{"id":"https://openalex.org/W2997418660","doi":"https://doi.org/10.1093/bib/bbz147","title":"Drug\u2013target prediction utilizing heterogeneous bio-linked network embeddings","display_name":"Drug\u2013target prediction utilizing heterogeneous bio-linked network embeddings","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W2997418660","doi":"https://doi.org/10.1093/bib/bbz147","mag":"2997418660"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz147","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/568/35934863/bbz147.pdf","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"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/22/1/568/35934863/bbz147.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5019653651","display_name":"Nansu Zong","orcid":"https://orcid.org/0000-0003-0066-9524"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Nansu Zong","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054614672","display_name":"Rachael Sze Nga Wong","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I4210133661","display_name":"La Jolla Bioengineering Institute","ror":"https://ror.org/03sgbh608","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210133661"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachael Sze Nga Wong","raw_affiliation_strings":["Department of Bioengineering, UC San Diego, 9500 Gilman Drive, San Diego, CA 92093-0412, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, UC San Diego, 9500 Gilman Drive, San Diego, CA 92093-0412, USA","institution_ids":["https://openalex.org/I4210133661","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100397981","display_name":"Yue Yu","orcid":"https://orcid.org/0000-0002-7620-6078"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yue Yu","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003128469","display_name":"Andrew Wen","orcid":"https://orcid.org/0000-0001-9090-8028"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Wen","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010869663","display_name":"Ming Huang","orcid":"https://orcid.org/0000-0001-7367-3626"},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"funder","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming Huang","raw_affiliation_strings":["Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Health Sciences Research, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100369033","display_name":"Ning Li","orcid":"https://orcid.org/0000-0002-6224-1809"},"institutions":[{"id":"https://openalex.org/I123431417","display_name":"Scripps Research Institute","ror":"https://ror.org/02dxx6824","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I123431417"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ning Li","raw_affiliation_strings":["Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA, 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA, 92037, USA","institution_ids":["https://openalex.org/I123431417"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5019653651"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.1107,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.78087141,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"568","last_page":"580"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9990000128746033,"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":0.9732999801635742,"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":0.7352954149246216},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.7188085913658142},{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.615486741065979},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5221201181411743},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5062650442123413},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49005377292633057},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4655986726284027}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7352954149246216},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.7188085913658142},{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.615486741065979},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5221201181411743},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5062650442123413},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49005377292633057},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4655986726284027},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bib/bbz147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz147","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/568/35934863/bbz147.pdf","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"}],"best_oa_location":{"id":"doi:10.1093/bib/bbz147","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbz147","pdf_url":"https://academic.oup.com/bib/article-pdf/22/1/568/35934863/bbz147.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":78,"referenced_works":["https://openalex.org/W90362830","https://openalex.org/W1544009106","https://openalex.org/W1594145284","https://openalex.org/W1802476567","https://openalex.org/W1861993554","https://openalex.org/W1888005072","https://openalex.org/W1966716734","https://openalex.org/W1971106435","https://openalex.org/W1976526581","https://openalex.org/W1984084871","https://openalex.org/W2018408116","https://openalex.org/W2019707847","https://openalex.org/W2062584010","https://openalex.org/W2066201825","https://openalex.org/W2068258779","https://openalex.org/W2079745490","https://openalex.org/W2083045667","https://openalex.org/W2100672820","https://openalex.org/W2106029302","https://openalex.org/W2113951828","https://openalex.org/W2119412782","https://openalex.org/W2123531184","https://openalex.org/W2127069089","https://openalex.org/W2139516171","https://openalex.org/W2139736926","https://openalex.org/W2145578524","https://openalex.org/W2148145769","https://openalex.org/W2153838454","https://openalex.org/W2154139219","https://openalex.org/W2154718035","https://openalex.org/W2154851992","https://openalex.org/W2154896031","https://openalex.org/W2155958387","https://openalex.org/W2158698691","https://openalex.org/W2159482845","https://openalex.org/W2159583324","https://openalex.org/W2165125496","https://openalex.org/W2165428180","https://openalex.org/W2167212630","https://openalex.org/W2183717576","https://openalex.org/W2213443318","https://openalex.org/W2259538443","https://openalex.org/W2295730657","https://openalex.org/W2306570595","https://openalex.org/W2318276819","https://openalex.org/W2419892062","https://openalex.org/W2479004024","https://openalex.org/W2494614593","https://openalex.org/W2558217333","https://openalex.org/W2607497028","https://openalex.org/W2623060321","https://openalex.org/W2729788619","https://openalex.org/W2744720080","https://openalex.org/W2753953057","https://openalex.org/W2767891136","https://openalex.org/W2770261575","https://openalex.org/W2771169143","https://openalex.org/W2787612455","https://openalex.org/W2798932700","https://openalex.org/W2892341857","https://openalex.org/W2897730209","https://openalex.org/W2900487223","https://openalex.org/W2962756421","https://openalex.org/W2977393556","https://openalex.org/W2982327501","https://openalex.org/W3104097132","https://openalex.org/W3105705953","https://openalex.org/W4210483668","https://openalex.org/W4210702584","https://openalex.org/W4294216483","https://openalex.org/W6603694148","https://openalex.org/W6633912811","https://openalex.org/W6639315830","https://openalex.org/W6686420396","https://openalex.org/W6697600683","https://openalex.org/W6753508912","https://openalex.org/W6756602674","https://openalex.org/W6814377679"],"related_works":["https://openalex.org/W2060724872","https://openalex.org/W4238897586","https://openalex.org/W2082094785","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2202198356","https://openalex.org/W3087203342","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472"],"abstract_inverted_index":{"Abstract":[0],"To":[1],"enable":[2],"modularization":[3,210],"for":[4,149,188],"network-based":[5,128,205],"prediction,":[6,217],"we":[7,46,73,144,176],"conducted":[8,145],"a":[9,23,43,59,70,81,169,178,204,236],"review":[10,82],"of":[11,22,51,83,85,101,104,157,180,198,211,244],"known":[12],"methods":[13,92,129],"conducting":[14],"the":[15,20,32,48,75,86,111,116,122,126,140,155,158,181,185,190,209,212,242],"various":[16],"subtasks":[17],"corresponding":[18],"to":[19,30,114,225,239],"creation":[21],"drug\u2013target":[24,164],"prediction":[25,77,147,206],"framework":[26,207],"and":[27,93,136,153,194,215,223],"associated":[28],"benchmarking":[29,98,200],"determine":[31,115],"highest-performing":[33],"approaches.":[34],"Accordingly,":[35],"our":[36,199],"contributions":[37],"are":[38],"as":[39,130,132,166,233,235],"follows:":[40],"(i)":[41],"from":[42,65,69,110],"network":[44,63,182],"perspective,":[45,72],"benchmarked":[47],"association-mining":[49],"performance":[50],"32":[52],"distinct":[53,108,151],"subnetwork":[54],"permutations,":[55],"arranging":[56],"based":[57,79],"on":[58,80,203],"comprehensive":[60],"heterogeneous":[61],"biomedical":[62],"derived":[64],"12":[66],"repositories;":[67],"(ii)":[68],"methodological":[71],"identified":[74],"best":[76,117],"strategy":[78,99,159],"combinations":[84],"components":[87],"with":[88,184,208],"off-the-shelf":[89],"classification,":[90],"inference":[91],"graph":[94],"embedding":[95],"methods.":[96],"Our":[97],"consisted":[100],"two":[102,112],"series":[103],"experiments,":[105],"totaling":[106],"six":[107],"tasks":[109,148],"perspectives,":[113],"prediction.":[118,141],"We":[119],"demonstrated":[120],"that":[121],"proposed":[123],"method":[124],"outperformed":[125],"existing":[127],"well":[131,234],"how":[133],"combinatorial":[134],"networks":[135],"methodologies":[137],"can":[138,219],"influence":[139],"In":[142,174],"addition,":[143],"disease-specific":[146],"20":[150],"diseases":[152],"showed":[154],"reliability":[156],"in":[160],"predicting":[161,189],"75":[162],"novel":[163],"associations":[165],"shown":[167],"by":[168],"validation":[170],"utilizing":[171],"DrugBank":[172],"5.1.0.":[173],"particular,":[175],"revealed":[177],"connection":[179],"topology":[183],"biological":[186],"explanations":[187],"diseases,":[191],"\u2018Asthma\u2019":[192],"\u2018Hypertension\u2019,":[193],"\u2018Dementia\u2019.":[195],"The":[196],"results":[197],"produced":[201],"knowledge":[202],"feature":[213,227],"selection":[214],"association":[216],"which":[218],"be":[220],"easily":[221],"adapted":[222],"extended":[224],"other":[226],"sources":[228],"or":[229],"machine":[230],"learning":[231],"algorithms":[232],"performed":[237],"baseline":[238],"comprehensively":[240],"evaluate":[241],"utility":[243],"incorporating":[245],"varying":[246],"data":[247],"sources.":[248]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2020-01-10T00:00:00"}
