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Our pDNN reproduces behavioral and neural activity patterns observed in affected children, including lower performance accuracy, slower learning rates, neural hyperexcitability, and reduced neural differentiation of numerical problems. Crucially, pDNN models reveal aberrancies in the geometry of manifold structure, providing a comprehensive view of how neural excitability influences both learning performance and the internal structure of neural representations. Our findings not only advance knowledge of the neurophysiological underpinnings of learning differences but also open avenues for targeted, personalized strategies designed to bridge cognitive gaps in affected children. This work reveals the power of digital twins integrating artificial intelligence and neuroscience to uncover mechanisms underlying neurodevelopmental disorders.<\/jats:p>","DOI":"10.1126\/sciadv.adq9990","type":"journal-article","created":{"date-parts":[[2025,6,6]],"date-time":"2025-06-06T17:58:24Z","timestamp":1749232704000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":11,"title":["Personalized deep neural networks reveal mechanisms of math learning disabilities in children"],"prefix":"10.1126","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6725-561X","authenticated-orcid":true,"given":"Anthony","family":"Strock","sequence":"first","affiliation":[{"name":"Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3055-4472","authenticated-orcid":true,"given":"Percy K.","family":"Mistry","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1622-9857","authenticated-orcid":true,"given":"Vinod","family":"Menon","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA."},{"name":"Department of Neurology &amp; Neurological Sciences, Stanford University, Stanford, CA 94305, USA."},{"name":"Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA."},{"name":"Graduate School of Education, Stanford University, Stanford, CA 94305, USA."}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"221","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1037\/0012-1649.37.2.231"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1111\/desc.12671"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1044\/1092-4388(2009\/07-0144)"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cognition.2017.05.016"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1097\/DBP.0b013e318209edef"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.tine.2013.06.006"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1037\/0022-0663.97.3.493"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.econedurev.2011.09.006"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.2307\/145737"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.34133\/icomputing.0055"},{"key":"e_1_3_2_12_2","doi-asserted-by":"crossref","unstructured":"I. 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