{"id":"https://openalex.org/W4409474031","doi":"https://doi.org/10.1109/jbhi.2025.3561197","title":"Integrating Transformer and Graph Attention Network for circRNA-miRNA Interaction Prediction","display_name":"Integrating Transformer and Graph Attention Network for circRNA-miRNA Interaction Prediction","publication_year":2025,"publication_date":"2025-04-15","ids":{"openalex":"https://openalex.org/W4409474031","doi":"https://doi.org/10.1109/jbhi.2025.3561197","pmid":"https://pubmed.ncbi.nlm.nih.gov/40232907"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3561197","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3561197","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5063624362","display_name":"Mengmeng Wei","orcid":"https://orcid.org/0009-0009-9453-7653"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng-Meng Wei","raw_affiliation_strings":["School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":"https://orcid.org/0009-0009-9453-7653","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436059","display_name":"Lei Wang","orcid":"https://orcid.org/0000-0003-0184-307X"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Wang","raw_affiliation_strings":["School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China"],"raw_orcid":"https://orcid.org/0000-0003-0184-307X","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014724927","display_name":"Bo-Wei Zhao","orcid":"https://orcid.org/0000-0001-8200-6016"},"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"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo-Wei Zhao","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China","College of Computer and Information Science, School of Software, Southwest University, Chongqing, China"],"raw_orcid":"https://orcid.org/0000-0001-8200-6016","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"College of Computer and Information Science, School of Software, Southwest University, Chongqing, China","institution_ids":["https://openalex.org/I142108993"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045680312","display_name":"Xiaorui Su","orcid":"https://orcid.org/0000-0001-5468-6085"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiao-Rui Su","raw_affiliation_strings":["Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China","Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019805735","display_name":"Zhu\u2010Hong You","orcid":"https://orcid.org/0000-0003-1266-2696"},"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"]},{"id":"https://openalex.org/I4210165264","display_name":"Guangxi Academy of Sciences","ror":"https://ror.org/054x1kd82","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210165264"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, China","Guangxi Academy of Science, Nanning, China"],"raw_orcid":"https://orcid.org/0000-0003-1266-2696","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Guangxi Academy of Science, Nanning, China","institution_ids":["https://openalex.org/I4210165264"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100891253","display_name":"De-Shuang Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I4394709157","display_name":"Eastern Institute of Technology, Ningbo","ror":"https://ror.org/036mbz113","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"De-Shuang Huang","raw_affiliation_strings":["Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, China","Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, China"],"raw_orcid":"https://orcid.org/0000-0002-6759-2691","affiliations":[{"raw_affiliation_string":"Ningbo Institute of Digital Twin, Eastern Institute of Technology, Ningbo, China","institution_ids":["https://openalex.org/I4394709157"]},{"raw_affiliation_string":"Eastern Institute for Advanced Study, Eastern Institute of Technology, Ningbo, China","institution_ids":["https://openalex.org/I4394709157"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":18.3741,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.99604504,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"29","issue":"8","first_page":"6105","last_page":"6113"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11765","display_name":"Circular RNAs in diseases","score":0.9860000014305115,"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":0.6654599905014038},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5269414186477661},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4358072578907013},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38238534331321716},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34678709506988525},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.29489827156066895},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1279725730419159}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6654599905014038},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5269414186477661},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4358072578907013},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38238534331321716},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34678709506988525},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.29489827156066895},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1279725730419159},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000079962","descriptor_name":"RNA, Circular","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3561197","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3561197","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40232907","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40232907","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3588239447","display_name":null,"funder_award_id":"61702444","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G369388814","display_name":null,"funder_award_id":"62273284","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4306865477","display_name":null,"funder_award_id":"ZR2022LZL003","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G7911954467","display_name":null,"funder_award_id":"62172355","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"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1888005072","https://openalex.org/W2031593782","https://openalex.org/W2064165694","https://openalex.org/W2143668817","https://openalex.org/W2154851992","https://openalex.org/W2393319904","https://openalex.org/W2605363845","https://openalex.org/W2616072553","https://openalex.org/W2759136286","https://openalex.org/W2807602500","https://openalex.org/W2896457183","https://openalex.org/W2904089587","https://openalex.org/W2942409680","https://openalex.org/W2973172555","https://openalex.org/W2990448851","https://openalex.org/W3004927487","https://openalex.org/W3098523662","https://openalex.org/W3200356212","https://openalex.org/W4200597037","https://openalex.org/W4239025696","https://openalex.org/W4286373989","https://openalex.org/W4291825018","https://openalex.org/W4296394114","https://openalex.org/W4296777868","https://openalex.org/W4309366575","https://openalex.org/W4312187515","https://openalex.org/W4361017398","https://openalex.org/W4385520543","https://openalex.org/W4387092668","https://openalex.org/W4390075127","https://openalex.org/W4390187230","https://openalex.org/W4390970052","https://openalex.org/W4400762160","https://openalex.org/W4401009333","https://openalex.org/W4401485218","https://openalex.org/W6621906925","https://openalex.org/W6745537798","https://openalex.org/W6745609711","https://openalex.org/W6803512735"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"CircRNA-miRNA":[0],"interaction":[1],"(CMI)":[2],"plays":[3],"a":[4,65,181],"crucial":[5],"role":[6],"in":[7,21,187],"the":[8,13,32,72,83,90,106,115,121,134,147,176],"gene":[9],"regulatory":[10],"network":[11],"of":[12,34,92,129,149,164,178],"cell.":[14],"Numerous":[15],"experiments":[16],"have":[17],"shown":[18],"that":[19,146,154],"abnormalities":[20],"CMI":[22,42,116],"can":[23],"impact":[24],"molecular":[25,47,53],"functions":[26],"and":[27,55,74,94,101,131,136,160,170],"physiological":[28],"processes,":[29],"leading":[30],"to":[31,88,158],"occurrence":[33],"specific":[35],"diseases.":[36],"Current":[37],"computational":[38],"models":[39],"for":[40,124,184],"predicting":[41],"typically":[43],"focus":[44],"on":[45,71,133],"local":[46],"entity":[48],"relationships,":[49],"thereby":[50],"neglecting":[51],"inherent":[52],"attributes":[54],"global":[56,111],"structural":[57,112],"information.":[58],"To":[59],"address":[60],"these":[61],"limitations,":[62],"we":[63],"propose":[64],"multi-feature":[66,123],"fusion":[67],"prediction":[68,148],"model":[69],"based":[70],"transformer":[73,84],"graph":[75],"attention":[76],"network,":[77],"named":[78],"EGATCMI.":[79],"Specifically,":[80],"EGATCMI":[81,109,118,179],"combines":[82],"architecture":[85],"with":[86],"Word2vec":[87],"pre-train":[89],"sequence":[91,98,102],"circRNA":[93],"miRNA,":[95],"capturing":[96],"their":[97],"feature":[99,113],"representation":[100],"similarity.":[103],"By":[104],"leveraging":[105],"self-attention":[107],"mechanism,":[108],"extracts":[110],"from":[114],"network.":[117],"effectively":[119],"integrates":[120],"obtained":[122],"prediction,":[125],"achieving":[126],"AUC":[127],"values":[128],"0.9106":[130],"0.9470":[132],"CMI-9905":[135],"CircBank":[137],"datasets,":[138],"respectively,":[139],"outperforming":[140],"existing":[141],"methods.":[142],"In":[143],"case":[144],"studies":[145],"interactions":[150],"between":[151],"three":[152],"miRNAs":[153],"are":[155],"closely":[156],"related":[157],"diseases":[159],"circRNAs,":[161],"8":[162],"out":[163],"10":[165],"pairs":[166],"were":[167],"accurately":[168],"predicted":[169],"validated.":[171],"Extensive":[172],"experimental":[173],"results":[174],"demonstrate":[175],"potential":[177],"as":[180],"reliable":[182],"tool":[183],"candidate":[185],"screening":[186],"biological":[188],"investigations.":[189]},"counts_by_year":[{"year":2026,"cited_by_count":26},{"year":2025,"cited_by_count":13}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
