{"id":"https://openalex.org/W4412468353","doi":"https://doi.org/10.1186/s12859-025-06186-1","title":"Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution","display_name":"Cross-attention graph neural networks for inferring gene regulatory networks with skewed degree distribution","publication_year":2025,"publication_date":"2025-07-16","ids":{"openalex":"https://openalex.org/W4412468353","doi":"https://doi.org/10.1186/s12859-025-06186-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/40670912"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06186-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06186-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06186-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06186-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102653791","display_name":"Jiaqi Xiong","orcid":null},"institutions":[{"id":"https://openalex.org/I187400657","display_name":"South China Normal University","ror":"https://ror.org/01kq0pv72","country_code":"CN","type":"education","lineage":["https://openalex.org/I187400657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaqi Xiong","raw_affiliation_strings":["Aberdeen Institute of Data Science and Artificial Intelligence, South China Normal University, Guangzhou, 528225, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aberdeen Institute of Data Science and Artificial Intelligence, South China Normal University, Guangzhou, 528225, China","institution_ids":["https://openalex.org/I187400657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112114244","display_name":"Nan Yin","orcid":"https://orcid.org/0000-0002-9792-6066"},"institutions":[{"id":"https://openalex.org/I200769079","display_name":"Hong Kong University of Science and Technology","ror":"https://ror.org/00q4vv597","country_code":"HK","type":"education","lineage":["https://openalex.org/I200769079"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Nan Yin","raw_affiliation_strings":["Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China. yinnan8911@gmail.com","Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China. yinnan8911@gmail.com","institution_ids":["https://openalex.org/I200769079","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China","institution_ids":["https://openalex.org/I200769079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062585318","display_name":"Shiyang Liang","orcid":"https://orcid.org/0000-0002-6941-2404"},"institutions":[{"id":"https://openalex.org/I4210120701","display_name":"The 180th Hospital of PLA","ror":"https://ror.org/01ye08k77","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210120701"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiyang Liang","raw_affiliation_strings":["Department of Internal Medicine, The No. 944 Hospital of Joint Logistic Support Force of PLA, Xiongguan Road, Jiu Quan, 735000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Internal Medicine, The No. 944 Hospital of Joint Logistic Support Force of PLA, Xiongguan Road, Jiu Quan, 735000, China","institution_ids":["https://openalex.org/I4210120701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100369545","display_name":"Haoyang Li","orcid":"https://orcid.org/0000-0003-3544-5563"},"institutions":[{"id":"https://openalex.org/I187400657","display_name":"South China Normal University","ror":"https://ror.org/01kq0pv72","country_code":"CN","type":"education","lineage":["https://openalex.org/I187400657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyang Li","raw_affiliation_strings":["Aberdeen Institute of Data Science and Artificial Intelligence, South China Normal University, Guangzhou, 528225, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aberdeen Institute of Data Science and Artificial Intelligence, South China Normal University, Guangzhou, 528225, China","institution_ids":["https://openalex.org/I187400657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101481532","display_name":"Yingxu Wang","orcid":"https://orcid.org/0000-0003-3284-1464"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Yingxu Wang","raw_affiliation_strings":["Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Machine Learning, Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115637394","display_name":"Duo Ai","orcid":null},"institutions":[{"id":"https://openalex.org/I4210158926","display_name":"Xijing Hospital","ror":"https://ror.org/05cqe9350","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210158926"]},{"id":"https://openalex.org/I9916479","display_name":"Air Force Medical University","ror":"https://ror.org/00ms48f15","country_code":"CN","type":"education","lineage":["https://openalex.org/I9916479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Duo Ai","raw_affiliation_strings":["Department of Dermatology, Xijing Hospital, Fourth Military Medical University, No 127 of West Changle Road, Xi'an, 710032, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Dermatology, Xijing Hospital, Fourth Military Medical University, No 127 of West Changle Road, Xi'an, 710032, Shaanxi, China","institution_ids":["https://openalex.org/I9916479","https://openalex.org/I4210158926"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100670459","display_name":"Jingjie Wang","orcid":"https://orcid.org/0000-0002-2192-7193"},"institutions":[{"id":"https://openalex.org/I4210154136","display_name":"Tang Du Hospital","ror":"https://ror.org/04yvdan45","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210154136"]},{"id":"https://openalex.org/I9916479","display_name":"Air Force Medical University","ror":"https://ror.org/00ms48f15","country_code":"CN","type":"education","lineage":["https://openalex.org/I9916479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jingjie Wang","raw_affiliation_strings":["Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Shaanxi, 710038, China. jingjiefmmu@163.com","Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Shaanxi, 710038, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Shaanxi, 710038, China. jingjiefmmu@163.com","institution_ids":["https://openalex.org/I9916479","https://openalex.org/I4210154136"]},{"raw_affiliation_string":"Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Shaanxi, 710038, China","institution_ids":["https://openalex.org/I4210154136","https://openalex.org/I9916479"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100670459","https://openalex.org/A5112114244"],"corresponding_institution_ids":["https://openalex.org/I200769079","https://openalex.org/I4210154136","https://openalex.org/I889458895","https://openalex.org/I9916479"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3603,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.81437796,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"179","last_page":"179"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.7597000002861023,"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":0.7597000002861023,"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":0.07460000365972519,"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":0.030500000342726707,"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/degree-distribution","display_name":"Degree distribution","score":0.7113178968429565},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5503178238868713},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5489221811294556},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5124278664588928},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5097147822380066},{"id":"https://openalex.org/keywords/degree","display_name":"Degree (music)","score":0.5092097520828247},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43887701630592346},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4361409544944763},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3851056694984436},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32045239210128784},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.24888953566551208},{"id":"https://openalex.org/keywords/complex-network","display_name":"Complex network","score":0.18599197268486023},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.13807284832000732},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.07185035943984985}],"concepts":[{"id":"https://openalex.org/C87414783","wikidata":"https://www.wikidata.org/wiki/Q1002603","display_name":"Degree distribution","level":3,"score":0.7113178968429565},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5503178238868713},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5489221811294556},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5124278664588928},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5097147822380066},{"id":"https://openalex.org/C2775997480","wikidata":"https://www.wikidata.org/wiki/Q586277","display_name":"Degree (music)","level":2,"score":0.5092097520828247},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43887701630592346},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4361409544944763},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3851056694984436},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32045239210128784},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24888953566551208},{"id":"https://openalex.org/C34947359","wikidata":"https://www.wikidata.org/wiki/Q665189","display_name":"Complex network","level":2,"score":0.18599197268486023},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.13807284832000732},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.07185035943984985},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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":"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06186-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06186-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06186-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40670912","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40670912","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d58205548a6743d9a39246f2e841fb46","is_oa":true,"landing_page_url":"https://doaj.org/article/d58205548a6743d9a39246f2e841fb46","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-21 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12265278","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12265278","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06186-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06186-1","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06186-1","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412468353.pdf","grobid_xml":"https://content.openalex.org/works/W4412468353.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1175879704","https://openalex.org/W1558526836","https://openalex.org/W1707446633","https://openalex.org/W1965637582","https://openalex.org/W2099692224","https://openalex.org/W2106961470","https://openalex.org/W2115199224","https://openalex.org/W2123734813","https://openalex.org/W2132951277","https://openalex.org/W2148944713","https://openalex.org/W2414912604","https://openalex.org/W2470223656","https://openalex.org/W2498761000","https://openalex.org/W2512653609","https://openalex.org/W2769550393","https://openalex.org/W2774736917","https://openalex.org/W2809324976","https://openalex.org/W2897807203","https://openalex.org/W2909647016","https://openalex.org/W2949475756","https://openalex.org/W3008638899","https://openalex.org/W3033392434","https://openalex.org/W3095716988","https://openalex.org/W3098000306","https://openalex.org/W3119261195","https://openalex.org/W3152889963","https://openalex.org/W3184872791","https://openalex.org/W3216588755","https://openalex.org/W4221092895","https://openalex.org/W4284665181","https://openalex.org/W4298004368","https://openalex.org/W4311574756","https://openalex.org/W4362601455","https://openalex.org/W4379117479","https://openalex.org/W4383551705","https://openalex.org/W4386316616","https://openalex.org/W4386620529","https://openalex.org/W4394014672","https://openalex.org/W4400103610","https://openalex.org/W4401200660","https://openalex.org/W4401536884","https://openalex.org/W4401670694","https://openalex.org/W6600339963","https://openalex.org/W6601955380","https://openalex.org/W6696711281","https://openalex.org/W6871841648"],"related_works":["https://openalex.org/W4293160469","https://openalex.org/W2963945385","https://openalex.org/W2146137903","https://openalex.org/W1587202469","https://openalex.org/W2256700515","https://openalex.org/W2619014136","https://openalex.org/W2013497788","https://openalex.org/W1993303705","https://openalex.org/W2046130977","https://openalex.org/W2013285130"],"abstract_inverted_index":{"BACKGROUND:":[0],"Inferring":[1],"Gene":[2],"Regulatory":[3],"Networks":[4],"(GRNs)":[5],"from":[6],"gene":[7,107],"expression":[8],"data":[9],"is":[10],"a":[11,54,58],"pivotal":[12],"challenge":[13],"in":[14],"systems":[15],"biology.":[16],"Most":[17],"existing":[18,83],"methods":[19,85],"fail":[20],"to":[21,48,64],"consider":[22],"the":[23,30,66,103],"skewed":[24,67,99],"degree":[25,68,100],"distribution":[26],"of":[27,32,73,105],"genes,":[28],"complicating":[29],"application":[31],"directed":[33],"graph":[34,61],"embedding":[35,62],"methods.":[36],"RESULTS:":[37],"The":[38,79,110],"Cross-Attention":[39],"Complex":[40],"Dual":[41],"Graph":[42],"Embedding":[43],"Model":[44],"(XATGRN)":[45],"was":[46],"proposed":[47],"address":[49],"this":[50],"issue.":[51],"It":[52],"employs":[53],"cross-attention":[55],"mechanism":[56],"and":[57,76,112],"dual":[59],"complex":[60,106],"approach":[63],"manage":[65],"distribution,":[69,101],"ensuring":[70],"precise":[71],"prediction":[72],"regulatory":[74,108],"relationships":[75],"their":[77],"directionality.":[78],"model":[80],"consistently":[81],"outperforms":[82],"state-of-the-art":[84],"across":[86],"various":[87],"datasets.":[88],"CONCLUSIONS:":[89],"XATGRN":[90],"provides":[91],"an":[92],"effective":[93],"solution":[94],"for":[95],"inferring":[96],"GRNs":[97],"with":[98],"enhancing":[102],"understanding":[104],"mechanisms.":[109],"codes":[111],"detailed":[113],"requirements":[114],"have":[115],"been":[116],"released":[117],"on":[118],"Github:":[119],"(":[120],"https://github.com/kikixiong/XATGRN":[121],").":[122]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}