{"id":"https://openalex.org/W4403390513","doi":"https://doi.org/10.1109/jbhi.2024.3476490","title":"Hierarchical Graph Transformer With Contrastive Learning for Gene Regulatory Network Inference","display_name":"Hierarchical Graph Transformer With Contrastive Learning for Gene Regulatory Network Inference","publication_year":2024,"publication_date":"2024-10-14","ids":{"openalex":"https://openalex.org/W4403390513","doi":"https://doi.org/10.1109/jbhi.2024.3476490","pmid":"https://pubmed.ncbi.nlm.nih.gov/39401117"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3476490","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3476490","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":null,"display_name":"Wentao Cui","orcid":"https://orcid.org/0000-0002-1404-3971"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wentao Cui","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027022795","display_name":"Qingqing Long","orcid":"https://orcid.org/0009-0003-7105-361X"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingqing Long","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100429118","display_name":"Wenhao Liu","orcid":"https://orcid.org/0000-0003-4571-6523"},"institutions":[{"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/I4210167311","display_name":"Institute of Zoology","ror":"https://ror.org/05skxkv18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210167311"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Liu","raw_affiliation_strings":["State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210167311","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100766597","display_name":"Fang Chen","orcid":"https://orcid.org/0000-0002-4410-7040"},"institutions":[{"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/I4210167311","display_name":"Institute of Zoology","ror":"https://ror.org/05skxkv18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210167311"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Fang","raw_affiliation_strings":["State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210167311","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040824554","display_name":"Xuezhi Wang","orcid":"https://orcid.org/0000-0001-5222-248X"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuezhi Wang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Pengfei Wang","orcid":"https://orcid.org/0000-0003-1075-0684"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengfei Wang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065865669","display_name":"Yuanchun Zhou","orcid":"https://orcid.org/0000-0003-2144-1131"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanchun Zhou","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"],"apc_list":null,"apc_paid":null,"fwci":0.2271,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5794337,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"29","issue":"1","first_page":"690","last_page":"699"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9861999750137329,"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":0.9861999750137329,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9846000075340271,"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":0.9782000184059143,"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/inference","display_name":"Inference","score":0.6701751947402954},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6553411483764648},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4891872704029083},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.42182159423828125},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.417140930891037},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3423053026199341},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2856453061103821},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16718745231628418},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15757977962493896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12171542644500732},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09964683651924133}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6701751947402954},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6553411483764648},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4891872704029083},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.42182159423828125},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.417140930891037},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3423053026199341},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2856453061103821},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16718745231628418},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15757977962493896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12171542644500732},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09964683651924133},{"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":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":"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":"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":"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":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":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":"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":"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":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"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/jbhi.2024.3476490","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3476490","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:39401117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39401117","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2076513103","https://openalex.org/W2077132193","https://openalex.org/W2090808827","https://openalex.org/W2106555403","https://openalex.org/W2111384508","https://openalex.org/W2151870437","https://openalex.org/W2337819340","https://openalex.org/W2776035257","https://openalex.org/W2782454362","https://openalex.org/W2900569176","https://openalex.org/W2901292166","https://openalex.org/W2904574059","https://openalex.org/W2952535935","https://openalex.org/W2964315448","https://openalex.org/W2996140569","https://openalex.org/W2997831639","https://openalex.org/W3024161231","https://openalex.org/W3045910546","https://openalex.org/W3095716988","https://openalex.org/W3127245931","https://openalex.org/W3186348651","https://openalex.org/W3193795275","https://openalex.org/W3205207815","https://openalex.org/W4205848861","https://openalex.org/W4226005254","https://openalex.org/W4283592141","https://openalex.org/W4288384137","https://openalex.org/W4290930137","https://openalex.org/W4294991206","https://openalex.org/W4304690684","https://openalex.org/W4362664882","https://openalex.org/W4366464224","https://openalex.org/W4382198799","https://openalex.org/W4385955324","https://openalex.org/W4386699707","https://openalex.org/W4388870182","https://openalex.org/W4391044567","https://openalex.org/W4391126196","https://openalex.org/W4392231300","https://openalex.org/W4394764901","https://openalex.org/W4399141298","https://openalex.org/W4401200719","https://openalex.org/W4403862485","https://openalex.org/W6631190155","https://openalex.org/W6631943919","https://openalex.org/W6679868779","https://openalex.org/W6726873649","https://openalex.org/W6761613834","https://openalex.org/W6846765560"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Gene":[0],"regulatory":[1,17],"networks":[2,169],"(GRNs)":[3],"are":[4,150],"crucial":[5],"for":[6,57,110,170],"understanding":[7],"gene":[8,130,134,162,167],"regulation":[9,23],"and":[10,24,35],"cellular":[11,27],"processes.":[12,28],"Inferring":[13],"GRNs":[14],"helps":[15],"uncover":[16],"pathways,":[18],"shedding":[19],"light":[20],"on":[21],"the":[22,30,52,62,82,144],"development":[25,63],"of":[26,32,64,129,174],"With":[29],"rise":[31],"high-throughput":[33],"sequencing":[34],"advancements":[36],"in":[37,54,143,184],"computational":[38,40],"technology,":[39],"models":[41],"have":[42],"emerged":[43],"as":[44,136],"cost-effective":[45],"alternatives":[46],"to":[47,84,91,139,152,165],"traditional":[48],"experimental":[49],"studies.":[50],"Moreover,":[51],"surge":[53],"ChIP-seq":[55],"data":[56],"TF-DNA":[58],"binding":[59],"has":[60],"catalyzed":[61],"graph":[65,123],"neural":[66],"network":[67],"(GNN)-based":[68],"methods,":[69],"greatly":[70],"advancing":[71],"GRN":[72,111,185],"inference":[73],"capabilities.":[74],"However,":[75],"most":[76],"existing":[77],"GNN-based":[78,101],"methods":[79],"suffer":[80],"from":[81],"inability":[83],"capture":[85],"long-distance":[86],"structural":[87,118],"semantic":[88],"correlations":[89],"due":[90],"transitive":[92],"interactions.":[93],"In":[94],"this":[95],"paper,":[96],"we":[97,160],"introduce":[98],"a":[99,121,127],"novel":[100],"model":[102],"named":[103],"Hierarchical":[104],"Graph":[105],"Transformer":[106],"with":[107,141,156],"Contrastive":[108],"Learning":[109],"(HGTCGRN)":[112],"inference.":[113,186],"HGTCGRN":[114,180],"excels":[115],"at":[116],"capturing":[117],"semantics":[119],"using":[120],"hierarchical":[122],"Transformer,":[124],"which":[125],"introduces":[126],"series":[128],"family":[131],"nodes":[132,138,142],"representing":[133],"functions":[135],"virtual":[137],"interact":[140],"GRNS.":[145],"These":[146],"semantic-aware":[147],"virtual-node":[148],"embeddings":[149],"aggregated":[151],"produce":[153],"node":[154],"representations":[155],"varying":[157],"emphasis.":[158],"Additionally,":[159],"leverage":[161],"ontology":[163],"information":[164],"construct":[166],"interaction":[168],"contrastive":[171],"learning":[172],"optimization":[173],"GRNs.":[175],"Experimental":[176],"results":[177],"demonstrate":[178],"that":[179],"achieves":[181],"superior":[182],"performance":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-15T08:11:43.952461","created_date":"2025-10-10T00:00:00"}
