{"id":"https://openalex.org/W7126028250","doi":"https://doi.org/10.1109/bibm66473.2025.11356471","title":"Predicting Gene Regulatory Relationship in Cancer Using LLM and Graph Neural Network from Known Regulations","display_name":"Predicting Gene Regulatory Relationship in Cancer Using LLM and Graph Neural Network from Known Regulations","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126028250","doi":"https://doi.org/10.1109/bibm66473.2025.11356471"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356471","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5102771953","display_name":"Yanran Liu","orcid":"https://orcid.org/0000-0003-0062-4473"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanran Liu","raw_affiliation_strings":["City University of Hong Kong,Department of Information Systems,Kowloon, Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Information Systems,Kowloon, Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124277225","display_name":"Dian Meng","orcid":null},"institutions":[{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Dian Meng","raw_affiliation_strings":["Yong Loo Lin School of Medicine, National University of Singapore,Department of Biomedical Informatics,Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yong Loo Lin School of Medicine, National University of Singapore,Department of Biomedical Informatics,Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021886812","display_name":"Xinlei Huang","orcid":"https://orcid.org/0009-0009-7183-9237"},"institutions":[{"id":"https://openalex.org/I2799850029","display_name":"Dongguan University of Technology","ror":"https://ror.org/01m8p7q42","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinlei Huang","raw_affiliation_strings":["School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China","institution_ids":["https://openalex.org/I2799850029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029275670","display_name":"Yidi Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I6469544","display_name":"City University of Macau","ror":"https://ror.org/04gpd4q15","country_code":"MO","type":"education","lineage":["https://openalex.org/I6469544"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Yidi Wang","raw_affiliation_strings":["University of Macau,State Key Laboratory of Internet of Things for Smart City,Department of Computer and Information Science,Macao,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Macau,State Key Laboratory of Internet of Things for Smart City,Department of Computer and Information Science,Macao,China","institution_ids":["https://openalex.org/I204512498","https://openalex.org/I6469544"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124279271","display_name":"Yijun Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I2799850029","display_name":"Dongguan University of Technology","ror":"https://ror.org/01m8p7q42","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yijun Zhou","raw_affiliation_strings":["School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China","institution_ids":["https://openalex.org/I2799850029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124274662","display_name":"Shiwei Ruan","orcid":null},"institutions":[{"id":"https://openalex.org/I2799850029","display_name":"Dongguan University of Technology","ror":"https://ror.org/01m8p7q42","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Ruan","raw_affiliation_strings":["School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China","institution_ids":["https://openalex.org/I2799850029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124196183","display_name":"Yi Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I2799850029","display_name":"Dongguan University of Technology","ror":"https://ror.org/01m8p7q42","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhong","raw_affiliation_strings":["School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China","institution_ids":["https://openalex.org/I2799850029"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124013640","display_name":"Yinghua Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210122949","display_name":"Dongguan People\u2019s Hospital","ror":"https://ror.org/022s5gm85","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210122949"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yinghua Chen","raw_affiliation_strings":["Dongguan People&#x0027;s Hospital Biobank, The Tenth Affiliated Hospital of Southern Medical University,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dongguan People&#x0027;s Hospital Biobank, The Tenth Affiliated Hospital of Southern Medical University,Dongguan,China","institution_ids":["https://openalex.org/I4210122949"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101934268","display_name":"Rui Luo","orcid":"https://orcid.org/0000-0003-0711-8039"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Rui Luo","raw_affiliation_strings":["City University of Hong Kong,Department of Systems Engineering,Kowloon, Hong Kong,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"City University of Hong Kong,Department of Systems Engineering,Kowloon, Hong Kong,China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035816463","display_name":"Xubin Zheng","orcid":"https://orcid.org/0000-0003-2322-857X"},"institutions":[{"id":"https://openalex.org/I2799850029","display_name":"Dongguan University of Technology","ror":"https://ror.org/01m8p7q42","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xubin Zheng","raw_affiliation_strings":["School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Great Bay University,Guangdong Provincial Key Laboratory of Mathematical and Neural Dynamical Systems, Dongguan Key Laboratory for Intelligence and Information Technology,Dongguan,China","institution_ids":["https://openalex.org/I2799850029"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1775","last_page":"1778"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.8521999716758728,"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":0.8521999716758728,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.027300000190734863,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.026799999177455902,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7190999984741211},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5889999866485596},{"id":"https://openalex.org/keywords/regulator-gene","display_name":"Regulator gene","score":0.5333999991416931},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4578000009059906},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4480000138282776},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.4397999942302704},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.4284999966621399},{"id":"https://openalex.org/keywords/directed-graph","display_name":"Directed graph","score":0.4133000075817108}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7190999984741211},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5889999866485596},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5511000156402588},{"id":"https://openalex.org/C33498276","wikidata":"https://www.wikidata.org/wiki/Q2138797","display_name":"Regulator gene","level":4,"score":0.5333999991416931},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4844000041484833},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4578000009059906},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4480000138282776},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4397999942302704},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.4284999966621399},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.4133000075817108},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.365200012922287},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.36010000109672546},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34869998693466187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3467000126838684},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3424000144004822},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.33809998631477356},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3197000026702881},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3084999918937683},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.3050999939441681},{"id":"https://openalex.org/C74197172","wikidata":"https://www.wikidata.org/wiki/Q1195339","display_name":"Directed acyclic graph","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.27379998564720154},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.25780001282691956},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2542000114917755},{"id":"https://openalex.org/C2991772755","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Gene interaction","level":3,"score":0.2526000142097473},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.2502000033855438}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356471","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.40478721261024475}],"awards":[{"id":"https://openalex.org/G2182508837","display_name":null,"funder_award_id":"32300554,62176164","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1979104937","https://openalex.org/W2062029454","https://openalex.org/W2151296343","https://openalex.org/W2911489562","https://openalex.org/W2911875851","https://openalex.org/W3021747854","https://openalex.org/W3152893301","https://openalex.org/W3175507592","https://openalex.org/W3205331816","https://openalex.org/W4281626913","https://openalex.org/W4322730846","https://openalex.org/W4382239112","https://openalex.org/W4403598089","https://openalex.org/W4406781476","https://openalex.org/W4409369229"],"related_works":[],"abstract_inverted_index":{"Predicting":[0],"gene":[1,48,66,84,112,160,173],"regulatory":[2,23,49,67,85,116,161],"relationship":[3,68],"is":[4],"crucial":[5],"to":[6,80],"reveal":[7],"cancer":[8],"mechanism":[9],"and":[10,25,63,100,122,133,141],"develop":[11],"targeted":[12],"therapies.":[13],"However,":[14],"current":[15],"computational":[16],"methods":[17],"typically":[18],"estimate":[19],"gene-gene":[20],"associations":[21],"without":[22],"directions":[24],"only":[26],"based":[27,109],"on":[28,110],"statistical":[29],"significance,":[30],"often":[31],"lacking":[32],"accuracy":[33,156],"after":[34],"validation":[35],"by":[36,88,102],"biological":[37,89],"experiments.":[38],"Therefore,":[39],"we":[40,77],"introduce":[41],"a":[42,94,105],"pipeline":[43,127,146],"named":[44],"LiGRNet":[45],"that":[46],"constructs":[47],"networks":[50,74],"as":[51],"signed":[52,71,95],"directed":[53,96],"graphs":[54],"using":[55],"large":[56],"language":[57],"models":[58],"(LLMs)":[59],"from":[60],"the":[61,82,171],"literature":[62],"predicts":[64],"potential":[65,115],"with":[69,104,120],"magnetic":[70],"graph":[72,97],"neural":[73],"(MSGNNs).":[75],"First,":[76],"teach":[78],"LLM":[79],"extract":[81],"known":[83],"relationships":[86,117],"proved":[87],"experiments":[90],"through":[91],"prompt.":[92],"Then,":[93],"was":[98],"constructed":[99],"learnt":[101],"MSGNN":[103],"link":[106],"prediction":[107],"framework":[108],"complex-valued":[111],"embeddings.":[113],"The":[114,145],"were":[118],"predicted":[119,172],"direction":[121],"sign.":[123],"We":[124],"apply":[125],"our":[126],"in":[128,157,175],"colorectal":[129,134],"cancer,":[130,132],"liver":[131,135],"metastasis":[136],"including":[137],"<tex":[138,148],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[139,149],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$11,000,19,000$</tex>,":[140],"1,300":[142],"literature,":[143],"respectively.":[144],"achieve":[147],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">$84.5":[150],"\\%,":[151,153],"80.7":[152],"93.3":[154],"\\%$</tex>":[155],"predicting":[158],"unknown":[159],"relationship.":[162],"External":[163],"cell":[164],"line":[165],"data":[166],"also":[167],"provide":[168],"evidence":[169],"for":[170],"regulation":[174],"these":[176],"cancers.":[177]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2026-01-30T00:00:00"}