few samples. Popular techniques include autoencoders, random forests and support vector machines. We also found that the field is heavily influenced by the use of The Cancer Genome Atlas dataset, which is accessible and contains many diverse experiments.Availability and implementationAll data and processing scripts are available at this GitLab repository: or in Zenodo: .Supplementary informationare available at Bioinformatics online.

Original languageEnglish
Article numberbtad021
JournalBioinformatics
Volume39
Issue number2
Number of pages8
ISSN1367-4803
DOIs
Publication statusPublished - 2023

    Research areas

  • CAUSAL INFERENCE, GENE, EXPRESSION, MODELS

ID: 339325886