{"id":"https://openalex.org/W2953661734","doi":"https://doi.org/10.1109/access.2019.2921019","title":"CoDP: Cooperative Driver Pathways Discovery With Matrix Factorization and Tri-Random Walk","display_name":"CoDP: Cooperative Driver Pathways Discovery With Matrix Factorization and Tri-Random Walk","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2953661734","doi":"https://doi.org/10.1109/access.2019.2921019","mag":"2953661734"},"language":"en","primary_location":{"id":"doi:10.1109/access.2019.2921019","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2921019","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08731889.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08731889.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101501447","display_name":"Ziying Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ziying Yang","raw_affiliation_strings":["College of Computer and Information Sciences, Southwest University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"College of Computer and Information Sciences, Southwest University, Chongqing, China","institution_ids":["https://openalex.org/I142108993"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027082940","display_name":"Guoxian Yu","orcid":"https://orcid.org/0000-0002-1667-6705"},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guoxian Yu","raw_affiliation_strings":["College of Computer and Information Sciences, Southwest University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"College of Computer and Information Sciences, Southwest University, Chongqing, China","institution_ids":["https://openalex.org/I142108993"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079800756","display_name":"Maozu Guo","orcid":"https://orcid.org/0000-0001-6228-6276"},"institutions":[{"id":"https://openalex.org/I62853816","display_name":"Beijing University of Civil Engineering and Architecture","ror":"https://ror.org/02yj0p855","country_code":"CN","type":"education","lineage":["https://openalex.org/I62853816"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Maozu Guo","raw_affiliation_strings":["College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China"],"affiliations":[{"raw_affiliation_string":"College of Electrical and Information Engineering, Beijing University of Civil Engineering and Architecture, Beijing, China","institution_ids":["https://openalex.org/I62853816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100384767","display_name":"Jun Wang","orcid":"https://orcid.org/0000-0002-5890-0365"},"institutions":[{"id":"https://openalex.org/I142108993","display_name":"Southwest University","ror":"https://ror.org/01kj4z117","country_code":"CN","type":"education","lineage":["https://openalex.org/I142108993"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Wang","raw_affiliation_strings":["College of Computer and Information Sciences, Southwest University, Chongqing, China"],"affiliations":[{"raw_affiliation_string":"College of Computer and Information Sciences, Southwest University, Chongqing, China","institution_ids":["https://openalex.org/I142108993"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101501447"],"corresponding_institution_ids":["https://openalex.org/I142108993"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.3436,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.59335954,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"7","issue":null,"first_page":"77738","last_page":"77749"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":0.9998000264167786,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9990000128746033,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9912999868392944,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.6132892370223999},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5961707234382629},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5615726709365845},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.46574318408966064},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4618943929672241},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.44426995515823364},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43363386392593384},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.4321478605270386},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4174688458442688},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4156123399734497},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.4147428274154663},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24208155274391174}],"concepts":[{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.6132892370223999},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5961707234382629},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5615726709365845},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.46574318408966064},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4618943929672241},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.44426995515823364},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43363386392593384},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.4321478605270386},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4174688458442688},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4156123399734497},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.4147428274154663},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24208155274391174},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2019.2921019","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2921019","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08731889.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:1a5172e26d714d0f8ad8e33af2fa3a35","is_oa":true,"landing_page_url":"https://doaj.org/article/1a5172e26d714d0f8ad8e33af2fa3a35","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 7, Pp 77738-77749 (2019)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2019.2921019","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2921019","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08731889.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5099999904632568}],"awards":[{"id":"https://openalex.org/G1023919524","display_name":null,"funder_award_id":", Grant","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3605984960","display_name":null,"funder_award_id":"XDJK2019B024","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4765083334","display_name":null,"funder_award_id":"618732","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5035564973","display_name":null,"funder_award_id":"XDJK2019D019","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G5564147583","display_name":null,"funder_award_id":"61872300","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6156912111","display_name":null,"funder_award_id":"2019B02","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G659245102","display_name":null,"funder_award_id":"61873214","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7148930410","display_name":null,"funder_award_id":"61871020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8892394904","display_name":null,"funder_award_id":"CQ CSTC","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8951484681","display_name":null,"funder_award_id":"Grant","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321550","display_name":"Chongqing Science and Technology Commission","ror":"https://ror.org/05w9erc61"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953661734.pdf","grobid_xml":"https://content.openalex.org/works/W2953661734.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W40540053","https://openalex.org/W101504470","https://openalex.org/W1501194546","https://openalex.org/W1902027874","https://openalex.org/W1971106435","https://openalex.org/W1975131084","https://openalex.org/W1980080677","https://openalex.org/W1984708567","https://openalex.org/W1998777645","https://openalex.org/W2000425266","https://openalex.org/W2000469371","https://openalex.org/W2003553411","https://openalex.org/W2009105270","https://openalex.org/W2009228902","https://openalex.org/W2014510815","https://openalex.org/W2015284016","https://openalex.org/W2023568503","https://openalex.org/W2041744082","https://openalex.org/W2042844479","https://openalex.org/W2043021563","https://openalex.org/W2044433401","https://openalex.org/W2045156863","https://openalex.org/W2048902349","https://openalex.org/W2050869737","https://openalex.org/W2055532123","https://openalex.org/W2059738518","https://openalex.org/W2064690543","https://openalex.org/W2070413419","https://openalex.org/W2088891952","https://openalex.org/W2089772680","https://openalex.org/W2095319945","https://openalex.org/W2096766502","https://openalex.org/W2100582962","https://openalex.org/W2102111081","https://openalex.org/W2102406841","https://openalex.org/W2105325784","https://openalex.org/W2109761160","https://openalex.org/W2113895678","https://openalex.org/W2114830914","https://openalex.org/W2116298046","https://openalex.org/W2116798163","https://openalex.org/W2117968640","https://openalex.org/W2121443461","https://openalex.org/W2121906867","https://openalex.org/W2122769974","https://openalex.org/W2122778851","https://openalex.org/W2123696077","https://openalex.org/W2125536613","https://openalex.org/W2125984976","https://openalex.org/W2126172213","https://openalex.org/W2126426563","https://openalex.org/W2136787567","https://openalex.org/W2140141449","https://openalex.org/W2141222510","https://openalex.org/W2147754310","https://openalex.org/W2152154355","https://openalex.org/W2152176732","https://openalex.org/W2161145604","https://openalex.org/W2163798887","https://openalex.org/W2164298117","https://openalex.org/W2165516140","https://openalex.org/W2313125707","https://openalex.org/W2568642260","https://openalex.org/W2611492308","https://openalex.org/W2743167137","https://openalex.org/W2744377419","https://openalex.org/W2774736917","https://openalex.org/W2915975108","https://openalex.org/W4294216483","https://openalex.org/W6601662664","https://openalex.org/W6630012955"],"related_works":["https://openalex.org/W2737319532","https://openalex.org/W2382997850","https://openalex.org/W4392896533","https://openalex.org/W2062945643","https://openalex.org/W2390968135","https://openalex.org/W2050308539","https://openalex.org/W3151405604","https://openalex.org/W3144241576","https://openalex.org/W2113725788","https://openalex.org/W1988174701"],"abstract_inverted_index":{"Discovering":[0],"driver":[1,54,173,236,242],"pathways":[2,36,218,243],"is":[3],"becoming":[4],"a":[5,46,99,145],"key":[6,222],"step":[7],"to":[8,16,51,63,105,107,126,148],"uncover":[9],"the":[10,25,79,120,123,150,164,168,185,204,213],"molecular":[11],"mechanism":[12],"underlying":[13],"cancer":[14,21,94,180],"and":[15,70,84,89,109,113,128,133,135,139,162,195,206,225,240],"explore":[17],"precise":[18],"treatments":[19],"for":[20,155],"patients.":[22],"Most":[23],"of":[24,76,82,93,122,152,227,251],"previous":[26],"works":[27],"focus":[28],"on":[29,119,159,177],"identifying":[30],"individual":[31],"pathways.":[32,55,140,174],"In":[33,41],"practice,":[34],"multiple":[35],"often":[37],"cooperatively":[38,189],"trigger":[39],"cancer.":[40,214,230],"this":[42],"study,":[43],"we":[44],"propose":[45],"new":[47],"approach":[48],"called":[49],"CoDP":[50,56,97,143,231,252],"discover":[52],"cooperative":[53,172,217,241],"firstly":[57],"uses":[58,116],"integrative":[59],"nonnegative":[60],"matrix":[61],"factorization":[62],"identify":[64],"cancer-related":[65],"comodules":[66],"(composed":[67],"with":[68,102,167,203,212,221],"genes":[69,108,132,192,237],"miRNAs)":[71],"by":[72],"fusing":[73],"four":[74],"types":[75],"data,":[77,88],"including":[78],"expression":[80],"profiles":[81],"miRNAs":[83,110,138,188,196],"genes,":[85,191],"miRNA-gene":[86],"interaction":[87,91],"gene-gene":[90],"data":[92],"samples.":[95],"Next,":[96],"builds":[98],"hybrid":[100,124],"network":[101,125],"nodes":[103],"corresponding":[104],"pathways,":[106,134],"in":[111,184],"comodules,":[112,187],"it":[114],"further":[115],"tri-random":[117],"walk":[118],"subnetworks":[121],"update":[127],"replenish":[129],"associations":[130,211],"between":[131,137],"those":[136],"After":[141],"that,":[142],"introduces":[144],"quantitative":[146],"function":[147],"quantify":[149],"coverage":[151,170],"pathway":[153,165],"sets":[154],"each":[156],"comodule":[157],"based":[158],"replenished":[160],"associations,":[161],"identifies":[163],"set":[166],"highest":[169],"as":[171],"Empirical":[175],"study":[176],"ovarian":[178,228],"(liver)":[179,229],"datasets":[181],"shows":[182],"that":[183],"identified":[186,216],"regulate":[190],"(i.e.,":[193,197],"TP53)":[194],"mir-10b)":[198],"are":[199,219,253],"statistical":[200],"significantly":[201],"associated":[202],"cancer,":[205],"others":[207],"may":[208],"have":[209],"potential":[210],"The":[215,249],"involved":[220],"biological":[223],"processes":[224],"carcinogenesis":[226],"also":[232],"uncovers":[233],"more":[234],"known":[235],"(over":[238,244],"300%)":[239],"200%)":[245],"than":[246],"existing":[247],"methods.":[248],"codes":[250],"available":[254],"at":[255],"http://mlda.swu.edu.cn/codes.php?name=CoDP.":[256]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
