{"id":"https://openalex.org/W3131175301","doi":"https://doi.org/10.1093/bioinformatics/btab110","title":"Graph contextualized attention network for predicting synthetic lethality in human cancers","display_name":"Graph contextualized attention network for predicting synthetic lethality in human cancers","publication_year":2021,"publication_date":"2021-02-16","ids":{"openalex":"https://openalex.org/W3131175301","doi":"https://doi.org/10.1093/bioinformatics/btab110","mag":"3131175301","pmid":"https://pubmed.ncbi.nlm.nih.gov/33609108"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab110","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab110","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/A5066627747","display_name":"Yahui Long","orcid":"https://orcid.org/0000-0002-2765-3007"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Yahui Long","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410000, China","School of Computer Science and Engineering, Nanyang Technological University , Singapore 639798, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410000, China","institution_ids":["https://openalex.org/I16609230"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University , Singapore 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100340964","display_name":"Min Wu","orcid":"https://orcid.org/0000-0003-0977-3600"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Min Wu","raw_affiliation_strings":["Machine Intellection Department, Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR) , Singapore 138632, Singapore"],"raw_orcid":"https://orcid.org/0000-0003-0977-3600","affiliations":[{"raw_affiliation_string":"Machine Intellection Department, Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR) , Singapore 138632, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072988055","display_name":"Yong Liu","orcid":"https://orcid.org/0000-0001-9031-9696"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Yong Liu","raw_affiliation_strings":["Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly, Nanyang Technological University , Singapore 639798, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint NTU-UBC Research Centre of Excellence in Active Living for the Elderly, Nanyang Technological University , Singapore 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014529529","display_name":"Jie Zheng","orcid":"https://orcid.org/0000-0001-6774-9786"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Zheng","raw_affiliation_strings":["School of Information Science and Technology, ShanghaiTech University , Shanghai, 201210, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, ShanghaiTech University , Shanghai, 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee Keong Kwoh","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University , Singapore 639798, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University , Singapore 639798, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026469278","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-2385-8272"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410000, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410000, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100418684","display_name":"Xiaoli Li","orcid":"https://orcid.org/0000-0002-0762-6562"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Xiaoli Li","raw_affiliation_strings":["Machine Intellection Department, Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR) , Singapore 138632, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Machine Intellection Department, Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR) , Singapore 138632, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026469278","https://openalex.org/A5100418684"],"corresponding_institution_ids":["https://openalex.org/I115228651","https://openalex.org/I16609230","https://openalex.org/I3005327000"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.9341,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.92284958,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":99},"biblio":{"volume":"37","issue":"16","first_page":"2432","last_page":"2440"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6690999865531921,"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":0.6690999865531921,"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":0.06689999997615814,"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":0.033399999141693115,"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":0.7063020467758179},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.6189504861831665},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5968325138092041},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5655839443206787},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.530206561088562},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5034412741661072},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46807798743247986},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.45634424686431885},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4490818977355957},{"id":"https://openalex.org/keywords/perceptron","display_name":"Perceptron","score":0.44772958755493164},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3406323194503784},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3281717002391815},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2735382318496704},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.1989937424659729}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7063020467758179},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.6189504861831665},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5968325138092041},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5655839443206787},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.530206561088562},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5034412741661072},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46807798743247986},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.45634424686431885},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4490818977355957},{"id":"https://openalex.org/C60908668","wikidata":"https://www.wikidata.org/wiki/Q690207","display_name":"Perceptron","level":3,"score":0.44772958755493164},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3406323194503784},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3281717002391815},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2735382318496704},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.1989937424659729},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab110","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab110","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33609108","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33609108","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6299999952316284,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1342612824","display_name":"MicroRNA\u5bf9\u57fa\u56e0\u7684\u8c03\u63a7\u4f5c\u7528\u53ca\u5176\u4e0e\u75be\u75c5\u5173\u8054\u5173\u7cfb\u7684\u8ba1\u7b97\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61873089","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7362438383","display_name":null,"funder_award_id":"201906130027","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1895317372","https://openalex.org/W1966182052","https://openalex.org/W1975414584","https://openalex.org/W2009931781","https://openalex.org/W2010391389","https://openalex.org/W2029346055","https://openalex.org/W2044511756","https://openalex.org/W2045953361","https://openalex.org/W2107975811","https://openalex.org/W2123688186","https://openalex.org/W2124156743","https://openalex.org/W2153166923","https://openalex.org/W2159906261","https://openalex.org/W2160584334","https://openalex.org/W2165492471","https://openalex.org/W2256553158","https://openalex.org/W2420913016","https://openalex.org/W2465015709","https://openalex.org/W2518731133","https://openalex.org/W2614103706","https://openalex.org/W2618439945","https://openalex.org/W2704159227","https://openalex.org/W2735914287","https://openalex.org/W2741508285","https://openalex.org/W2752877365","https://openalex.org/W2793951981","https://openalex.org/W2883529879","https://openalex.org/W2917858269","https://openalex.org/W2939312265","https://openalex.org/W2963277165","https://openalex.org/W2963984147","https://openalex.org/W2967109100","https://openalex.org/W2971769670","https://openalex.org/W2972528761","https://openalex.org/W2982352208","https://openalex.org/W2990747402","https://openalex.org/W2995178483","https://openalex.org/W3009246021","https://openalex.org/W3013279271","https://openalex.org/W3037489518","https://openalex.org/W3080295962","https://openalex.org/W3098487500","https://openalex.org/W6719270105"],"related_works":["https://openalex.org/W17155033","https://openalex.org/W3207760230","https://openalex.org/W1496222301","https://openalex.org/W4312814274","https://openalex.org/W3199964822","https://openalex.org/W4232132981","https://openalex.org/W4238046985","https://openalex.org/W3164948662","https://openalex.org/W3003242282","https://openalex.org/W3153597579"],"abstract_inverted_index":{"MOTIVATION:":[0],"Synthetic":[1],"Lethality":[2],"(SL)":[3],"plays":[4],"an":[5,45],"increasingly":[6],"critical":[7],"role":[8],"in":[9,38,79,256],"the":[10,32,56,81,141,161,175,186,190,198,204,217,250,277],"targeted":[11],"anticancer":[12],"therapeutics.":[13],"In":[14,85,105,244],"addition,":[15,86,245],"identifying":[16,257],"SL":[17,42,61,73,102,123,259],"interactions":[18,43],"can":[19,47],"create":[20],"opportunities":[21],"to":[22,54,92,118,131,158,184,202,211],"selectively":[23],"kill":[24],"cancer":[25],"cells":[26],"without":[27,99],"harming":[28],"normal":[29],"cells.":[30],"Given":[31],"high":[33],"cost":[34],"of":[35,41,59,83,163,219,252],"wet-lab":[36],"experiments,":[37],"silico":[39],"prediction":[40],"as":[44,140],"alternative":[46],"be":[48],"a":[49,110],"rapid":[50],"and":[51,165,168,171,192,195,265,273],"cost-effective":[52],"way":[53],"guide":[55],"experimental":[57,226],"screening":[58],"candidate":[60],"pairs.":[62,260],"Several":[63],"matrix":[64],"factorization-based":[65],"methods":[66,242],"have":[67],"recently":[68],"been":[69],"proposed":[70,254],"for":[71,96,122,136,144,149,174],"human":[72],"prediction.":[74,124],"However,":[75],"they":[76],"are":[77,267,284],"limited":[78],"capturing":[80],"dependencies":[82],"neighbors.":[84],"it":[87],"is":[88],"also":[89],"highly":[90],"challenging":[91],"make":[93],"accurate":[94],"predictions":[95],"new":[97],"genes":[98],"any":[100],"known":[101],"partners.":[103],"RESULTS:":[104],"this":[106],"work,":[107],"we":[108,126,153,207],"propose":[109],"novel":[111,258],"graph":[112],"contextualized":[113],"attention":[114,156,210],"network":[115],"named":[116],"GCATSL":[117,146,237],"learn":[119,169],"gene":[120],"representations":[121,173,194,214],"First,":[125],"leverage":[127],"different":[128,220,232],"data":[129,283],"sources":[130],"construct":[132],"multiple":[133],"feature":[134,142,151,221],"graphs":[135,222],"genes,":[137],"which":[138],"serve":[139],"inputs":[143],"our":[145,236,253],"method.":[147],"Second,":[148],"each":[150],"graph,":[152],"design":[154,208],"node-level":[155],"mechanism":[157],"effectively":[159],"capture":[160],"importance":[162,218],"local":[164,170,191],"global":[166,172,193],"neighbors":[167],"nodes,":[176],"respectively.":[177],"We":[178],"further":[179,248],"exploit":[180],"multi-layer":[181],"perceptron":[182],"(MLP)":[183],"aggregate":[185],"original":[187],"features":[188],"with":[189],"then":[196],"derive":[197,203],"feature-specific":[199,213],"representations.":[200],"Third,":[201],"final":[205],"representations,":[206],"feature-level":[209],"integrate":[212],"by":[215],"taking":[216],"into":[223],"account.":[224],"Extensive":[225],"results":[227],"on":[228,270],"three":[229],"datasets":[230],"under":[231,276],"settings":[233],"demonstrated":[234],"that":[235],"model":[238,255],"outperforms":[239],"14":[240],"state-of-the-art":[241],"consistently.":[243],"case":[246],"studies":[247],"validated":[249],"effectiveness":[251],"AVAILABILITYAND":[261],"IMPLEMENTATION:":[262],"Python":[263],"codes":[264],"dataset":[266],"freely":[268],"available":[269,285],"GitHub":[271],"(https://github.com/longyahui/GCATSL)":[272],"Zenodo":[274],"(https://zenodo.org/record/4522679)":[275],"MIT":[278],"license.":[279],"SUPPLEMENTARY":[280],"INFORMATION:":[281],"Supplementary":[282],"at":[286],"Bioinformatics":[287],"online.":[288]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}