{"id":"https://openalex.org/W2772272229","doi":"https://doi.org/10.1186/s12918-017-0477-2","title":"A unified frame of predicting side effects of drugs by using linear neighborhood similarity","display_name":"A unified frame of predicting side effects of drugs by using linear neighborhood similarity","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2772272229","doi":"https://doi.org/10.1186/s12918-017-0477-2","mag":"2772272229","pmid":"https://pubmed.ncbi.nlm.nih.gov/29297371"},"language":"en","primary_location":{"id":"doi:10.1186/s12918-017-0477-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0477-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-017-0477-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-017-0477-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100448121","display_name":"Wen Zhang","orcid":"https://orcid.org/0000-0001-5221-2628"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen Zhang","raw_affiliation_strings":["School of Computer, Wuhan University, Wuhan, 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer, Wuhan University, Wuhan, 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086600391","display_name":"Xiang Yue","orcid":"https://orcid.org/0000-0003-4547-1685"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Yue","raw_affiliation_strings":["International School of Software, Wuhan University, Wuhan, 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"International School of Software, Wuhan University, Wuhan, 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100415260","display_name":"Feng Liu","orcid":"https://orcid.org/0000-0002-3301-7613"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Liu","raw_affiliation_strings":["International School of Software, Wuhan University, Wuhan, 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"International School of Software, Wuhan University, Wuhan, 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114986023","display_name":"Yanlin Chen","orcid":"https://orcid.org/0009-0000-5600-8827"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanlin Chen","raw_affiliation_strings":["School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan University, Wuhan, 430072, China","institution_ids":["https://openalex.org/I37461747"]}]},{"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":false,"raw_author_name":"Shikui Tu","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101508701","display_name":"Xining Zhang","orcid":"https://orcid.org/0000-0002-9426-6453"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xining Zhang","raw_affiliation_strings":["School of Computer, Wuhan University, Wuhan, 430072, China. zhangxn@whu.edu.cn","School of Computer, Wuhan University, Wuhan, 430072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer, Wuhan University, Wuhan, 430072, China. zhangxn@whu.edu.cn","institution_ids":["https://openalex.org/I37461747"]},{"raw_affiliation_string":"School of Computer, Wuhan University, Wuhan, 430072, China","institution_ids":["https://openalex.org/I37461747"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101508701"],"corresponding_institution_ids":["https://openalex.org/I37461747"],"apc_list":{"value":2290,"currency":"USD","value_usd":2290},"apc_paid":{"value":2290,"currency":"USD","value_usd":2290},"fwci":6.1631,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.97094193,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"11","issue":"S6","first_page":"101","last_page":"101"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9323999881744385,"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":0.9323999881744385,"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":0.01679999940097332,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.009999999776482582,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.7150177955627441},{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.6625845432281494},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5229578614234924},{"id":"https://openalex.org/keywords/linear-model","display_name":"Linear model","score":0.45147979259490967},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4139013886451721},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3337544798851013},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3105004131793976},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2955949902534485},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16104531288146973},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.11814433336257935}],"concepts":[{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.7150177955627441},{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.6625845432281494},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5229578614234924},{"id":"https://openalex.org/C163175372","wikidata":"https://www.wikidata.org/wiki/Q3339222","display_name":"Linear model","level":2,"score":0.45147979259490967},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4139013886451721},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3337544798851013},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3105004131793976},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2955949902534485},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16104531288146973},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.11814433336257935},{"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}],"mesh":[{"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":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":4,"locations":[{"id":"doi:10.1186/s12918-017-0477-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0477-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-017-0477-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:29297371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29297371","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":"BMC systems biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:52a1b6798e8d423f95498b7fcd20266d","is_oa":false,"landing_page_url":"https://doaj.org/article/52a1b6798e8d423f95498b7fcd20266d","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Systems Biology, Vol 11, Iss S6, Pp 23-34 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4668054","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5751767","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12918-017-0477-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12918-017-0477-2","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/s12918-017-0477-2","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7099999785423279,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2772272229.pdf","grobid_xml":"https://content.openalex.org/works/W2772272229.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1161601223","https://openalex.org/W1969198379","https://openalex.org/W1971387816","https://openalex.org/W1976311337","https://openalex.org/W1977310857","https://openalex.org/W1979845492","https://openalex.org/W1980121140","https://openalex.org/W2002745879","https://openalex.org/W2009313526","https://openalex.org/W2018518196","https://openalex.org/W2031133736","https://openalex.org/W2039656193","https://openalex.org/W2040135138","https://openalex.org/W2044542784","https://openalex.org/W2047708582","https://openalex.org/W2049946556","https://openalex.org/W2051730284","https://openalex.org/W2053186076","https://openalex.org/W2065424176","https://openalex.org/W2074192927","https://openalex.org/W2085398335","https://openalex.org/W2120009105","https://openalex.org/W2125748363","https://openalex.org/W2127553917","https://openalex.org/W2136127280","https://openalex.org/W2137052779","https://openalex.org/W2138995863","https://openalex.org/W2142572836","https://openalex.org/W2151241390","https://openalex.org/W2152454589","https://openalex.org/W2154896031","https://openalex.org/W2170146596","https://openalex.org/W2171437346","https://openalex.org/W2234451305","https://openalex.org/W2339812959","https://openalex.org/W2508414719","https://openalex.org/W2570516417","https://openalex.org/W2572837991","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2411788938","https://openalex.org/W4206379684","https://openalex.org/W2375480909","https://openalex.org/W2353314428","https://openalex.org/W2012019886","https://openalex.org/W2166090428","https://openalex.org/W2381021552","https://openalex.org/W2354749003","https://openalex.org/W2366105490","https://openalex.org/W2377121353"],"abstract_inverted_index":{"BACKGROUND:":[0],"Drug":[1],"side":[2,19,51,62,80,123,129,134,161,174,190,204,222,234,245,254],"effects":[3,20,63,130,162,191,205,246,255],"are":[4],"one":[5],"of":[6,22,43,92,163,176,184,192,199,206,221,247,256],"main":[7],"concerns":[8],"in":[9,78,102,188,201],"the":[10,26,50,73,79,115,118,122,147,168,182,197,213,219,226,240],"drug":[11,18,104,128],"discovery,":[12],"which":[13,99],"gains":[14],"wide":[15],"attentions.":[16],"Investigating":[17],"is":[21,64,76,100],"great":[23,41],"importance,":[24],"and":[25,69,126,155,166,186,195,225],"computational":[27,44],"prediction":[28,236],"can":[29,217,231,243],"help":[30],"to":[31,71,159,171],"guide":[32],"wet":[33],"experiments.":[34],"As":[35],"far":[36],"as":[37,250,252],"we":[38,87,113,151],"known,":[39],"a":[40,89,103,138,142,260],"number":[42],"methods":[45,230,242],"have":[46],"been":[47],"proposed":[48,241],"for":[49,67],"effect":[52,81,124,135,175,223,235],"predictions.":[53,82],"The":[54,209],"assumption":[55],"that":[56,212],"similar":[57],"drugs":[58,249,258],"may":[59],"induce":[60],"same":[61],"usually":[65],"employed":[66],"modeling,":[68],"how":[70],"calculate":[72],"drug-drug":[74,93],"similarity":[75,94,116,216],"critical":[77],"RESULTS:":[83],"In":[84],"this":[85],"paper,":[86],"present":[88],"novel":[90],"measure":[91],"named":[95],"\"linear":[96],"neighborhood":[97,110,149,215,228],"similarity\",":[98],"calculated":[101],"feature":[105,119],"space":[106,120],"by":[107,131],"exploring":[108],"linear":[109,148,214,227],"relationship.":[111],"Then,":[112],"transfer":[114],"from":[117],"into":[121],"space,":[125],"predict":[127,160,172,244],"propagating":[132],"known":[133],"information":[136],"through":[137],"similarity-based":[139,229],"graph.":[140],"Under":[141],"unified":[143,261],"frame":[144],"based":[145],"on":[146],"similarity,":[150],"propose":[152,167],"method":[153,169],"\"LNSM\"":[154],"its":[156],"extension":[157],"\"LNSM-SMI\"":[158],"new":[164,193,248],"drugs,":[165,194],"\"LNSM-MSE\"":[170],"unobserved":[173,253],"approved":[177,207,257],"drugs.":[178,208],"CONCLUSIONS:":[179],"We":[180],"evaluate":[181,196],"performances":[183,198,220],"LNSM":[185],"LNSM-SMI":[187],"predicting":[189,202],"LNSM-MSE":[200],"missing":[203],"results":[210],"demonstrate":[211],"improve":[218],"prediction,":[224],"outperform":[232],"existing":[233],"methods.":[237],"More":[238],"importantly,":[239],"well":[251],"under":[259],"frame.":[262]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":14}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
