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Here we apply a transformer-based unsupervised clustering framework to longitudinal electronic health record data from over 100,000 patients across two UK cohorts, Clinical Practice Research Datalink Aurum and UK Biobank, to identify, validate and characterize subtypes of AD and PD. We uncover five reproducible subtypes for each condition, characterized by distinct comorbidity patterns, symptom trajectories, outcomes and genetic profiles. These include a high-mortality AD subtype with motor and cardiovascular features, and a genetically susceptible but clinically resilient PD subtype. We also identify metabolic\u2013inflammatory and vascular\u2013psychiatric phenotypes shared across AD and PD, suggesting cross-disease mechanisms. By integrating routinely collected electronic health record data with genetic analyses, our study provides a scalable framework for early, biologically informed subtyping, laying the groundwork for future targeted interventions in neurodegenerative diseases.<\/jats:p>","DOI":"10.1038\/s43587-026-01085-3","type":"journal-article","created":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T10:03:38Z","timestamp":1772100218000},"page":"612-625","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Subtyping Alzheimer\u2019s disease and Parkinson\u2019s disease using longitudinal electronic health records"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2351-2570","authenticated-orcid":false,"given":"Jie","family":"Lian","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-2549-7628","authenticated-orcid":false,"given":"Zhengxian","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben Omega","family":"Petrazzini","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7331-9416","authenticated-orcid":false,"given":"Shishir","family":"Rao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianqian","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guyu","family":"Zeng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nouman","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7324-6680","authenticated-orcid":false,"given":"Fatemeh","family":"Tabassi Mofrad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malgorzata","family":"Wamil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4807-4610","authenticated-orcid":false,"given":"Kazem","family":"Rahimi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,2,26]]},"reference":[{"key":"1085_CR1","doi-asserted-by":"publisher","DOI":"10.1016\/j.arr.2024.102414","volume":"100","author":"OF Sultana","year":"2024","unstructured":"Sultana, O. 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