{"id":"https://openalex.org/W4408745569","doi":"https://doi.org/10.1093/bib/bbaf118","title":"AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data","display_name":"AttentionGRN: a functional and directed graph transformer for gene regulatory network reconstruction from scRNA-seq data","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4408745569","doi":"https://doi.org/10.1093/bib/bbaf118","pmid":"https://pubmed.ncbi.nlm.nih.gov/40116659"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf118","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf118/62519420/bbaf118.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf118/62519420/bbaf118.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068590943","display_name":"Zhen Gao","orcid":"https://orcid.org/0000-0001-7427-6032"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen Gao","raw_affiliation_strings":["Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071754273","display_name":"Yansen Su","orcid":"https://orcid.org/0000-0002-3855-7133"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yansen Su","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007847166","display_name":"Jin Tang","orcid":"https://orcid.org/0000-0001-7680-8231"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin Tang","raw_affiliation_strings":["Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058512534","display_name":"Hyeonku Jin","orcid":"https://orcid.org/0009-0003-0855-9458"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaiwan Jin","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044032571","display_name":"Yun Ding","orcid":"https://orcid.org/0000-0002-2749-7710"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Ding","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101959312","display_name":"Ruifen Cao","orcid":"https://orcid.org/0000-0002-4223-3422"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui-Fen Cao","raw_affiliation_strings":["Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Computer Science and Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085214222","display_name":"Pi-Jing Wei","orcid":"https://orcid.org/0000-0003-2770-8781"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pi-Jing Wei","raw_affiliation_strings":["Anhui University , The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","Information Materials and Intelligent Sensing Laboratory of Anhui Province , The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","Information Materials and Intelligent Sensing Laboratory of Anhui Province, The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province , The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Institute of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110520920","display_name":"Zheng Chun-Hou","orcid":null},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China"],"affiliations":[{"raw_affiliation_string":"Anhui University , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education , School of Artificial Intelligence, , 111 Jiulong Road, Hefei 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"The Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University, 111 Jiulong Road, Hefei 230601, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5068590943"],"corresponding_institution_ids":["https://openalex.org/I143868143"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.0199,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.90410483,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9945999979972839,"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":0.9945999979972839,"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":0.9810000061988831,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9684000015258789,"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/transformer","display_name":"Transformer","score":0.5547192096710205},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5454947352409363},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4614694118499756},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4557676911354065},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.44520303606987},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37609240412712097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22623693943023682},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17985868453979492},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.17234346270561218},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1449519395828247},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10372909903526306}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5547192096710205},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5454947352409363},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4614694118499756},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4557676911354065},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.44520303606987},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37609240412712097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22623693943023682},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17985868453979492},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.17234346270561218},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1449519395828247},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10372909903526306},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":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},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf118","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf118/62519420/bbaf118.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40116659","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40116659","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11926986","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11926986","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf118","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf118","pdf_url":"https://academic.oup.com/bib/article-pdf/26/2/bbaf118/62519420/bbaf118.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1989873432","display_name":null,"funder_award_id":"2022AH020010","funder_id":"https://openalex.org/F4320321435","funder_display_name":"Anhui University"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2460525815","display_name":null,"funder_award_id":"62433001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2461069220","display_name":null,"funder_award_id":"62202004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2507855583","display_name":null,"funder_award_id":"202004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4784360784","display_name":null,"funder_award_id":"2020YFA0908700","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4830630615","display_name":null,"funder_award_id":"2202004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5700703483","display_name":null,"funder_award_id":"62322301","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6058138561","display_name":null,"funder_award_id":", No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8863666567","display_name":null,"funder_award_id":"and No.","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/F4320321435","display_name":"Anhui University","ror":"https://ror.org/05th6yx34"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408745569.pdf","grobid_xml":"https://content.openalex.org/works/W4408745569.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W2103912979","https://openalex.org/W2140258573","https://openalex.org/W2159675211","https://openalex.org/W2462053388","https://openalex.org/W2465917013","https://openalex.org/W2511896561","https://openalex.org/W2563605401","https://openalex.org/W2626990934","https://openalex.org/W2767756497","https://openalex.org/W2789254933","https://openalex.org/W2791453813","https://openalex.org/W2945217688","https://openalex.org/W2973083231","https://openalex.org/W2996140569","https://openalex.org/W2997831639","https://openalex.org/W3024161231","https://openalex.org/W3100379134","https://openalex.org/W3127245931","https://openalex.org/W3143143672","https://openalex.org/W3151227017","https://openalex.org/W3156304677","https://openalex.org/W3186348651","https://openalex.org/W3193795275","https://openalex.org/W3209046602","https://openalex.org/W3213399454","https://openalex.org/W4200379876","https://openalex.org/W4206804332","https://openalex.org/W4220837089","https://openalex.org/W4224260145","https://openalex.org/W4225278475","https://openalex.org/W4281559042","https://openalex.org/W4282919091","https://openalex.org/W4283769757","https://openalex.org/W4290930137","https://openalex.org/W4306966826","https://openalex.org/W4313340543","https://openalex.org/W4321452549","https://openalex.org/W4362460300","https://openalex.org/W4379117479","https://openalex.org/W4382022265","https://openalex.org/W4385754062","https://openalex.org/W4386051349","https://openalex.org/W4387840800","https://openalex.org/W4388034369","https://openalex.org/W4388870182","https://openalex.org/W4391126196","https://openalex.org/W4394014672","https://openalex.org/W4400103610","https://openalex.org/W4400603735","https://openalex.org/W4400904508","https://openalex.org/W4401200719","https://openalex.org/W6796801894"],"related_works":["https://openalex.org/W2131250617","https://openalex.org/W4233034052","https://openalex.org/W2371030422","https://openalex.org/W4310420093","https://openalex.org/W3154635860","https://openalex.org/W4226332880","https://openalex.org/W4298054035","https://openalex.org/W4366601060","https://openalex.org/W2364878181","https://openalex.org/W2189035925"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"enables":[4],"the":[5,49,77,86,96,115],"reconstruction":[6],"of":[7,51,79,117],"cell":[8,161],"type-specific":[9,162],"gene":[10,18,124,177],"regulatory":[11,178],"networks":[12,26],"(GRNs),":[13],"offering":[14],"detailed":[15],"insights":[16],"into":[17],"regulation":[19],"at":[20],"high":[21],"resolution.":[22],"While":[23],"graph":[24,63],"neural":[25],"have":[27],"become":[28],"widely":[29],"used":[30],"for":[31,164],"GRN":[32,80],"inference,":[33],"their":[34],"message-passing":[35],"mechanisms":[36],"are":[37,91],"often":[38],"limited":[39],"by":[40],"issues":[41],"such":[42],"as":[43],"over-smoothing":[44],"and":[45,75,101,121,131,172],"over-squashing,":[46],"which":[47,67],"hinder":[48],"preservation":[50],"essential":[52],"network":[53,98,119,133],"structure.":[54,134],"To":[55],"address":[56],"these":[57],"challenges,":[58],"we":[59,108],"propose":[60],"a":[61],"novel":[62,169],"transformer-based":[64],"model,":[65],"AttentionGRN,":[66],"leverages":[68],"soft":[69],"encoding":[70,112],"to":[71,93,113,126,159],"enhance":[72],"model":[73],"expressiveness":[74],"improve":[76],"accuracy":[78],"inference":[81],"from":[82],"scRNA-seq":[83],"data.":[84],"Furthermore,":[85,153],"GRN-oriented":[87],"message":[88],"aggregation":[89],"strategies":[90],"designed":[92],"capture":[94,127],"both":[95],"directed":[97,110,118],"structure":[99,111],"information":[100,103],"functional":[102,123,129],"inherent":[104],"in":[105],"GRNs.":[106],"Specifically,":[107],"design":[109],"facilitate":[114],"learning":[116],"topologies":[120],"employ":[122],"sampling":[125],"key":[128],"modules":[130],"global":[132],"Our":[135],"extensive":[136],"experiments,":[137],"conducted":[138],"on":[139],"88":[140],"datasets":[141],"across":[142],"two":[143],"distinct":[144],"tasks,":[145],"demonstrate":[146],"that":[147],"AttentionGRN":[148,154],"consistently":[149],"outperforms":[150],"existing":[151],"methods.":[152],"has":[155],"been":[156],"successfully":[157],"applied":[158],"reconstruct":[160],"GRNs":[163],"human":[165],"mature":[166],"hepatocytes,":[167],"revealing":[168],"hub":[170],"genes":[171],"previously":[173],"unidentified":[174],"transcription":[175],"factor-target":[176],"associations.":[179]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
