{"id":"https://openalex.org/W3200213084","doi":"https://doi.org/10.1109/tcbb.2021.3114281","title":"Deepgmd: A Graph-Neural-Network-Based Method to Detect Gene Regulator Module","display_name":"Deepgmd: A Graph-Neural-Network-Based Method to Detect Gene Regulator Module","publication_year":2021,"publication_date":"2021-09-21","ids":{"openalex":"https://openalex.org/W3200213084","doi":"https://doi.org/10.1109/tcbb.2021.3114281","mag":"3200213084","pmid":"https://pubmed.ncbi.nlm.nih.gov/34546926"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3114281","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3114281","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5100740091","display_name":"Ye Xiao","orcid":"https://orcid.org/0000-0003-2234-9185"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiao Ye","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101866995","display_name":"Yulin Wu","orcid":"https://orcid.org/0000-0001-7952-7136"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yulin Wu","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081558181","display_name":"Jiangsheng Pi","orcid":null},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiangsheng Pi","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100339336","display_name":"Hong Li","orcid":"https://orcid.org/0000-0001-5731-5335"},"institutions":[{"id":"https://openalex.org/I4210096013","display_name":"Shanghai Institute of Nutrition and Health","ror":"https://ror.org/00rytkh49","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210096013"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong Li","raw_affiliation_strings":["Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210096013","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115587783","display_name":"\u0411\u043e \u041b\u044e","orcid":"https://orcid.org/0000-0003-3045-628X"},"institutions":[{"id":"https://openalex.org/I4210161462","display_name":"Heilongjiang Institute of Technology","ror":"https://ror.org/05x0m9n95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210161462"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China"],"affiliations":[{"raw_affiliation_string":"Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China","institution_ids":["https://openalex.org/I4210161462","https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392447","display_name":"Yadong Wang","orcid":"https://orcid.org/0000-0001-6500-6217"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yadong Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100363203","display_name":"Junyi Li","orcid":"https://orcid.org/0000-0001-8045-5264"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I158809036","display_name":"Shenzhen Institute of Information Technology","ror":"https://ror.org/03wrf9427","country_code":"CN","type":"education","lineage":["https://openalex.org/I158809036"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyi Li","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100740091"],"corresponding_institution_ids":["https://openalex.org/I158809036","https://openalex.org/I204983213"],"apc_list":null,"apc_paid":null,"fwci":0.3218,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.56195849,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"19","issue":"6","first_page":"3366","last_page":"3373"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9986000061035156,"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":0.9983999729156494,"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/computer-science","display_name":"Computer science","score":0.7083057761192322},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5409466028213501},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5297302603721619},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5170077085494995},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4816707372665405},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4425346255302429},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39312151074409485},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3435133397579193},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33205294609069824}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7083057761192322},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5409466028213501},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5297302603721619},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5170077085494995},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4816707372665405},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4425346255302429},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39312151074409485},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3435133397579193},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33205294609069824},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3114281","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3114281","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34546926","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34546926","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1613448136","https://openalex.org/W1644724366","https://openalex.org/W1822745879","https://openalex.org/W1836465849","https://openalex.org/W1888005072","https://openalex.org/W1904365287","https://openalex.org/W1976208596","https://openalex.org/W1977556410","https://openalex.org/W2001554877","https://openalex.org/W2012921801","https://openalex.org/W2020547732","https://openalex.org/W2048971937","https://openalex.org/W2060705109","https://openalex.org/W2063280781","https://openalex.org/W2072367332","https://openalex.org/W2109384743","https://openalex.org/W2121947440","https://openalex.org/W2139997707","https://openalex.org/W2141224535","https://openalex.org/W2144544802","https://openalex.org/W2150926065","https://openalex.org/W2154851992","https://openalex.org/W2169387435","https://openalex.org/W2170984819","https://openalex.org/W2176431433","https://openalex.org/W2177432730","https://openalex.org/W2393319904","https://openalex.org/W2577326063","https://openalex.org/W2788730644","https://openalex.org/W2791975541","https://openalex.org/W2900007277","https://openalex.org/W2912917402","https://openalex.org/W2951271819","https://openalex.org/W2962756421","https://openalex.org/W2964015378","https://openalex.org/W2970771711","https://openalex.org/W2972530906","https://openalex.org/W2999729612","https://openalex.org/W3102647957","https://openalex.org/W3102714941","https://openalex.org/W3104097132","https://openalex.org/W3126033509","https://openalex.org/W4288102469","https://openalex.org/W4294558607","https://openalex.org/W6636447677","https://openalex.org/W6638667902","https://openalex.org/W6640036494","https://openalex.org/W6726873649","https://openalex.org/W6732195518","https://openalex.org/W6738964360","https://openalex.org/W6760423706"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2378076731","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W4286888643","https://openalex.org/W3210795196","https://openalex.org/W2071701083","https://openalex.org/W2383687187","https://openalex.org/W2156434174"],"abstract_inverted_index":{"Regulatory":[0],"module":[1,34],"mining":[2],"methods":[3],"divide":[4],"genes":[5],"into":[6,24,36],"multiple":[7],"gene":[8,20,25,33],"subgroups":[9],"and":[10,46,85,101,155,160,167],"explore":[11],"potential":[12],"biological":[13],"mechanisms":[14],"from":[15,146],"omics":[16],"data.":[17],"By":[18,96],"transforming":[19],"expression":[21],"profile":[22],"data":[23],"co-expression":[26],"network,":[27],"we":[28,74,108,141],"transform":[29],"the":[30,37,44,48,66,79,82,98,102,106,111,114,139,147,151,157],"task":[31],"of":[32,39,78,81,113],"detection":[35],"problem":[38],"finding":[40],"community":[41],"structure":[42],"in":[43],"graph,":[45],"introduce":[47],"latest":[49],"network":[50,55],"representation":[51],"learning":[52],"method-graph":[53],"neural":[54],"to":[56,62,70,120,163],"optimize":[57],"this":[58,118],"problem.":[59],"In":[60,138],"order":[61],"systematically":[63],"evaluate":[64,110],"whether":[65,92],"algorithm":[67,123,152],"allows":[68],"overlap":[69,93],"affect":[71],"such":[72],"problems,":[73],"make":[75],"two":[76],"variants":[77],"output":[80],"algorithm,":[83,107],"Deepgmd_cluster":[84],"Deepgmd.":[86],"The":[87,129],"difference":[88],"between":[89],"them":[90],"is":[91,94],"allowed.":[95],"comparing":[97],"known":[99],"modules":[100,103,145,148],"generated":[104],"by":[105,150],"can":[109],"quality":[112],"algorithm.":[115],"We":[116],"use":[117,156],"method":[119,134],"compare":[121],"our":[122,133],"with":[124],"some":[125,143],"current":[126],"mainstream":[127],"methods.":[128],"results":[130],"show":[131],"that":[132],"has":[135],"greater":[136],"advantages.":[137],"end,":[140],"analyze":[142],"typical":[144],"found":[149],"for":[153],"visualization,":[154],"GO":[158],"database":[159,162],"KEGG":[161],"perform":[164],"enrichment":[165],"analysis":[166,169],"pathway":[168],"on":[170],"these":[171],"modules.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
