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However, multi-omics data integration remains challenging due to the high-dimensionality, heterogeneity, and frequency of missing values across data types. Computational methods leveraging statistical and machine learning approaches have been developed to address these issues and uncover complex biological patterns, improving our understanding of disease mechanisms. Here, we comprehensively review state-of-the-art multi-omics integration methods with a focus on deep generative models, particularly variational autoencoders (VAEs) that have been widely used for data imputation, augmentation, and batch effect correction. We explore the technical aspects of VAE loss functions and regularisation techniques, including adversarial training, disentanglement, and contrastive learning. Moreover, we highlight recent advancements in foundation models and multimodal data integration, outlining future directions in precision medicine research.<\/jats:p>","DOI":"10.1093\/bib\/bbaf355","type":"journal-article","created":{"date-parts":[[2025,8,1]],"date-time":"2025-08-01T13:36:06Z","timestamp":1754055366000},"source":"Crossref","is-referenced-by-count":83,"title":["A technical review of multi-omics data integration methods: from classical statistical to deep generative approaches"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2377-8080","authenticated-orcid":false,"given":"Ana R","family":"Bai\u00e3o","sequence":"first","affiliation":[{"name":"INESC-ID , Rua Alves Redol 9, 1000-029 Lisboa ,","place":["Portugal"]},{"name":"Instituto Superior T\u00e9cnico (IST), Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3809-0817","authenticated-orcid":false,"given":"Zhaoxiang","family":"Cai","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , 214 Hawkesbury Road, Westmead, NSW 2145 ,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8419-7028","authenticated-orcid":false,"given":"Rebecca C","family":"Poulos","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , 214 Hawkesbury Road, Westmead, NSW 2145 ,","place":["Australia"]}]},{"given":"Phillip J","family":"Robinson","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , 214 Hawkesbury Road, Westmead, NSW 2145 ,","place":["Australia"]}]},{"given":"Roger R","family":"Reddel","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , 214 Hawkesbury Road, Westmead, NSW 2145 ,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5340-301X","authenticated-orcid":false,"given":"Qing","family":"Zhong","sequence":"additional","affiliation":[{"name":"ProCan\u00ae, Children\u2019s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney , 214 Hawkesbury Road, Westmead, NSW 2145 ,","place":["Australia"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1954-5487","authenticated-orcid":false,"given":"Susana","family":"Vinga","sequence":"additional","affiliation":[{"name":"INESC-ID , Rua Alves Redol 9, 1000-029 Lisboa ,","place":["Portugal"]},{"name":"Instituto Superior T\u00e9cnico (IST), Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa ,","place":["Portugal"]},{"name":"IDMEC, Instituto Superior T\u00e9cnico, Universidade de Lisboa , Av. Rovisco Pais, 1049-001 Lisboa ,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9967-5205","authenticated-orcid":false,"given":"Emanuel","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"INESC-ID , Rua Alves Redol 9, 1000-029 Lisboa ,","place":["Portugal"]},{"name":"Instituto Superior T\u00e9cnico (IST), Universidade de Lisboa , Av. 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