{"id":"https://openalex.org/W4379117479","doi":"https://doi.org/10.1109/tcbb.2023.3282212","title":"CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data","display_name":"CNNGRN: A Convolutional Neural Network-Based Method for Gene Regulatory Network Inference From Bulk Time-Series Expression Data","publication_year":2023,"publication_date":"2023-06-02","ids":{"openalex":"https://openalex.org/W4379117479","doi":"https://doi.org/10.1109/tcbb.2023.3282212","pmid":"https://pubmed.ncbi.nlm.nih.gov/37267145"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3282212","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3282212","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/A5068590943","display_name":"Zhen Gao","orcid":"https://orcid.org/0000-0001-7427-6032"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Gao","raw_affiliation_strings":["Anhui Province Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0001-7427-6032","affiliations":[{"raw_affiliation_string":"Anhui Province Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030720334","display_name":"Jin Tang","orcid":"https://orcid.org/0000-0001-8375-3590"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Tang","raw_affiliation_strings":["Anhui Province Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0001-8375-3590","affiliations":[{"raw_affiliation_string":"Anhui Province Key Laboratory of Multimodal Cognitive Computation, School of Computer Science and Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0003-3024-1705","affiliations":[{"raw_affiliation_string":"Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064185915","display_name":"Chun-Hou Zheng","orcid":"https://orcid.org/0000-0002-2695-1926"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["College of Artificial Intelligence, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0002-2695-1926","affiliations":[{"raw_affiliation_string":"College of Artificial Intelligence, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085214222","display_name":"Pi-Jing Wei","orcid":"https://orcid.org/0000-0003-2770-8781"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pi-Jing Wei","raw_affiliation_strings":["Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0003-2770-8781","affiliations":[{"raw_affiliation_string":"Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":null,"apc_paid":null,"fwci":2.1527,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.87491401,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"5","first_page":"2853","last_page":"2861"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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/T10621","display_name":"Gene Regulatory Network Analysis","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9939000010490417,"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":0.9923999905586243,"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":0.7102278470993042},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6744034290313721},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6697496771812439},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6451884508132935},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.6382325887680054},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.636300802230835},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5659976601600647},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5256605744361877},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5036348700523376},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.4587097764015198},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4374655783176422},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.43114301562309265},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32208937406539917},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.23426583409309387},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18846863508224487},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14024695754051208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7102278470993042},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6744034290313721},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6697496771812439},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6451884508132935},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.6382325887680054},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.636300802230835},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5659976601600647},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5256605744361877},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5036348700523376},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.4587097764015198},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4374655783176422},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.43114301562309265},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32208937406539917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.23426583409309387},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18846863508224487},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14024695754051208},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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}],"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":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3282212","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3282212","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:37267145","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37267145","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":[{"display_name":"Partnerships for the goals","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G8602029459","display_name":null,"funder_award_id":"2108085QF267","funder_id":"https://openalex.org/F4320334897","funder_display_name":"Natural Science Foundation of Anhui Province"}],"funders":[{"id":"https://openalex.org/F4320334897","display_name":"Natural Science Foundation of Anhui Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1553008332","https://openalex.org/W1989689639","https://openalex.org/W1993418188","https://openalex.org/W2039747539","https://openalex.org/W2056311436","https://openalex.org/W2063833044","https://openalex.org/W2076513103","https://openalex.org/W2084332810","https://openalex.org/W2103912979","https://openalex.org/W2105129830","https://openalex.org/W2109384743","https://openalex.org/W2117650761","https://openalex.org/W2126345910","https://openalex.org/W2139997707","https://openalex.org/W2140899665","https://openalex.org/W2142836135","https://openalex.org/W2159675211","https://openalex.org/W2160255151","https://openalex.org/W2161922735","https://openalex.org/W2232370058","https://openalex.org/W2274656501","https://openalex.org/W2460716387","https://openalex.org/W2555391902","https://openalex.org/W2770463049","https://openalex.org/W2791183315","https://openalex.org/W2803928488","https://openalex.org/W2891454102","https://openalex.org/W2892035503","https://openalex.org/W2899545492","https://openalex.org/W2901292166","https://openalex.org/W2902700395","https://openalex.org/W2920876032","https://openalex.org/W2949956784","https://openalex.org/W2954716046","https://openalex.org/W2962858109","https://openalex.org/W2964689826","https://openalex.org/W2977435326","https://openalex.org/W2988020351","https://openalex.org/W2998917483","https://openalex.org/W3042307925","https://openalex.org/W3042878854","https://openalex.org/W3093153369","https://openalex.org/W3095716988","https://openalex.org/W3114111133","https://openalex.org/W3120280121","https://openalex.org/W3127245931","https://openalex.org/W3128158089","https://openalex.org/W3128925966","https://openalex.org/W3132547172","https://openalex.org/W3142178348","https://openalex.org/W3159076767","https://openalex.org/W3176710272","https://openalex.org/W3199285124","https://openalex.org/W3217444066","https://openalex.org/W4242577767","https://openalex.org/W4282932623","https://openalex.org/W6718744960"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W2055243143","https://openalex.org/W4321487865","https://openalex.org/W2381031055","https://openalex.org/W2366070815","https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Gene":[0],"regulatory":[1,106],"networks":[2],"(GRNs)":[3],"participate":[4],"in":[5,16,66,195],"many":[6,20],"biological":[7,196],"processes,":[8],"and":[9,110,143,150],"reconstructing":[10],"them":[11],"plays":[12],"an":[13],"important":[14],"role":[15],"systems":[17],"biology.":[18],"Although":[19],"advanced":[21],"methods":[22,53],"have":[23,189],"been":[24,190],"proposed":[25],"for":[26],"GRN":[27,80,117],"reconstruction,":[28],"their":[29],"predictive":[30],"performance":[31,172],"is":[32,40,135],"far":[33],"from":[34,81],"the":[35,56,61,104,111,125,145,162,178],"ideal":[36],"standard,":[37],"so":[38],"it":[39],"urgent":[41],"to":[42,48,137,160,177,192],"design":[43],"a":[44,73,93],"more":[45,94],"effective":[46],"method":[47],"reconstruct":[49],"GRN.":[50,67],"Moreover,":[51,153],"most":[52],"only":[54],"consider":[55],"gene":[57,100],"expression":[58,84,101],"data,":[59],"ignoring":[60],"network":[62,89,112],"structure":[63,113],"information":[64],"contained":[65],"In":[68,132],"this":[69],"study,":[70],"we":[71],"propose":[72],"supervised":[74],"model":[75,130],"named":[76],"CNNGRN,":[77],"which":[78],"infers":[79],"bulk":[82],"time-series":[83],"data":[85,102],"via":[86],"convolutional":[87],"neural":[88],"(CNN)":[90],"model,":[91],"with":[92],"informative":[95],"feature.":[96],"Bulk":[97],"time":[98],"series":[99],"imply":[103],"intricate":[105,139],"associations":[107,147],"between":[108,148],"genes,":[109],"feature":[114,154],"of":[115,141],"ground-truth":[116],"contains":[118],"rich":[119],"neighbor":[120],"information.":[121],"Hence,":[122],"CNNGRN":[123,169,188],"integrates":[124],"above":[126],"two":[127],"features":[128,140],"as":[129],"inputs.":[131],"addition,":[133],"CNN":[134],"adopted":[136],"extract":[138],"genes":[142,184],"infer":[144],"potential":[146],"regulators":[149],"target":[151],"genes.":[152],"importance":[155],"visualization":[156],"experiments":[157],"are":[158],"implemented":[159],"seek":[161],"key":[163],"features.":[164],"Experimental":[165],"results":[166],"show":[167],"that":[168],"achieved":[170],"competitive":[171],"on":[173,187],"benchmark":[174],"datasets":[175],"compared":[176],"state-of-the-art":[179],"computational":[180],"methods.":[181],"Finally,":[182],"hub":[183],"identified":[185],"based":[186],"confirmed":[191],"be":[193],"involved":[194],"processes":[197],"through":[198],"literature.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
