{"id":"https://openalex.org/W4296780663","doi":"https://doi.org/10.1093/bioinformatics/btac636","title":"MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk","display_name":"MPVNN: Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk","publication_year":2022,"publication_date":"2022-09-19","ids":{"openalex":"https://openalex.org/W4296780663","doi":"https://doi.org/10.1093/bioinformatics/btac636","pmid":"https://pubmed.ncbi.nlm.nih.gov/36124954"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5026/47153905/btac636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5026/47153905/btac636.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044187321","display_name":"Gourab Ghosh Roy","orcid":"https://orcid.org/0000-0001-9420-5653"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I79619799","display_name":"University of Birmingham","ror":"https://ror.org/03angcq70","country_code":"GB","type":"education","lineage":["https://openalex.org/I79619799"]}],"countries":["AU","GB"],"is_corresponding":true,"raw_author_name":"Gourab Ghosh Roy","raw_affiliation_strings":["School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK","School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0001-9420-5653","affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK","institution_ids":["https://openalex.org/I79619799"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061048717","display_name":"Nicholas Geard","orcid":"https://orcid.org/0000-0003-0069-2281"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nicholas Geard","raw_affiliation_strings":["School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067214173","display_name":"Karin Verspoor","orcid":"https://orcid.org/0000-0002-8661-1544"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I82951845","display_name":"RMIT University","ror":"https://ror.org/04ttjf776","country_code":"AU","type":"education","lineage":["https://openalex.org/I82951845"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Karin Verspoor","raw_affiliation_strings":["School of Computing Technologies, RMIT University , Melbourne 3000, Australia","School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia"],"raw_orcid":"https://orcid.org/0000-0002-8661-1544","affiliations":[{"raw_affiliation_string":"School of Computing Technologies, RMIT University , Melbourne 3000, Australia","institution_ids":["https://openalex.org/I82951845"]},{"raw_affiliation_string":"School of Computing and Information Systems, University of Melbourne , Melbourne 3052, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011186506","display_name":"Shan He","orcid":"https://orcid.org/0000-0003-1694-1465"},"institutions":[{"id":"https://openalex.org/I79619799","display_name":"University of Birmingham","ror":"https://ror.org/03angcq70","country_code":"GB","type":"education","lineage":["https://openalex.org/I79619799"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shan He","raw_affiliation_strings":["School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK"],"raw_orcid":"https://orcid.org/0000-0003-1694-1465","affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Birmingham , Birmingham B15 2TT, UK","institution_ids":["https://openalex.org/I79619799"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044187321"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I79619799"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.2993,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.79569374,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"38","issue":"22","first_page":"5026","last_page":"5032"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3093999922275543,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.3093999922275543,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.1501999944448471,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.13439999520778656,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.6363145112991333},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5280393362045288},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.47141334414482117},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44765743613243103},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39486801624298096},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32733893394470215},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30225449800491333}],"concepts":[{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.6363145112991333},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5280393362045288},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.47141334414482117},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44765743613243103},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39486801624298096},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32733893394470215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30225449800491333},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D051057","descriptor_name":"Proto-Oncogene Proteins c-akt","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051057","descriptor_name":"Proto-Oncogene Proteins c-akt","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051057","descriptor_name":"Proto-Oncogene Proteins c-akt","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5026/47153905/btac636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36124954","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36124954","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/f9a83c4b-bf15-4645-b79b-7df69467ad44","is_oa":true,"landing_page_url":"https://research.birmingham.ac.uk/en/publications/f9a83c4b-bf15-4645-b79b-7df69467ad44","pdf_url":null,"source":{"id":"https://openalex.org/S4306402634","display_name":"University of Birmingham Research Portal (University of Birmingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I79619799","host_organization_name":"University of Birmingham","host_organization_lineage":["https://openalex.org/I79619799"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"He, S, Ghosh Roy, G, Geard, N & Verspoor, K 2022, 'MPVNN : Mutated Pathway Visible Neural Network architecture for interpretable prediction of cancer-specific survival risk', Bioinformatics. https://doi.org/10.1093/bioinformatics/btac636","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac636","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac636","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/22/5026/47153905/btac636.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320339","display_name":"University of Birmingham","ror":"https://ror.org/03angcq70"},{"id":"https://openalex.org/F4320320974","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4296780663.pdf","grobid_xml":"https://content.openalex.org/works/W4296780663.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1987776395","https://openalex.org/W1992661964","https://openalex.org/W2007946604","https://openalex.org/W2102942095","https://openalex.org/W2112289645","https://openalex.org/W2129925362","https://openalex.org/W2138388653","https://openalex.org/W2471304467","https://openalex.org/W2741564801","https://openalex.org/W2753919178","https://openalex.org/W2790179710","https://openalex.org/W2795989238","https://openalex.org/W2808686685","https://openalex.org/W2893868814","https://openalex.org/W2921485464","https://openalex.org/W2945976633","https://openalex.org/W2998556046","https://openalex.org/W3017786087","https://openalex.org/W3028304854","https://openalex.org/W3036901136","https://openalex.org/W3047163763","https://openalex.org/W3147894994","https://openalex.org/W3199585733","https://openalex.org/W3199772305","https://openalex.org/W3211168122","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"MOTIVATION:":[0],"Survival":[1],"risk":[2,105,144],"prediction":[3,106,145],"using":[4,39,70,82],"gene":[5,83],"expression":[6],"data":[7,85,156,166],"is":[8,141,150],"important":[9,142],"in":[10,14,143],"making":[11],"treatment":[12],"decisions":[13],"cancer.":[15],"Standard":[16],"neural":[17,34],"network":[18,35],"(NN)":[19],"survival":[20,104,115],"analysis":[21,116],"models":[22],"are":[23,37,159,167],"black":[24],"boxes":[25],"with":[26],"a":[27,60,91],"lack":[28],"of":[29,78,107,130],"interpretability.":[30],"More":[31],"interpretable":[32],"visible":[33],"architectures":[36],"designed":[38,69],"biological":[40],"pathway":[41,49,73,80,98,139],"knowledge.":[42],"But":[43],"they":[44],"do":[45],"not":[46],"model":[47],"how":[48],"structures":[50],"can":[51],"change":[52],"for":[53,146],"particular":[54,147],"cancer":[55,148],"types.":[56],"RESULTS:":[57],"We":[58,118],"propose":[59],"novel":[61],"Mutated":[62],"Pathway":[63],"Visible":[64],"Neural":[65],"Network":[66],"(MPVNN)":[67],"architecture,":[68],"prior":[71],"signaling":[72],"knowledge":[74],"and":[75,99,113,157],"random":[76],"replacement":[77],"known":[79],"edges":[81],"mutation":[84],"simulating":[86],"signal":[87,134],"flow":[88,135],"disruption.":[89],"As":[90],"case":[92],"study,":[93],"we":[94],"use":[95],"the":[96,137],"PI3K-Akt":[97,138],"demonstrate":[100],"overall":[101],"improved":[102],"cancer-specific":[103],"MPVNN":[108,122],"over":[109],"other":[110],"similar-sized":[111],"NN":[112],"standard":[114],"methods.":[117],"show":[119],"that":[120,140],"trained":[121],"architecture":[123],"interpretation,":[124],"which":[125],"points":[126],"to":[127],"smaller":[128],"sets":[129],"genes":[131],"connected":[132],"by":[133],"within":[136],"types,":[149],"reliable.":[151],"AVAILABILITY":[152],"AND":[153],"IMPLEMENTATION:":[154],"The":[155],"code":[158],"available":[160,168],"at":[161,169],"https://github.com/gourabghoshroy/MPVNN.":[162],"SUPPLEMENTARY":[163],"INFORMATION:":[164],"Supplementary":[165],"Bioinformatics":[170],"online.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
