{"id":"https://openalex.org/W3209941363","doi":"https://doi.org/10.1093/bib/bbab449","title":"A similarity-based deep learning approach for determining the frequencies of drug side effects","display_name":"A similarity-based deep learning approach for determining the frequencies of drug side effects","publication_year":2021,"publication_date":"2021-10-01","ids":{"openalex":"https://openalex.org/W3209941363","doi":"https://doi.org/10.1093/bib/bbab449","mag":"3209941363","pmid":"https://pubmed.ncbi.nlm.nih.gov/34718402"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab449","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab449","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/A5103090768","display_name":"Haochen Zhao","orcid":"https://orcid.org/0000-0002-3854-4682"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haochen Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116548940","display_name":"Shaokai Wang","orcid":"https://orcid.org/0009-0003-2741-7914"},"institutions":[{"id":"https://openalex.org/I151746483","display_name":"University of Waterloo","ror":"https://ror.org/01aff2v68","country_code":"CA","type":"education","lineage":["https://openalex.org/I151746483"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Shaokai Wang","raw_affiliation_strings":["School of David R. Cheriton School of Computer Science, University of Waterloo, Canada"],"affiliations":[{"raw_affiliation_string":"School of David R. Cheriton School of Computer Science, University of Waterloo, Canada","institution_ids":["https://openalex.org/I151746483"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041593217","display_name":"Kai Zheng","orcid":"https://orcid.org/0000-0001-9275-1239"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001452497","display_name":"Qichang Zhao","orcid":"https://orcid.org/0000-0002-8319-9793"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qichang Zhao","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100755257","display_name":"Feng Zhu","orcid":"https://orcid.org/0000-0001-8069-0053"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Zhu","raw_affiliation_strings":["College of Pharmaceutical Sciences in Zhejiang University, China"],"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences in Zhejiang University, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100438360","display_name":"Jianxin Wang","orcid":"https://orcid.org/0000-0003-1516-0480"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jianxin Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.089,"has_fulltext":false,"cited_by_count":44,"citation_normalized_percentile":{"value":0.94497616,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"23","issue":"1","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":0.9997000098228455,"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":0.9997000098228455,"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/T11943","display_name":"Pharmacovigilance and Adverse Drug Reactions","score":0.9896000027656555,"subfield":{"id":"https://openalex.org/subfields/3005","display_name":"Toxicology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9749000072479248,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.8010593056678772},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6479450464248657},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5598313212394714},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5422372221946716},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4876624345779419},{"id":"https://openalex.org/keywords/side-chain","display_name":"Side chain","score":0.44105905294418335},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42997226119041443},{"id":"https://openalex.org/keywords/far-side-of-the-moon","display_name":"Far side of the Moon","score":0.41842859983444214},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32156050205230713},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2715985178947449},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.17287874221801758},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10072359442710876}],"concepts":[{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.8010593056678772},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6479450464248657},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5598313212394714},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5422372221946716},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4876624345779419},{"id":"https://openalex.org/C204921945","wikidata":"https://www.wikidata.org/wiki/Q899689","display_name":"Side chain","level":3,"score":0.44105905294418335},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42997226119041443},{"id":"https://openalex.org/C107195362","wikidata":"https://www.wikidata.org/wiki/Q816838","display_name":"Far side of the Moon","level":2,"score":0.41842859983444214},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32156050205230713},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2715985178947449},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.17287874221801758},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10072359442710876},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C8058405","wikidata":"https://www.wikidata.org/wiki/Q46255","display_name":"Geophysics","level":1,"score":0.0},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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/bbab449","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab449","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:34718402","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34718402","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":0.699999988079071,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G2668227021","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320320064","funder_display_name":"Scottish Funding Council"},{"id":"https://openalex.org/G4043378463","display_name":null,"funder_award_id":"61832019","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8740223855","display_name":null,"funder_award_id":"61772552","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320320064","display_name":"Scottish Funding Council","ror":"https://ror.org/056bwcz71"},{"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":53,"referenced_works":["https://openalex.org/W1484138821","https://openalex.org/W1601670221","https://openalex.org/W1969112208","https://openalex.org/W1977878526","https://openalex.org/W1982499183","https://openalex.org/W2002673340","https://openalex.org/W2003027810","https://openalex.org/W2015874712","https://openalex.org/W2017567635","https://openalex.org/W2019650183","https://openalex.org/W2029599836","https://openalex.org/W2047708582","https://openalex.org/W2049946556","https://openalex.org/W2058882666","https://openalex.org/W2060240021","https://openalex.org/W2068871297","https://openalex.org/W2074041943","https://openalex.org/W2077057698","https://openalex.org/W2119002393","https://openalex.org/W2131347449","https://openalex.org/W2142572836","https://openalex.org/W2145578524","https://openalex.org/W2157142912","https://openalex.org/W2166467489","https://openalex.org/W2202042777","https://openalex.org/W2234451305","https://openalex.org/W2512831247","https://openalex.org/W2615117870","https://openalex.org/W2767669124","https://openalex.org/W2767891136","https://openalex.org/W2777416523","https://openalex.org/W2783132606","https://openalex.org/W2895757710","https://openalex.org/W2896605526","https://openalex.org/W2902773418","https://openalex.org/W2916888356","https://openalex.org/W2920795827","https://openalex.org/W2951434717","https://openalex.org/W2955202322","https://openalex.org/W2963323306","https://openalex.org/W3022502706","https://openalex.org/W3030186245","https://openalex.org/W3080709495","https://openalex.org/W3085898256","https://openalex.org/W3100591234","https://openalex.org/W3137198614","https://openalex.org/W3160752125","https://openalex.org/W3174291985","https://openalex.org/W6669564591","https://openalex.org/W6730069992","https://openalex.org/W6785332826","https://openalex.org/W6792009056","https://openalex.org/W6797244631"],"related_works":["https://openalex.org/W2785332413","https://openalex.org/W2411788938","https://openalex.org/W2616782662","https://openalex.org/W3151349532","https://openalex.org/W2767671145","https://openalex.org/W2491102388","https://openalex.org/W4238542335","https://openalex.org/W2314508957","https://openalex.org/W3150243100","https://openalex.org/W2567278004"],"abstract_inverted_index":{"The":[0,177,207],"side":[1,16,39,55,65,78,99,122,141,168],"effects":[2,17,40,56],"of":[3,18,41,64,76,120,144,171,200],"drugs":[4,19,42,96,146,173],"present":[5],"growing":[6],"concern":[7],"attention":[8],"in":[9,174,204],"the":[10,15,37,62,74,84,118,126,140,161,167,175,198],"healthcare":[11],"system.":[12],"Accurately":[13],"identifying":[14],"is":[20,160,183],"very":[21],"important":[22],"for":[23,116],"drug":[24,77,121],"development":[25],"and":[26,43,59,134,210,218],"risk":[27],"assessment.":[28],"Some":[29],"computational":[30],"models":[31],"have":[32],"been":[33],"developed":[34],"to":[35,94,138,186],"predict":[36,53,73,139,166],"potential":[38],"provided":[44],"satisfactory":[45],"performance.":[46],"However,":[47],"most":[48],"existing":[49,70,127],"methods":[50,71],"can":[51,72,135,165],"only":[52],"whether":[54],"will":[57],"occur":[58],"cannot":[60,91],"determine":[61],"frequency":[63,75,101,154],"effects.":[66,123],"Although":[67],"a":[68,108],"few":[69],"effects,":[79],"they":[80,90],"strongly":[81],"depend":[82],"on":[83],"known":[85,98,149],"drug-side":[86,150],"effect":[87,100,142,151,169],"relationships.":[88],"Therefore,":[89],"be":[92,136],"applied":[93,137],"new":[95,145,172],"without":[97,147],"information.":[102,155],"In":[103,191],"this":[104,159],"paper,":[105],"we":[106],"develop":[107],"novel":[109],"similarity-based":[110],"deep":[111],"learning":[112],"method,":[113],"named":[114],"SDPred,":[115],"determining":[117],"frequencies":[119,143,170],"Compared":[124],"with":[125],"state-of-the-art":[128],"models,":[129],"SDPred":[130,182,208],"integrates":[131],"rich":[132],"features":[133],"any":[148],"association":[152],"or":[153],"To":[156],"our":[157,201],"knowledge,":[158],"first":[162],"work":[163],"that":[164,181],"population.":[176],"comparison":[178],"results":[179],"indicate":[180],"much":[184],"superior":[185],"all":[187],"previously":[188],"reported":[189],"models.":[190],"addition,":[192],"some":[193],"case":[194],"studies":[195],"also":[196],"demonstrate":[197],"effectiveness":[199],"proposed":[202],"method":[203],"practical":[205],"applications.":[206],"software":[209],"data":[211],"are":[212],"freely":[213],"available":[214],"at":[215],"https://github.com/zhc940702/SDPred,":[216],"https://zenodo.org/record/5112573":[217],"https://hub.docker.com/r/zhc940702/sdpred.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":14},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":4}],"updated_date":"2026-04-11T08:14:18.477133","created_date":"2025-10-10T00:00:00"}
