{"id":"https://openalex.org/W3042748728","doi":"https://doi.org/10.1109/tcbb.2021.3054738","title":"EPGAT: Gene Essentiality Prediction With Graph Attention Networks","display_name":"EPGAT: Gene Essentiality Prediction With Graph Attention Networks","publication_year":2021,"publication_date":"2021-01-26","ids":{"openalex":"https://openalex.org/W3042748728","doi":"https://doi.org/10.1109/tcbb.2021.3054738","mag":"3042748728","pmid":"https://pubmed.ncbi.nlm.nih.gov/33497339"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3054738","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3054738","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2007.09671","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020402687","display_name":"Jo\u00e3o Schapke","orcid":"https://orcid.org/0000-0001-6794-7758"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Jo\u00e3o Schapke","raw_affiliation_strings":["Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil"],"raw_orcid":"https://orcid.org/0000-0001-6794-7758","affiliations":[{"raw_affiliation_string":"Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048925954","display_name":"Anderson Rocha Tavares","orcid":"https://orcid.org/0000-0002-8530-6468"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Anderson Tavares","raw_affiliation_strings":["Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-8530-6468","affiliations":[{"raw_affiliation_string":"Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039060913","display_name":"Mariana Recamonde\u2010Mendoza","orcid":"https://orcid.org/0000-0003-2800-1032"},"institutions":[{"id":"https://openalex.org/I130442723","display_name":"Universidade Federal do Rio Grande do Sul","ror":"https://ror.org/041yk2d64","country_code":"BR","type":"education","lineage":["https://openalex.org/I130442723"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Mariana Recamonde-Mendoza","raw_affiliation_strings":["Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-2800-1032","affiliations":[{"raw_affiliation_string":"Institute of Informatics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil","institution_ids":["https://openalex.org/I130442723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I130442723"],"apc_list":null,"apc_paid":null,"fwci":2.2206,"has_fulltext":false,"cited_by_count":37,"citation_normalized_percentile":{"value":0.8882459,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"1615","last_page":"1626"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9998999834060669,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.994700014591217,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9915000200271606,"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":0.6708698272705078},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6262592077255249},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5284887552261353},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4996373653411865},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.447378009557724},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.43931224942207336},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.42863205075263977},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.42412126064300537},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3865883946418762},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36509451270103455},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33674904704093933},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3143177032470703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22743967175483704},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12779638171195984}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6708698272705078},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6262592077255249},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5284887552261353},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4996373653411865},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.447378009557724},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.43931224942207336},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.42863205075263977},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.42412126064300537},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3865883946418762},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36509451270103455},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33674904704093933},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3143177032470703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22743967175483704},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12779638171195984},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"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":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbb.2021.3054738","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3054738","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33497339","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33497339","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/ACM transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2007.09671","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2007.09671","pdf_url":"https://arxiv.org/pdf/2007.09671","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2007.09671","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2007.09671","pdf_url":"https://arxiv.org/pdf/2007.09671","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"text"},"sustainable_development_goals":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1501856433","https://openalex.org/W1544582011","https://openalex.org/W1973758399","https://openalex.org/W1998152384","https://openalex.org/W2005740247","https://openalex.org/W2006683252","https://openalex.org/W2007245700","https://openalex.org/W2008632223","https://openalex.org/W2030530458","https://openalex.org/W2036799174","https://openalex.org/W2037935996","https://openalex.org/W2049803706","https://openalex.org/W2077820538","https://openalex.org/W2095612544","https://openalex.org/W2095705004","https://openalex.org/W2099651125","https://openalex.org/W2101234009","https://openalex.org/W2105295234","https://openalex.org/W2109196093","https://openalex.org/W2111967267","https://openalex.org/W2113553645","https://openalex.org/W2115746733","https://openalex.org/W2116341502","https://openalex.org/W2118258530","https://openalex.org/W2130687290","https://openalex.org/W2130790725","https://openalex.org/W2133776083","https://openalex.org/W2135526239","https://openalex.org/W2140948740","https://openalex.org/W2161257056","https://openalex.org/W2180291937","https://openalex.org/W2201354711","https://openalex.org/W2311607323","https://openalex.org/W2326727950","https://openalex.org/W2334956771","https://openalex.org/W2467366894","https://openalex.org/W2512143001","https://openalex.org/W2519887557","https://openalex.org/W2543582635","https://openalex.org/W2563010899","https://openalex.org/W2578600712","https://openalex.org/W2766453196","https://openalex.org/W2766676715","https://openalex.org/W2766955181","https://openalex.org/W2770671706","https://openalex.org/W2790765877","https://openalex.org/W2790937047","https://openalex.org/W2899771611","https://openalex.org/W2900569176","https://openalex.org/W2908485946","https://openalex.org/W2912802963","https://openalex.org/W2912984848","https://openalex.org/W2915554882","https://openalex.org/W2917858269","https://openalex.org/W2918342466","https://openalex.org/W2949280944","https://openalex.org/W2949676527","https://openalex.org/W2962756421","https://openalex.org/W2963403868","https://openalex.org/W2964015378","https://openalex.org/W2972935357","https://openalex.org/W2991321419","https://openalex.org/W3005749954","https://openalex.org/W3015490653","https://openalex.org/W3020930839","https://openalex.org/W3087747512","https://openalex.org/W3096561213","https://openalex.org/W4288419263","https://openalex.org/W6674330103","https://openalex.org/W6675354045","https://openalex.org/W6726873649","https://openalex.org/W6739901393","https://openalex.org/W6760045743"],"related_works":["https://openalex.org/W2130939068","https://openalex.org/W3163717165","https://openalex.org/W2932872266","https://openalex.org/W2114466827","https://openalex.org/W249159571","https://openalex.org/W2791736663","https://openalex.org/W2806770614","https://openalex.org/W2129949791","https://openalex.org/W2131550814","https://openalex.org/W1710460698"],"abstract_inverted_index":{"Identifying":[0],"essential":[1,46,194],"genes":[2,195],"and":[3,16,31,63,151,155,178,189,196],"proteins":[4],"is":[5,51],"a":[6,10,157,187],"critical":[7],"step":[8],"towards":[9],"better":[11],"understanding":[12],"of":[13,34,61],"human":[14],"biology":[15],"pathology.":[17],"Computational":[18],"approaches":[19],"helped":[20],"to":[21,44,69,144,192],"mitigate":[22],"experimental":[23],"constraints":[24],"by":[25],"exploring":[26],"machine":[27],"learning":[28],"(ML)":[29],"methods":[30,66,154],"the":[32,162,170,183],"correlation":[33],"essentiality":[35,110,136],"with":[36,137,176],"biological":[37],"information,":[38],"especially":[39],"protein-protein":[40],"interaction":[41],"(PPI)":[42],"networks,":[43,114],"predict":[45],"genes.":[47],"Nonetheless,":[48],"their":[49],"performance":[50,160],"still":[52],"limited,":[53],"as":[54,75,122],"network-based":[55,150],"centralities":[56],"are":[57,67,95],"not":[58],"exclusive":[59],"proxies":[60],"essentiality,":[62],"traditional":[64],"ML":[65],"unable":[68],"learn":[70],"from":[71,112,118,142],"non-euclidean":[72],"domains":[73],"such":[74],"graphs.":[76],"Given":[77],"these":[78],"limitations,":[79],"we":[80],"proposed":[81,184],"EPGAT,":[82],"an":[83],"approach":[84,173,185],"for":[85,128],"Essentiality":[86],"Prediction":[87],"based":[88],"on":[89,102],"Graph":[90,97],"Attention":[91],"Networks":[92,99],"(GATs),":[93],"which":[94],"attention-based":[96],"Neural":[98],"(GNNs),":[100],"operating":[101],"graph-structured":[103],"data.":[104,181],"Our":[105,146],"model":[106,147],"directly":[107],"learns":[108],"gene":[109,135],"patterns":[111],"PPI":[113],"integrating":[115],"additional":[116],"evidence":[117],"multiomics":[119],"data":[120],"encoded":[121],"node":[123],"attributes.":[124],"We":[125],"benchmarked":[126],"EPGAT":[127,168],"four":[129],"organisms,":[130],"including":[131],"humans,":[132],"accurately":[133],"predicting":[134],"ROC":[138],"AUC":[139],"score":[140],"ranging":[141],"0.78":[143],"0.97.":[145],"significantly":[148],"outperformed":[149],"shallow":[152],"ML-based":[153],"achieved":[156],"very":[158],"competitive":[159],"against":[161],"state-of-the-art":[163],"node2vec":[164],"embedding":[165],"method.":[166],"Notably,":[167],"was":[169],"most":[171],"robust":[172],"in":[174],"scenarios":[175],"limited":[177],"imbalanced":[179],"training":[180],"Thus,":[182],"offers":[186],"powerful":[188],"effective":[190],"way":[191],"identify":[193],"proteins.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":2}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
