{"id":"https://openalex.org/W4405022389","doi":"https://doi.org/10.26599/bdma.2024.9020043","title":"Multiplex Networks and Pan-Cancer Multiomics-Based Driver Gene Identification Using Graph Neural Networks","display_name":"Multiplex Networks and Pan-Cancer Multiomics-Based Driver Gene Identification Using Graph Neural Networks","publication_year":2024,"publication_date":"2024-12-01","ids":{"openalex":"https://openalex.org/W4405022389","doi":"https://doi.org/10.26599/bdma.2024.9020043"},"language":"en","primary_location":{"id":"doi:10.26599/bdma.2024.9020043","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020043","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://doi.org/10.26599/bdma.2024.9020043","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100687807","display_name":"Xingyi Li","orcid":"https://orcid.org/0000-0002-6004-4174"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xingyi Li","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100638184","display_name":"Junming Li","orcid":"https://orcid.org/0000-0003-1409-3634"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junming Li","raw_affiliation_strings":["School of Software, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100550950","display_name":"Jun Hao","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Hao","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088826157","display_name":"Xingyu Liao","orcid":"https://orcid.org/0000-0002-0061-1317"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingyu Liao","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University,Changsha,China,410083","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University,Xi&#x0027;an,China,710072","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100687807"],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":null,"apc_paid":null,"fwci":2.5751,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.90343388,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"7","issue":"4","first_page":"1262","last_page":"1272"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9976000189781189,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9323999881744385,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6489933729171753},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6113042831420898},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5999565124511719},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5548904538154602},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5301975607872009},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5215863585472107},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5166031122207642},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.47847434878349304},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43920373916625977},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4338280260562897},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23817157745361328},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21286123991012573},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.16010606288909912}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6489933729171753},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6113042831420898},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5999565124511719},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5548904538154602},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5301975607872009},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5215863585472107},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5166031122207642},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.47847434878349304},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43920373916625977},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4338280260562897},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23817157745361328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21286123991012573},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.16010606288909912},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.26599/bdma.2024.9020043","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020043","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:cdf29296fca5490cb7271fcfe0e78f28","is_oa":false,"landing_page_url":"https://doaj.org/article/cdf29296fca5490cb7271fcfe0e78f28","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Big Data Mining and Analytics, Vol 7, Iss 4, Pp 1262-1272 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.26599/bdma.2024.9020043","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2024.9020043","pdf_url":null,"source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6401715041","display_name":null,"funder_award_id":"62202383","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G890272252","display_name":null,"funder_award_id":"2022YFD1801200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1566129332","https://openalex.org/W2010707723","https://openalex.org/W2079561996","https://openalex.org/W2092741708","https://openalex.org/W2100625056","https://openalex.org/W2103017472","https://openalex.org/W2148266291","https://openalex.org/W2154851992","https://openalex.org/W2157658519","https://openalex.org/W2158485828","https://openalex.org/W2162151166","https://openalex.org/W2166898290","https://openalex.org/W2295598076","https://openalex.org/W2509717357","https://openalex.org/W2522417827","https://openalex.org/W2522911430","https://openalex.org/W2904929499","https://openalex.org/W2915583118","https://openalex.org/W2949066452","https://openalex.org/W2951560185","https://openalex.org/W2951934944","https://openalex.org/W2976952765","https://openalex.org/W2997686727","https://openalex.org/W2998119497","https://openalex.org/W2998647770","https://openalex.org/W3014947099","https://openalex.org/W3031889339","https://openalex.org/W3101369110","https://openalex.org/W3156270925","https://openalex.org/W3198168376","https://openalex.org/W3206417123","https://openalex.org/W3210378911","https://openalex.org/W4211089684","https://openalex.org/W4212844381","https://openalex.org/W4243979784","https://openalex.org/W4283031272","https://openalex.org/W4293516388","https://openalex.org/W4294216483","https://openalex.org/W4295885518","https://openalex.org/W4315865919","https://openalex.org/W4377000536","https://openalex.org/W4379469027","https://openalex.org/W4391033917","https://openalex.org/W4392607741","https://openalex.org/W4394879987","https://openalex.org/W6726873649","https://openalex.org/W6745537798","https://openalex.org/W6751494907"],"related_works":["https://openalex.org/W3006199032","https://openalex.org/W1963826946","https://openalex.org/W2087421209","https://openalex.org/W4375867731","https://openalex.org/W2547948671","https://openalex.org/W4281783318","https://openalex.org/W2023853334","https://openalex.org/W2001010891","https://openalex.org/W2565428513","https://openalex.org/W3135623036"],"abstract_inverted_index":{"Identifying":[0],"cancer":[1,13,108],"driver":[2,70,109],"genes":[3],"has":[4,144,168],"paramount":[5],"significance":[6],"in":[7,69,175,183],"elucidating":[8],"the":[9,31,43,58,74,120,124,148,151,158,161,169],"intricate":[10,188],"mechanisms":[11],"underlying":[12],"development,":[14],"progression,":[15],"and":[16,22,60,93,123,134,157,178],"therapeutic":[17],"interventions.":[18],"Abundant":[19],"omics":[20],"data":[21,96],"interactome":[23],"networks":[24,92,100],"provided":[25],"by":[26,147],"numerous":[27],"extensive":[28],"databases":[29],"enable":[30],"application":[32],"of":[33,62,76,132,142,191],"graph":[34,98],"deep":[35,44,85],"learning":[36,45,86,117],"techniques":[37],"that":[38],"incorporate":[39],"network":[40],"structures":[41],"into":[42],"framework.":[46],"However,":[47],"most":[48],"existing":[49],"models":[50],"primarily":[51],"focus":[52],"on":[53,119],"individual":[54],"network,":[55],"inevitably":[56],"neglecting":[57],"incompleteness":[59],"noise":[61],"interactions.":[63],"Moreover,":[64],"samples":[65,136],"with":[66,102],"imbalanced":[67],"classes":[68],"gene":[71,115],"identification":[72],"hamper":[73],"performance":[75],"models.":[77],"To":[78],"address":[79],"this,":[80],"we":[81],"propose":[82],"a":[83],"novel":[84],"framework":[87],"MMGN,":[88],"which":[89,111],"integrates":[90],"multiplex":[91],"pan-cancer":[94],"multiomics":[95],"using":[97],"neural":[99],"combined":[101],"negative":[103,135],"sample":[104],"inference":[105],"to":[106,171],"discover":[107],"genes,":[110],"not":[112],"only":[113],"enhances":[114],"feature":[116],"based":[118],"mutual":[121],"information":[122],"consensus":[125],"regularizer,":[126],"but":[127],"also":[128],"achieves":[129],"balanced":[130],"class":[131],"positive":[133],"for":[137,186],"model":[138],"training.":[139],"The":[140],"reliability":[141],"MMGN":[143,167,192],"been":[145],"verified":[146],"Area":[149,159],"Under":[150,160],"Receiver":[152],"Operating":[153],"Characteristic":[154],"curves":[155],"(AUROC)":[156],"Precision-Recall":[162],"Curves":[163],"(AUPRC).":[164],"We":[165],"believe":[166],"potential":[170],"provide":[172],"new":[173],"prospects":[174],"precision":[176],"oncology":[177],"may":[179],"find":[180],"broader":[181],"applications":[182],"predicting":[184],"biomarkers":[185],"other":[187],"diseases.":[189],"Implementations":[190],"can":[193],"be":[194],"found":[195],"at":[196],"https://github.com/xingyili/MMGN.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-15T08:27:34.491423","created_date":"2025-10-10T00:00:00"}
