{"id":"https://openalex.org/W2469049024","doi":"https://doi.org/10.1093/bioinformatics/btw342","title":"A probabilistic approach for collective similarity-based drug\u2013drug interaction prediction","display_name":"A probabilistic approach for collective similarity-based drug\u2013drug interaction prediction","publication_year":2016,"publication_date":"2016-06-26","ids":{"openalex":"https://openalex.org/W2469049024","doi":"https://doi.org/10.1093/bioinformatics/btw342","mag":"2469049024","pmid":"https://pubmed.ncbi.nlm.nih.gov/27354693"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw342","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/20/3175/25040491/btw342.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/20/3175/25040491/btw342.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109398524","display_name":"Dhanya Sridhar","orcid":null},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dhanya Sridhar","raw_affiliation_strings":["1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077611411","display_name":"Shobeir Fakhraei","orcid":"https://orcid.org/0000-0001-8532-6023"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shobeir Fakhraei","raw_affiliation_strings":["1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA","2 Computer Science Department, University of Maryland, College Park, MD 20740, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"2 Computer Science Department, University of Maryland, College Park, MD 20740, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086169451","display_name":"Lise Getoor","orcid":null},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lise Getoor","raw_affiliation_strings":["1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Computer Science Department, University of California Santa Cruz, Santa Cruz, CA 95050, USA","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5109398524"],"corresponding_institution_ids":["https://openalex.org/I185103710"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":11.1743,"has_fulltext":false,"cited_by_count":142,"citation_normalized_percentile":{"value":0.98513557,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"32","issue":"20","first_page":"3175","last_page":"3182"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6679999828338623,"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":0.6679999828338623,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.17110000550746918,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.030400000512599945,"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/computer-science","display_name":"Computer science","score":0.8043936491012573},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.7301371097564697},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6204203963279724},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5585677623748779},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5126892328262329},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5080983638763428},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47095638513565063},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.4206514358520508},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.414201945066452},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3792865574359894}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8043936491012573},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.7301371097564697},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6204203963279724},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5585677623748779},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5126892328262329},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5080983638763428},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47095638513565063},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.4206514358520508},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.414201945066452},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3792865574359894},{"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/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008962","descriptor_name":"Models, Theoretical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw342","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/20/3175/25040491/btw342.pdf","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:27354693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27354693","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},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/20/3175","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/20/3175","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw342","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/20/3175/25040491/btw342.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W37334738","https://openalex.org/W188755909","https://openalex.org/W1659833910","https://openalex.org/W1835243625","https://openalex.org/W1955951250","https://openalex.org/W1969763365","https://openalex.org/W1984084871","https://openalex.org/W1991681722","https://openalex.org/W2004320937","https://openalex.org/W2013181441","https://openalex.org/W2024985940","https://openalex.org/W2048435239","https://openalex.org/W2053076602","https://openalex.org/W2079745490","https://openalex.org/W2091439417","https://openalex.org/W2091582819","https://openalex.org/W2096439168","https://openalex.org/W2098889731","https://openalex.org/W2105536900","https://openalex.org/W2109482131","https://openalex.org/W2126671570","https://openalex.org/W2135007932","https://openalex.org/W2135037015","https://openalex.org/W2138512826","https://openalex.org/W2139135964","https://openalex.org/W2139736926","https://openalex.org/W2161607603","https://openalex.org/W2170146596","https://openalex.org/W2200548835","https://openalex.org/W2249358283","https://openalex.org/W2298551783","https://openalex.org/W2400113734","https://openalex.org/W6601519200","https://openalex.org/W6607784695","https://openalex.org/W6648018980"],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W2965083567","https://openalex.org/W4235240664","https://openalex.org/W1838576100","https://openalex.org/W2345647014","https://openalex.org/W2002739602","https://openalex.org/W2201192772","https://openalex.org/W3136891595","https://openalex.org/W2535030201","https://openalex.org/W1964819397"],"abstract_inverted_index":{"MOTIVATION:":[0],"As":[1],"concurrent":[2],"use":[3,95],"of":[4,27,47,63,71,87,127,149,157],"multiple":[5,61,88],"medications":[6],"becomes":[7],"ubiquitous":[8],"among":[9,145],"patients,":[10],"it":[11],"is":[12],"crucial":[13],"to":[14],"characterize":[15],"both":[16,134],"adverse":[17],"and":[18,37,42,52,65,91,99,122,160],"synergistic":[19],"interactions":[20,30,140],"between":[21],"drugs.":[22,72],"Statistical":[23],"methods":[24,57,112],"for":[25,79],"prediction":[26,117],"putative":[28],"drug-drug":[29],"(DDIs)":[31],"can":[32],"guide":[33],"in":[34,131],"vitro":[35],"testing":[36],"cut":[38],"down":[39],"significant":[40],"cost":[41],"effort.":[43],"With":[44],"the":[45,69,96,146],"abundance":[46],"experimental":[48],"data":[49],"characterizing":[50],"drugs":[51],"their":[53],"associated":[54],"targets,":[55],"such":[56],"must":[58],"effectively":[59],"fuse":[60],"sources":[62,144],"information":[64],"perform":[66],"inference":[67],"over":[68,133],"network":[70,86],"RESULTS:":[73],"We":[74,94,108,136],"propose":[75],"a":[76,85,114],"probabilistic":[77,102],"approach":[78],"jointly":[80],"inferring":[81],"unknown":[82],"DDIs":[83],"from":[84],"drug-based":[89],"similarities":[90],"known":[92],"interactions.":[93],"highly":[97],"scalable":[98],"easily":[100],"extensible":[101],"programming":[103],"framework":[104],"Probabilistic":[105],"Soft":[106],"Logic":[107],"compare":[109],"against":[110],"two":[111],"including":[113],"state-of-the-art":[115],"DDI":[116],"system":[118],"across":[119],"three":[120],"experiments":[121],"show":[123],"best":[124],"performing":[125],"improvements":[126],"more":[128],"than":[129],"50%":[130],"AUPR":[132],"baselines.":[135],"find":[137],"five":[138],"novel":[139],"validated":[141],"by":[142],"external":[143],"top-ranked":[147],"predictions":[148],"our":[150],"model.":[151],"AVAILABILITY":[152],"AND":[153],"IMPLEMENTATION:":[154],"Final":[155],"versions":[156],"all":[158],"datasets":[159],"implementations":[161],"will":[162],"be":[163],"made":[164],"publicly":[165],"available.":[166],"CONTACT:":[167],"dsridhar@ucsc.edu.":[168]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":13},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":25},{"year":2022,"cited_by_count":22},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":24},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}