{"id":"https://openalex.org/W4281636170","doi":"https://doi.org/10.1093/bioinformatics/btac345","title":"Deep structure integrative representation of multi-omics data for cancer subtyping","display_name":"Deep structure integrative representation of multi-omics data for cancer subtyping","publication_year":2022,"publication_date":"2022-05-26","ids":{"openalex":"https://openalex.org/W4281636170","doi":"https://doi.org/10.1093/bioinformatics/btac345","pmid":"https://pubmed.ncbi.nlm.nih.gov/35639657"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac345","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac345","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5021610428","display_name":"Bo Yang","orcid":"https://orcid.org/0000-0001-6200-8727"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CA","CN"],"is_corresponding":true,"raw_author_name":"Bo Yang","raw_affiliation_strings":["Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada","School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China","Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada"],"raw_orcid":"https://orcid.org/0000-0001-6200-8727","affiliations":[{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , Toronto, ON M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China","institution_ids":["https://openalex.org/I27599042"]},{"raw_affiliation_string":"Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada","institution_ids":["https://openalex.org/I185261750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064498084","display_name":"Yan Yang","orcid":"https://orcid.org/0000-0003-3681-0139"},"institutions":[{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Yang","raw_affiliation_strings":["School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Xi\u2019an Polytechnic University , Xi\u2019an, 710048, China","institution_ids":["https://openalex.org/I27599042"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044122736","display_name":"Xueping Su","orcid":null},"institutions":[{"id":"https://openalex.org/I27599042","display_name":"Xi'an Polytechnic University","ror":"https://ror.org/03442p831","country_code":"CN","type":"education","lineage":["https://openalex.org/I27599042"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueping Su","raw_affiliation_strings":["School of Electronics and Information, Xi\u2019an Polytechnic University , Xi\u2019an 710048, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Electronics and Information, Xi\u2019an Polytechnic University , Xi\u2019an 710048, China","institution_ids":["https://openalex.org/I27599042"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5021610428"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I27599042"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0073,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.73792394,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"38","issue":"13","first_page":"3337","last_page":"3342"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7577000260353088,"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":0.7577000260353088,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.060100000351667404,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.04259999841451645,"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/subtyping","display_name":"Subtyping","score":0.8756546974182129},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.62928706407547},{"id":"https://openalex.org/keywords/subspace-topology","display_name":"Subspace topology","score":0.5816693305969238},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.5650273561477661},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5431496500968933},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.474604070186615},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.46071964502334595},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42873597145080566},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4165467619895935},{"id":"https://openalex.org/keywords/nonlinear-dimensionality-reduction","display_name":"Nonlinear dimensionality reduction","score":0.4114955961704254},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39275026321411133},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.39270728826522827},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3020337224006653},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14063012599945068},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.09639260172843933}],"concepts":[{"id":"https://openalex.org/C83852419","wikidata":"https://www.wikidata.org/wiki/Q2713292","display_name":"Subtyping","level":2,"score":0.8756546974182129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.62928706407547},{"id":"https://openalex.org/C32834561","wikidata":"https://www.wikidata.org/wiki/Q660730","display_name":"Subspace topology","level":2,"score":0.5816693305969238},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.5650273561477661},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5431496500968933},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.474604070186615},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.46071964502334595},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42873597145080566},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4165467619895935},{"id":"https://openalex.org/C151876577","wikidata":"https://www.wikidata.org/wiki/Q7049464","display_name":"Nonlinear dimensionality reduction","level":3,"score":0.4114955961704254},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39275026321411133},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39270728826522827},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3020337224006653},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14063012599945068},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.09639260172843933},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac345","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac345","pdf_url":null,"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:35639657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35639657","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.41999998688697815}],"awards":[{"id":"https://openalex.org/G2570735729","display_name":null,"funder_award_id":"61902301","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G708289198","display_name":null,"funder_award_id":"61806159","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1548779692","https://openalex.org/W1593648249","https://openalex.org/W1977556410","https://openalex.org/W1987219048","https://openalex.org/W1991154912","https://openalex.org/W1993962865","https://openalex.org/W2003056152","https://openalex.org/W2008929650","https://openalex.org/W2109363337","https://openalex.org/W2110940238","https://openalex.org/W2132914434","https://openalex.org/W2168517816","https://openalex.org/W2245966294","https://openalex.org/W2321627895","https://openalex.org/W2396849069","https://openalex.org/W2624701078","https://openalex.org/W2626481916","https://openalex.org/W2765654979","https://openalex.org/W2783685429","https://openalex.org/W2792874817","https://openalex.org/W2803273701","https://openalex.org/W2809034148","https://openalex.org/W2884724578","https://openalex.org/W2898401672","https://openalex.org/W2909364225","https://openalex.org/W2913268845","https://openalex.org/W2940629765","https://openalex.org/W2950878899","https://openalex.org/W2954752948","https://openalex.org/W2963165461","https://openalex.org/W2966833448","https://openalex.org/W3003192283","https://openalex.org/W3007910141","https://openalex.org/W3143649444","https://openalex.org/W3148185623","https://openalex.org/W3165527726","https://openalex.org/W3185773261","https://openalex.org/W3186062074","https://openalex.org/W3186475033","https://openalex.org/W3187466590","https://openalex.org/W3208283713","https://openalex.org/W4252676770","https://openalex.org/W6644682428","https://openalex.org/W6652524677","https://openalex.org/W6739094974","https://openalex.org/W6766085377","https://openalex.org/W6802007102"],"related_works":["https://openalex.org/W2396009657","https://openalex.org/W2799110842","https://openalex.org/W3032826521","https://openalex.org/W2391332606","https://openalex.org/W1462775415","https://openalex.org/W1987896487","https://openalex.org/W4229853287","https://openalex.org/W2233322082","https://openalex.org/W2540547653","https://openalex.org/W1875839244"],"abstract_inverted_index":{"MOTIVATION:":[0],"Cancer":[1,8,129],"is":[2,10,43],"a":[3,11,62,104],"heterogeneous":[4],"group":[5],"of":[6,124],"diseases.":[7],"subtyping":[9],"crucial":[12],"and":[13,19,48,80,93,102],"critical":[14],"step":[15],"to":[16,29,45,53],"diagnosis,":[17],"prognosis":[18],"treatment.":[20],"Since":[21],"high-throughput":[22],"sequencing":[23],"technologies":[24],"provide":[25],"an":[26,38],"unprecedented":[27],"opportunity":[28],"rapidly":[30],"collect":[31],"multi-omics":[32,51,82,100],"data":[33,52,101,126,153],"for":[34,73],"the":[35,87,142],"same":[36],"individuals,":[37],"urgent":[39],"need":[40],"in":[41,90,96,117],"current":[42],"how":[44],"effectively":[46],"represent":[47],"integrate":[49],"these":[50],"achieve":[54],"clinically":[55],"meaningful":[56],"cancer":[57,74],"subtyping.":[58],"RESULTS:":[59],"We":[60],"propose":[61],"novel":[63],"deep":[64,110],"learning":[65],"model,":[66],"called":[67],"Deep":[68],"Structure":[69],"Integrative":[70],"Representation":[71],"(DSIR),":[72],"subtypes":[75],"dentification":[76],"by":[77,108],"integrating":[78],"representation":[79],"clustering":[81],"data.":[83],"DSIR":[84,136],"simultaneously":[85],"captures":[86],"global":[88],"structures":[89,95],"sparse":[91],"subspace":[92,98],"local":[94],"manifold":[97],"from":[99,127],"constructs":[103],"consensus":[105],"similarity":[106],"matrix":[107],"utilizing":[109],"neural":[111],"networks.":[112],"Extensive":[113],"tests":[114],"are":[115,154],"performed":[116],"12":[118],"different":[119],"cancers":[120],"on":[121],"three":[122],"levels":[123],"omics":[125],"The":[128,132],"Genome":[130],"Atlas.":[131],"results":[133],"demonstrate":[134],"that":[135],"obtains":[137],"more":[138],"significant":[139],"performances":[140],"than":[141],"state-of-the-art":[143],"integrative":[144],"methods.":[145],"AVAILABILITY":[146],"AND":[147],"IMPLEMENTATION:":[148],"https://github.com/Polytech-bioinf/Deep-structure-integrative-representation.git.":[149],"SUPPLEMENTARY":[150],"INFORMATION:":[151],"Supplementary":[152],"available":[155],"at":[156],"Bioinformatics":[157],"online.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}