{"id":"https://openalex.org/W4285794944","doi":"https://doi.org/10.1093/bib/bbac296","title":"Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug\u2013drug interactions prediction","display_name":"Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug\u2013drug interactions prediction","publication_year":2022,"publication_date":"2022-07-18","ids":{"openalex":"https://openalex.org/W4285794944","doi":"https://doi.org/10.1093/bib/bbac296","pmid":"https://pubmed.ncbi.nlm.nih.gov/35849817"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac296","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac296","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/A5100441863","display_name":"Xudong Zhang","orcid":"https://orcid.org/0000-0003-2671-8275"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xudong Zhang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102965143","display_name":"Gan Wang","orcid":"https://orcid.org/0000-0003-1663-7834"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Gan Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061578352","display_name":"Xiangyu Meng","orcid":"https://orcid.org/0000-0001-5696-3090"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangyu Meng","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100375587","display_name":"Shuang Wang","orcid":"https://orcid.org/0000-0002-6779-9537"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuang Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100716053","display_name":"Ying Zhang","orcid":"https://orcid.org/0009-0003-6424-6675"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Zhang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049425478","display_name":"Alfonso Rodr\u00edguez\u2010Pat\u00f3n","orcid":"https://orcid.org/0000-0001-7289-2114"},"institutions":[{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Alfonso Rodriguez-Paton","raw_affiliation_strings":["Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Campus de Montegancedo , Boadilla del Monte 28660, Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Faculty of Computer Science, Polytechnical University of Madrid, Campus de Montegancedo , Boadilla del Monte 28660, Madrid, Spain","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373521","display_name":"Jianmin Wang","orcid":"https://orcid.org/0000-0001-8910-0929"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Jianmin Wang","raw_affiliation_strings":["The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicin, Yonsei University , Incheon 21983, Korea"],"affiliations":[{"raw_affiliation_string":"The Interdisciplinary Graduate Program in Integrative Biotechnology and Translational Medicin, Yonsei University , Incheon 21983, Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100333854","display_name":"Xun Wang","orcid":"https://orcid.org/0000-0002-2741-433X"},"institutions":[{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xun Wang","raw_affiliation_strings":["College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, China University of Petroleum , Qingdao 266580, China","institution_ids":["https://openalex.org/I4210162190"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100333854","https://openalex.org/A5100373521"],"corresponding_institution_ids":["https://openalex.org/I193775966","https://openalex.org/I4210162190"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":7.3598,"has_fulltext":false,"cited_by_count":56,"citation_normalized_percentile":{"value":0.97777453,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"23","issue":"5","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":1.0,"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":1.0,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9702000021934509,"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":0.7982079386711121},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5664774179458618},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4824724495410919},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.42954784631729126},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.42643237113952637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42299383878707886},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3946811556816101},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38321158289909363},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21824994683265686},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.08825746178627014},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.0860505998134613}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7982079386711121},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5664774179458618},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4824724495410919},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.42954784631729126},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.42643237113952637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42299383878707886},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3946811556816101},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38321158289909363},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21824994683265686},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08825746178627014},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.0860505998134613},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","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":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac296","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac296","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:35849817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35849817","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":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2787410821","display_name":null,"funder_award_id":"21CX06018A","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G4037723416","display_name":null,"funder_award_id":"61873280","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6059194225","display_name":null,"funder_award_id":"61972416","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6683504761","display_name":null,"funder_award_id":"ZR2021QF023","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G833021299","display_name":null,"funder_award_id":"2021YFA1000102\uff0c2021YFA1000103","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W2009313526","https://openalex.org/W2029775948","https://openalex.org/W2112460877","https://openalex.org/W2115896407","https://openalex.org/W2157331557","https://openalex.org/W2255466643","https://openalex.org/W2264517602","https://openalex.org/W2591704587","https://openalex.org/W2597646117","https://openalex.org/W2598912124","https://openalex.org/W2604272474","https://openalex.org/W2612690371","https://openalex.org/W2760923572","https://openalex.org/W2767891136","https://openalex.org/W2790602452","https://openalex.org/W2798749466","https://openalex.org/W2802200505","https://openalex.org/W2944851425","https://openalex.org/W2948035163","https://openalex.org/W2950898568","https://openalex.org/W2963285578","https://openalex.org/W2963925437","https://openalex.org/W2965993245","https://openalex.org/W3018980093","https://openalex.org/W3024534448","https://openalex.org/W3033077186","https://openalex.org/W3109916301","https://openalex.org/W3187647935","https://openalex.org/W3205082786","https://openalex.org/W3206585172","https://openalex.org/W4205463297","https://openalex.org/W4212774754","https://openalex.org/W4213448676","https://openalex.org/W4224326349","https://openalex.org/W4282921483","https://openalex.org/W6685562342","https://openalex.org/W6690815549","https://openalex.org/W6733741073","https://openalex.org/W6750627587","https://openalex.org/W6769627184","https://openalex.org/W6787273344","https://openalex.org/W6805850347","https://openalex.org/W6810860524"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4224009465","https://openalex.org/W4286629047","https://openalex.org/W4306321456","https://openalex.org/W4285260836","https://openalex.org/W3046775127","https://openalex.org/W3170094116","https://openalex.org/W4205958290","https://openalex.org/W4381956280"],"abstract_inverted_index":{"Multi-drug":[0],"combinations":[1],"for":[2,99,179,229],"the":[3,23,42,48,75,82,104,114,132,140,147,155,162,172,177,185,216,230,240],"treatment":[4,18],"of":[5,17,22,41,50,77,108,164,171,226,239],"complex":[6],"diseases":[7],"are":[8,32,44,245],"gradually":[9],"becoming":[10],"an":[11],"important":[12],"treatment,":[13],"and":[14,38,53,79,112,126,149,182,209,234,236,243],"this":[15,86],"type":[16],"can":[19,167],"take":[20],"advantage":[21],"synergistic":[24],"effects":[25],"among":[26],"drugs.":[27],"However,":[28],"drug-drug":[29],"interactions":[30,228],"(DDIs)":[31],"not":[33,137],"just":[34],"all":[35],"beneficial.":[36],"Accurate":[37],"rapid":[39],"identifications":[40],"DDIs":[43,59,100,213],"essential":[45],"to":[46,129,159,175,187,223],"enhance":[47],"effectiveness":[49],"combination":[51],"therapy":[52],"avoid":[54],"unintended":[55],"side":[56],"effects.":[57],"Traditional":[58],"prediction":[60],"methods":[61,204],"use":[62,154,170],"only":[63,138],"drug":[64,68,194],"sequence":[65],"information":[66,73],"or":[67],"graph":[69,116],"information,":[70],"which":[71,136,166],"ignores":[72],"about":[74],"position":[76],"atoms":[78],"edges":[80],"in":[81,205],"spatial":[83,118],"structure.":[84],"In":[85,215],"paper,":[87],"we":[88,153,220],"propose":[89],"Molormer,":[90,165],"a":[91,95],"method":[92,201],"based":[93],"on":[94,211],"lightweight":[96],"attention":[97,124,142],"mechanism":[98,125,143],"prediction.":[101],"Molormer":[102,121,222],"takes":[103],"two-dimension":[105],"(2D)":[106],"structures":[107],"drugs":[109,231],"as":[110,161],"input":[111],"encodes":[113],"molecular":[115,134],"with":[117,193],"information.":[119],"Besides,":[120],"uses":[122],"lightweight-based":[123],"self-attention":[127],"distilling":[128],"process":[130],"spatially":[131],"encoded":[133],"graph,":[135],"retains":[139],"multi-headed":[141],"but":[144],"also":[145,183],"reduces":[146],"computational":[148],"storage":[150],"costs.":[151],"Finally,":[152],"Siamese":[156],"network":[157],"architecture":[158,163],"serve":[160],"make":[168,224],"full":[169],"limited":[173],"data":[174],"train":[176],"model":[178],"better":[180],"performance":[181],"limit":[184],"differences":[186],"some":[188],"extent":[189],"between":[190],"networks":[191],"dealing":[192],"features.":[195],"Experiments":[196],"show":[197],"that":[198],"our":[199],"proposed":[200],"outperforms":[202],"state-of-the-art":[203],"Accuracy,":[206],"Precision,":[207],"Recall":[208],"F1":[210],"multi-label":[212],"dataset.":[214],"case":[217],"study":[218],"section,":[219],"used":[221],"predictions":[225],"new":[227],"Aliskiren,":[232],"Selexipag":[233],"Vorapaxar":[235],"validated":[237],"parts":[238],"predictions.":[241],"Code":[242],"models":[244],"available":[246],"at":[247],"https://github.com/IsXudongZhang/Molormer.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
