{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,15]],"date-time":"2026-05-15T07:20:52Z","timestamp":1778829652924,"version":"3.51.4"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,9,19]],"date-time":"2022-09-19T00:00:00Z","timestamp":1663545600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000855","name":"University of Birmingham","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000855","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001782","name":"University of Melbourne","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001782","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Survival risk prediction using gene expression data is important in making treatment decisions in cancer. Standard neural network (NN) survival analysis models are black boxes with a lack of interpretability. More interpretable visible neural network architectures are designed using biological pathway knowledge. But they do not model how pathway structures can change for particular cancer types.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a novel Mutated Pathway Visible Neural Network (MPVNN) architecture, designed using prior signaling pathway knowledge and random replacement of known pathway edges using gene mutation data simulating signal flow disruption. As a case study, we use the PI3K-Akt pathway and demonstrate overall improved cancer-specific survival risk prediction of MPVNN over other similar-sized NN and standard survival analysis methods. We show that trained MPVNN architecture interpretation, which points to smaller sets of genes connected by signal flow within the PI3K-Akt pathway that is important in risk prediction for particular cancer types, is reliable.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The data and code are available at https:\/\/github.com\/gourabghoshroy\/MPVNN.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac636","type":"journal-article","created":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T10:29:58Z","timestamp":1663669798000},"page":"5026-5032","source":"Crossref","is-referenced-by-count":17,"title":["MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9420-5653","authenticated-orcid":false,"given":"Gourab","family":"Ghosh Roy","sequence":"first","affiliation":[{"name":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK"},{"name":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Geard","sequence":"additional","affiliation":[{"name":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8661-1544","authenticated-orcid":false,"given":"Karin","family":"Verspoor","sequence":"additional","affiliation":[{"name":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"},{"name":"School of Computing Technologies, RMIT University , Melbourne 3000, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1694-1465","authenticated-orcid":false,"given":"Shan","family":"He","sequence":"additional","affiliation":[{"name":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,9,19]]},"reference":[{"key":"2022112014201377200_btac636-B2","first-page":"8","author":"Biran","year":"2017"},{"key":"2022112014201377200_btac636-B3","first-page":"735","author":"Chapfuwa","year":"2018"},{"key":"2022112014201377200_btac636-B4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.compbiomed.2014.02.006","article-title":"Risk classification of cancer survival using ANN with gene expression data from multiple laboratories","volume":"48","author":"Chen","year":"2014","journal-title":"Comput. 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