{"id":"https://openalex.org/W4226005254","doi":"https://doi.org/10.1093/bib/bbac148","title":"GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions","display_name":"GraphTGI: an attention-based graph embedding model for predicting TF-target gene interactions","publication_year":2022,"publication_date":"2022-04-14","ids":{"openalex":"https://openalex.org/W4226005254","doi":"https://doi.org/10.1093/bib/bbac148","pmid":"https://pubmed.ncbi.nlm.nih.gov/35511108"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac148","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","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":false,"raw_author_name":"Zhi-Hua Du","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","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":false,"raw_author_name":"Yang-Han Wu","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, 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/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":"Yu-An Huang","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047093288","display_name":"Jie Chen","orcid":"https://orcid.org/0000-0002-9811-1694"},"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":false,"raw_author_name":"Jie Chen","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063005114","display_name":"Gui-Qing Pan","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":false,"raw_author_name":"Gui-Qing Pan","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"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/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lun Hu","raw_affiliation_strings":["College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, 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":false,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","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, 3688 Nanhai Avenue, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Software Engineering, ShenZhen University, 3688 Nanhai Avenue, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017713277","https://openalex.org/A5100393871"],"corresponding_institution_ids":["https://openalex.org/I180726961"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.4103,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.80777366,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"23","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.47589999437332153,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.47589999437332153,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4413999915122986,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.02590000070631504,"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":0.6272959113121033},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6015222072601318},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5582585334777832},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4252101182937622},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39767682552337646},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19521936774253845},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.19491958618164062}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6272959113121033},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6015222072601318},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5582585334777832},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4252101182937622},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39767682552337646},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19521936774253845},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.19491958618164062}],"mesh":[{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac148","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac148","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35511108","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35511108","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"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/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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1522301498","https://openalex.org/W1976260744","https://openalex.org/W1992442866","https://openalex.org/W2015416439","https://openalex.org/W2017840637","https://openalex.org/W2059699217","https://openalex.org/W2129795133","https://openalex.org/W2136640051","https://openalex.org/W2198606573","https://openalex.org/W2401562190","https://openalex.org/W2737543579","https://openalex.org/W2765323781","https://openalex.org/W2782454362","https://openalex.org/W2786016794","https://openalex.org/W2787740662","https://openalex.org/W2885815722","https://openalex.org/W2896262061","https://openalex.org/W2912083425","https://openalex.org/W2951529022","https://openalex.org/W2962711740","https://openalex.org/W2963468488","https://openalex.org/W2974274234","https://openalex.org/W3019246273","https://openalex.org/W3021338900","https://openalex.org/W3080500495","https://openalex.org/W3096561213","https://openalex.org/W3126579909","https://openalex.org/W3130819465","https://openalex.org/W3174990076","https://openalex.org/W6631190155","https://openalex.org/W6745316256","https://openalex.org/W6748402259","https://openalex.org/W6754929296","https://openalex.org/W6776579259"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2081900870","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W4402327032"],"abstract_inverted_index":{"MOTIVATION:":[0],"Interaction":[1],"between":[2,93],"transcription":[3,94],"factor":[4],"(TF)":[5],"and":[6,84,96,160,176,193,227,240],"its":[7],"target":[8,97],"genes":[9,98],"establishes":[10],"the":[11,20,36,52,71,74,90,104,107,111,116,120,131,143,182,186,194,199,215,222,241],"knowledge":[12,158],"foundation":[13],"for":[14,44],"biological":[15,29],"researches":[16],"in":[17,214,244],"transcriptional":[18],"regulation,":[19],"number":[21],"of":[22,38,73,106,113,146,171,185,210],"which":[23,168],"is,":[24],"however,":[25],"still":[26],"limited":[27],"by":[28,102,127],"techniques.":[30],"Existing":[31],"computational":[32],"methods":[33],"relevant":[34],"to":[35,65,123],"prediction":[37,144,153,183],"TF-target":[39,67,76,133,147,230],"interactions":[40,69,92,149,232],"are":[41,247],"mostly":[42],"proposed":[43,117,187,200],"predicting":[45,51],"binding":[46],"sites,":[47],"rather":[48],"than":[49],"directly":[50],"interactions.":[53],"To":[54,110],"this":[55,125,139],"end,":[56],"we":[57,141],"propose":[58,161],"here":[59],"a":[60,151,156,162,172,177,190,234],"graph":[61,159,173],"attention-based":[62,174],"autoencoder":[63],"model":[64,118,165,201,224],"predict":[66,229],"gene":[68,77,86,134,148,231],"using":[70],"information":[72],"known":[75,108,132],"interaction":[78,135],"network":[79],"combined":[80],"with":[81,205],"two":[82],"sequential":[83],"chemical":[85],"characters,":[87],"considering":[88],"that":[89,198,221],"unobserved":[91],"factors":[95],"can":[99,225],"be":[100],"predicted":[101],"learning":[103,128,164],"pattern":[105],"ones.":[109],"best":[112],"our":[114,245],"knowledge,":[115],"is":[119,169,219],"first":[121],"attempt":[122],"solve":[124],"problem":[126,154],"patterns":[129],"from":[130],"network.":[136],"RESULTS:":[137],"In":[138],"paper,":[140],"formulate":[142],"task":[145],"as":[150],"link":[152],"on":[155,189,233],"complex":[157],"deep":[163],"called":[166],"GraphTGI,":[167],"composed":[170],"encoder":[175],"bilinear":[178],"decoder.":[179],"We":[180],"evaluated":[181],"performance":[184,204],"method":[188],"real":[191],"dataset,":[192],"experimental":[195],"results":[196],"show":[197],"yields":[202],"outstanding":[203],"an":[206],"average":[207],"AUC":[208],"value":[209],"0.8864":[211],"+/-":[212],"0.0057":[213],"5-fold":[216],"cross-validation.":[217],"It":[218],"anticipated":[220],"GraphTGI":[223],"effectively":[226],"efficiently":[228],"large":[235],"scale.":[236],"AVAILABILITY:":[237],"Python":[238],"code":[239],"datasets":[242],"used":[243],"studies":[246],"made":[248],"available":[249],"at":[250],"https://github.com/YanghanWu/GraphTGI.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}