{"id":"https://openalex.org/W4381327801","doi":"https://doi.org/10.1371/journal.pcbi.1011207","title":"Knowledge graph embedding for profiling the interaction between transcription factors and their target genes","display_name":"Knowledge graph embedding for profiling the interaction between transcription factors and their target genes","publication_year":2023,"publication_date":"2023-06-20","ids":{"openalex":"https://openalex.org/W4381327801","doi":"https://doi.org/10.1371/journal.pcbi.1011207","pmid":"https://pubmed.ncbi.nlm.nih.gov/37339154"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011207","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011207","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1011207","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054130157","display_name":"Yang-Han Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yang-Han Wu","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017713277","display_name":"Yu\u2010An Huang","orcid":"https://orcid.org/0000-0002-5346-2394"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu-An Huang","raw_affiliation_strings":["School of Computer Science, Northwesterm Polytechnical University, Xi'an, Shaanxi, China"],"raw_orcid":"https://orcid.org/0000-0002-5346-2394","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwesterm Polytechnical University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100393871","display_name":"Jianqiang Li","orcid":"https://orcid.org/0000-0002-2208-962X"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian-Qiang Li","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019805735","display_name":"Zhu\u2010Hong You","orcid":"https://orcid.org/0000-0003-1266-2696"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["School of Computer Science, Northwesterm Polytechnical University, Xi'an, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwesterm Polytechnical University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078808331","display_name":"Pengwei Hu","orcid":"https://orcid.org/0000-0001-5974-7932"},"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/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peng-Wei Hu","raw_affiliation_strings":["Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, \u00dcr\u00fcmqi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, \u00dcr\u00fcmqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008221100","display_name":"Lun Hu","orcid":"https://orcid.org/0000-0002-1591-8549"},"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/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lun Hu","raw_affiliation_strings":["Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, \u00dcr\u00fcmqi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, \u00dcr\u00fcmqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035919267","display_name":"Victor C. M. Leung","orcid":"https://orcid.org/0000-0003-3529-2640"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Victor C. M. Leung","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China"],"raw_orcid":"https://orcid.org/0000-0003-3529-2640","affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007272827","display_name":"Zhihua Du","orcid":"https://orcid.org/0000-0002-7213-2198"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhi-Hua Du","raw_affiliation_strings":["College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guang-dong, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007272827","https://openalex.org/A5008221100","https://openalex.org/A5017713277","https://openalex.org/A5019805735","https://openalex.org/A5035919267","https://openalex.org/A5054130157","https://openalex.org/A5078808331","https://openalex.org/A5100393871"],"corresponding_institution_ids":["https://openalex.org/I17145004","https://openalex.org/I180726961","https://openalex.org/I19820366","https://openalex.org/I4210106108"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.9374,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.72110946,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"6","first_page":"e1011207","last_page":"e1011207"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9970999956130981,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9948999881744385,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.627219021320343},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5873480439186096},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.513465940952301},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.48304635286331177},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43198710680007935},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41304171085357666},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3751414120197296},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35655298829078674},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3356844484806061},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21320131421089172}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.627219021320343},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5873480439186096},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.513465940952301},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.48304635286331177},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43198710680007935},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41304171085357666},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3751414120197296},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35655298829078674},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3356844484806061},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21320131421089172}],"mesh":[{"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":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010363","descriptor_name":"Pattern Recognition, Automated","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011207","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011207","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37339154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37339154","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10313080","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10313080","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10313080/pdf/pcbi.1011207.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011207","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011207","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:0d93afc4389346c4b5ba2ca4a8d8ddf5","is_oa":true,"landing_page_url":"https://doaj.org/article/0d93afc4389346c4b5ba2ca4a8d8ddf5","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":"PLoS Computational Biology, Vol 19, Iss 6, p e1011207 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011207","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011207","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1024446419","display_name":null,"funder_award_id":"2023A1515010992","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G1242154059","display_name":null,"funder_award_id":"R2020A045","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G1366773193","display_name":null,"funder_award_id":"2019ZT08X603","funder_id":"https://openalex.org/F4320334009","funder_display_name":"Guangdong Provincial Pearl River Talents Program"},{"id":"https://openalex.org/G1578964211","display_name":null,"funder_award_id":"Grant 62176164","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3332848674","display_name":null,"funder_award_id":"R2020A045","funder_id":"https://openalex.org/F4320326705","funder_display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality"},{"id":"https://openalex.org/G3918337656","display_name":null,"funder_award_id":"2019JC01X235","funder_id":"https://openalex.org/F4320334009","funder_display_name":"Guangdong Provincial Pearl River Talents Program"},{"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/G5403815052","display_name":null,"funder_award_id":"2019ZT08X603","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5737382697","display_name":null,"funder_award_id":"R2020A045","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6246565750","display_name":null,"funder_award_id":"2019ZT08X603","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G7279309214","display_name":null,"funder_award_id":"62176164","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null},{"id":"https://openalex.org/F4320326705","display_name":"Science, Technology and Innovation Commission of Shenzhen Municipality","ror":null},{"id":"https://openalex.org/F4320334009","display_name":"Guangdong Provincial Pearl River Talents Program","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W952995637","https://openalex.org/W1019830208","https://openalex.org/W1527927437","https://openalex.org/W1975987535","https://openalex.org/W1976260744","https://openalex.org/W2076513103","https://openalex.org/W2106555403","https://openalex.org/W2157581457","https://openalex.org/W2175370850","https://openalex.org/W2198606573","https://openalex.org/W2513179542","https://openalex.org/W2537679995","https://openalex.org/W2767434619","https://openalex.org/W2782454362","https://openalex.org/W2785792383","https://openalex.org/W2789273478","https://openalex.org/W2951529022","https://openalex.org/W2963468488","https://openalex.org/W2974274234","https://openalex.org/W2979750740","https://openalex.org/W2991357552","https://openalex.org/W2997831639","https://openalex.org/W3080500495","https://openalex.org/W3093194543","https://openalex.org/W3126579909","https://openalex.org/W3130819465","https://openalex.org/W3173198890","https://openalex.org/W3174990076","https://openalex.org/W4226005254","https://openalex.org/W4280508205","https://openalex.org/W4281488864","https://openalex.org/W4287339628","https://openalex.org/W4290930137","https://openalex.org/W4294558607","https://openalex.org/W4296024012","https://openalex.org/W4313250874"],"related_works":["https://openalex.org/W3036264823","https://openalex.org/W3206528106","https://openalex.org/W2123605750","https://openalex.org/W2912814903","https://openalex.org/W2088740331","https://openalex.org/W2950907416","https://openalex.org/W3038102983","https://openalex.org/W2082479932","https://openalex.org/W4281484020","https://openalex.org/W2932872266"],"abstract_inverted_index":{"Interactions":[0],"between":[1],"transcription":[2],"factor":[3,128],"and":[4,53,82,129,163,187,195,223],"target":[5,130],"gene":[6,12,51,112],"form":[7],"the":[8,120,165,174,178,190,202,213,221],"main":[9],"part":[10],"of":[11,29,122,126,173,185,192,204,207,215],"regulation":[13],"network":[14],"in":[15,22,33,84,189,230],"human,":[16],"which":[17],"are":[18,39],"still":[19,58],"complicating":[20],"factors":[21],"biological":[23],"research.":[24],"Specifically,":[25],"for":[26,97,137],"nearly":[27],"half":[28],"those":[30],"interactions":[31,52],"recorded":[32],"established":[34],"database,":[35],"their":[36,54],"interaction":[37,124],"types":[38,125,139],"yet":[40],"to":[41,49,62,220],"be":[42],"confirmed.":[43],"Although":[44],"several":[45],"computational":[46],"methods":[47],"exist":[48],"predict":[50,63],"type,":[55],"there":[56],"is":[57,152],"no":[59],"method":[60,167,180],"available":[61],"them":[64],"solely":[65],"based":[66],"on":[67,89,104,140,168],"topology":[68,105],"information.":[69],"To":[70],"this":[71,98,116,231],"end,":[72],"we":[73,94,118],"proposed":[74,166,179],"here":[75],"a":[76,85,90,133,141,157,171,205],"graph-based":[77],"prediction":[78,149,194,222],"model":[79,102],"called":[80],"KGE-TGI":[81,101],"trained":[83],"multi-task":[86],"learning":[87],"manner":[88],"knowledge":[91,216],"graph":[92],"that":[93,151,212,224],"specially":[95],"constructed":[96,156],"problem.":[99,232],"The":[100],"relies":[103],"information":[106,217],"rather":[107],"than":[108],"being":[109],"driven":[110],"by":[111],"expression":[113],"data.":[114],"In":[115,200],"paper,":[117],"formulate":[119],"task":[121],"predicting":[123],"transcript":[127],"genes":[131],"as":[132,161],"multi-label":[134],"classification":[135],"problem":[136,150],"link":[138,148,193,196],"heterogeneous":[142],"graph,":[143],"coupled":[144],"with":[145],"solving":[146],"another":[147],"inherently":[153],"related.":[154],"We":[155],"ground":[158],"truth":[159],"dataset":[160],"benchmark":[162],"evaluated":[164],"it.":[169],"As":[170],"result":[172],"5-fold":[175],"cross":[176],"experiments,":[177],"achieved":[181],"average":[182],"AUC":[183],"values":[184],"0.9654":[186],"0.9339":[188],"tasks":[191],"type":[197],"classification,":[198],"respectively.":[199],"addition,":[201],"results":[203],"series":[206],"comparison":[208],"experiments":[209],"also":[210],"prove":[211],"introduction":[214],"significantly":[218],"benefits":[219],"our":[225],"methodology":[226],"achieve":[227],"state-of-the-art":[228],"performance":[229]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
