{"id":"https://openalex.org/W4296907511","doi":"https://doi.org/10.1093/bib/bbac403","title":"Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism","display_name":"Predicting cell line-specific synergistic drug combinations through a relational graph convolutional network with attention mechanism","publication_year":2022,"publication_date":"2022-09-22","ids":{"openalex":"https://openalex.org/W4296907511","doi":"https://doi.org/10.1093/bib/bbac403","pmid":"https://pubmed.ncbi.nlm.nih.gov/36136353"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac403","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac403","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/A5020548567","display_name":"Peng Zhang","orcid":"https://orcid.org/0000-0001-8780-0892"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peng Zhang","raw_affiliation_strings":["Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073963268","display_name":"Shikui Tu","orcid":"https://orcid.org/0000-0001-6270-0449"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shikui Tu","raw_affiliation_strings":["Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100448121","display_name":"Wen Zhang","orcid":"https://orcid.org/0000-0001-5221-2628"},"institutions":[{"id":"https://openalex.org/I204823248","display_name":"Huazhong Agricultural University","ror":"https://ror.org/023b72294","country_code":"CN","type":"education","lineage":["https://openalex.org/I204823248"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wen Zhang","raw_affiliation_strings":["Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of informatics, Huazhong Agricultural University , Wuhan 430070, China"],"affiliations":[{"raw_affiliation_string":"Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of informatics, Huazhong Agricultural University , Wuhan 430070, China","institution_ids":["https://openalex.org/I204823248"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5111716317","display_name":"Lei Xu","orcid":"https://orcid.org/0000-0002-2752-1573"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Xu","raw_affiliation_strings":["Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Center for Cognitive Machines and Computational Health (CMaCH), Shanghai Jiao Tong University , Shanghai 200240, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5073963268","https://openalex.org/A5100448121"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I204823248"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":5.43,"has_fulltext":false,"cited_by_count":38,"citation_normalized_percentile":{"value":0.96365422,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"23","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.994700014591217,"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/encoder","display_name":"Encoder","score":0.6804094910621643},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6660981178283691},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5410037040710449},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5400979518890381},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4973624050617218},{"id":"https://openalex.org/keywords/line","display_name":"Line (geometry)","score":0.46782439947128296},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44843193888664246},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.44233983755111694},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.41368624567985535},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.34882819652557373},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.31212180852890015},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11766192317008972}],"concepts":[{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6804094910621643},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6660981178283691},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5410037040710449},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5400979518890381},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4973624050617218},{"id":"https://openalex.org/C198352243","wikidata":"https://www.wikidata.org/wiki/Q37105","display_name":"Line (geometry)","level":2,"score":0.46782439947128296},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44843193888664246},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.44233983755111694},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.41368624567985535},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.34882819652557373},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.31212180852890015},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11766192317008972},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004338","descriptor_name":"Drug Combinations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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/bbac403","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac403","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:36136353","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36136353","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":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5899999737739563}],"awards":[{"id":"https://openalex.org/G1311322377","display_name":null,"funder_award_id":"62072206","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2415283116","display_name":null,"funder_award_id":"62172273","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1696775091","https://openalex.org/W1757990252","https://openalex.org/W1984694945","https://openalex.org/W2012401213","https://openalex.org/W2012420916","https://openalex.org/W2015789827","https://openalex.org/W2040904830","https://openalex.org/W2060737851","https://openalex.org/W2061136308","https://openalex.org/W2095705004","https://openalex.org/W2126726407","https://openalex.org/W2137988419","https://openalex.org/W2153372063","https://openalex.org/W2223501982","https://openalex.org/W2299417213","https://openalex.org/W2304111010","https://openalex.org/W2604314403","https://openalex.org/W2608863179","https://openalex.org/W2767891136","https://openalex.org/W2775061087","https://openalex.org/W2786016794","https://openalex.org/W2907272802","https://openalex.org/W2938206352","https://openalex.org/W2942883778","https://openalex.org/W2950860419","https://openalex.org/W2951449549","https://openalex.org/W2960677646","https://openalex.org/W2964054038","https://openalex.org/W2964321699","https://openalex.org/W2990138404","https://openalex.org/W2992010506","https://openalex.org/W2995448904","https://openalex.org/W2998807596","https://openalex.org/W3006302308","https://openalex.org/W3006386963","https://openalex.org/W3011657074","https://openalex.org/W3014482292","https://openalex.org/W3032005109","https://openalex.org/W3032089175","https://openalex.org/W3035302862","https://openalex.org/W3047749858","https://openalex.org/W3088123593","https://openalex.org/W3093030756","https://openalex.org/W3093687066","https://openalex.org/W3096561213","https://openalex.org/W3102269903","https://openalex.org/W3126516421","https://openalex.org/W3127930610","https://openalex.org/W3130506522","https://openalex.org/W3139532774","https://openalex.org/W3142239405","https://openalex.org/W3143789190","https://openalex.org/W3165195325","https://openalex.org/W3178697201","https://openalex.org/W3188733779","https://openalex.org/W3195831412","https://openalex.org/W3199618438","https://openalex.org/W4206405364","https://openalex.org/W4212966936","https://openalex.org/W6631190155","https://openalex.org/W6639832135","https://openalex.org/W6674330103","https://openalex.org/W6689127954","https://openalex.org/W6720006811","https://openalex.org/W6729210268","https://openalex.org/W6769589523","https://openalex.org/W6771692986","https://openalex.org/W6775006995","https://openalex.org/W6778669669","https://openalex.org/W6779477267","https://openalex.org/W6792916831","https://openalex.org/W6798971917"],"related_works":["https://openalex.org/W2159052453","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3167935049","https://openalex.org/W3029198973","https://openalex.org/W2891286602"],"abstract_inverted_index":{"Identifying":[0],"synergistic":[1],"drug":[2,84,134],"combinations":[3],"(SDCs)":[4],"is":[5,19,87,129,151,190,196],"a":[6,55,99,104],"great":[7],"challenge":[8],"due":[9],"to":[10,113,131,143,192,201],"the":[11,15,31,91,111,117,133,140,171,209,213,218],"combinatorial":[12],"complexity":[13],"and":[14,102,115,195],"fact":[16],"that":[17,148,188,205],"SDC":[18,92],"cell":[20,32,47,63,72,77,96,124,164,181,203,227],"line":[21,33,48],"specific.":[22],"The":[23,154],"existing":[24],"computational":[25],"methods":[26,194],"either":[27],"did":[28,38],"not":[29,39,168],"consider":[30],"specificity":[34],"of":[35,94,120,139,220],"SDC,":[36],"or":[37],"perform":[40],"well":[41,75],"by":[42,89],"building":[43],"model":[44,82],"for":[45,61,83,122,179],"each":[46,180],"independently.":[49],"In":[50],"this":[51],"paper,":[52],"we":[53],"present":[54],"novel":[56,225],"encoder-decoder":[57],"network":[58,108],"named":[59],"SDCNet":[60,66,189],"predicting":[62,224],"line-specific":[64,78,165,228],"SDCs.":[65,229],"learns":[67],"common":[68,155],"patterns":[69,156],"across":[70],"different":[71,95,123,137,207],"lines":[73,97,204],"as":[74,76,98,110],"features":[79,135],"in":[80,163,223],"one":[81],"combinations.":[85],"This":[86],"realized":[88],"considering":[90],"graphs":[93],"relational":[100,105],"graph,":[101],"constructing":[103],"graph":[106],"convolutional":[107],"(R-GCN)":[109],"encoder":[112],"learn":[114],"fuse":[116],"deep":[118],"representations":[119],"drugs":[121],"lines.":[125],"An":[126],"attention":[127],"mechanism":[128],"devised":[130],"integrate":[132],"from":[136,208],"layers":[138],"R-GCN":[141],"according":[142],"their":[144],"relative":[145],"importance":[146],"so":[147],"representation":[149],"learning":[150],"further":[152],"enhanced.":[153],"are":[157,206],"exploited":[158],"through":[159],"partial":[160],"parameter":[161],"sharing":[162],"decoders,":[166],"which":[167],"only":[169],"reconstruct":[170],"known":[172],"SDCs":[173],"but":[174],"also":[175,197],"predict":[176],"new":[177,202],"ones":[178],"line.":[182],"Experiments":[183],"on":[184],"various":[185],"datasets":[186],"demonstrate":[187],"superior":[191],"state-of-the-art":[193],"robust":[198],"when":[199],"generalized":[200],"training":[210],"ones.":[211],"Finally,":[212],"case":[214],"study":[215],"again":[216],"confirms":[217],"effectiveness":[219],"our":[221],"method":[222],"reliable":[226]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":10},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":3}],"updated_date":"2026-04-06T07:47:59.780226","created_date":"2025-10-10T00:00:00"}
