{"id":"https://openalex.org/W3113654230","doi":"https://doi.org/10.1093/bioinformatics/btaa1024","title":"Heterogeneous graph inference with matrix completion for computational drug repositioning","display_name":"Heterogeneous graph inference with matrix completion for computational drug repositioning","publication_year":2020,"publication_date":"2020-11-26","ids":{"openalex":"https://openalex.org/W3113654230","doi":"https://doi.org/10.1093/bioinformatics/btaa1024","mag":"3113654230","pmid":"https://pubmed.ncbi.nlm.nih.gov/33331887"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1024","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5456/36855873/btaa1024.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/36/22-23/5456/36855873/btaa1024.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004356703","display_name":"Mengyun Yang","orcid":"https://orcid.org/0000-0002-2703-533X"},"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"]},{"id":"https://openalex.org/I206324368","display_name":"Shaoyang University","ror":"https://ror.org/03fx09x73","country_code":"CN","type":"education","lineage":["https://openalex.org/I206324368"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengyun Yang","raw_affiliation_strings":["School of Science, Shaoyang University , Shaoyang 422000, China","The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Shaoyang University , Shaoyang 422000, China","institution_ids":["https://openalex.org/I206324368"]},{"raw_affiliation_string":"The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068875177","display_name":"Lan Huang","orcid":"https://orcid.org/0000-0003-2394-2300"},"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":"Lan Huang","raw_affiliation_strings":["The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038763794","display_name":"Yunpei Xu","orcid":null},"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":"Yunpei Xu","raw_affiliation_strings":["The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065367210","display_name":"Chengqian Lu","orcid":"https://orcid.org/0000-0001-9201-6912"},"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":"Chengqian Lu","raw_affiliation_strings":["The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0001-9201-6912","affiliations":[{"raw_affiliation_string":"The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"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":["The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0003-1516-0480","affiliations":[{"raw_affiliation_string":"The Hunan Provincial Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100438360"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":2.7145,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.92172188,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"36","issue":"22-23","first_page":"5456","last_page":"5464"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9607999920845032,"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":0.9607999920845032,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.013399999588727951,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.006399999838322401,"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/matrix-completion","display_name":"Matrix completion","score":0.7625851631164551},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.750960111618042},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6577569842338562},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.6467868685722351},{"id":"https://openalex.org/keywords/heterogeneous-network","display_name":"Heterogeneous network","score":0.6201279163360596},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5084018111228943},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4370175898075104},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4256495237350464},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40858209133148193},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3864845931529999},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33986079692840576},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.33671432733535767},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.2584608793258667},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.19030365347862244}],"concepts":[{"id":"https://openalex.org/C2778459887","wikidata":"https://www.wikidata.org/wiki/Q6787865","display_name":"Matrix completion","level":3,"score":0.7625851631164551},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.750960111618042},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6577569842338562},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.6467868685722351},{"id":"https://openalex.org/C158207573","wikidata":"https://www.wikidata.org/wiki/Q5747224","display_name":"Heterogeneous network","level":4,"score":0.6201279163360596},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5084018111228943},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4370175898075104},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4256495237350464},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40858209133148193},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3864845931529999},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33986079692840576},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33671432733535767},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.2584608793258667},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.19030365347862244},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C108037233","wikidata":"https://www.wikidata.org/wiki/Q11375","display_name":"Wireless network","level":3,"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/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1024","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5456/36855873/btaa1024.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:33331887","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33331887","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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa1024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1024","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5456/36855873/btaa1024.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":[{"id":"https://openalex.org/G4126902417","display_name":null,"funder_award_id":"61972423","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3113654230.pdf","grobid_xml":"https://content.openalex.org/works/W3113654230.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1987219048","https://openalex.org/W1994658365","https://openalex.org/W1998898494","https://openalex.org/W2011359124","https://openalex.org/W2020132970","https://openalex.org/W2031954078","https://openalex.org/W2062533676","https://openalex.org/W2079558799","https://openalex.org/W2093313266","https://openalex.org/W2100929382","https://openalex.org/W2103972604","https://openalex.org/W2113072832","https://openalex.org/W2119412782","https://openalex.org/W2124001239","https://openalex.org/W2128049108","https://openalex.org/W2145578524","https://openalex.org/W2148797284","https://openalex.org/W2151357092","https://openalex.org/W2154654747","https://openalex.org/W2170146596","https://openalex.org/W2183717576","https://openalex.org/W2346950316","https://openalex.org/W2397757171","https://openalex.org/W2473876819","https://openalex.org/W2790385355","https://openalex.org/W2807209585","https://openalex.org/W2809363952","https://openalex.org/W2810953629","https://openalex.org/W2888358121","https://openalex.org/W2896002881","https://openalex.org/W2922405516","https://openalex.org/W2946099214","https://openalex.org/W2950860419","https://openalex.org/W2960557205","https://openalex.org/W2996505894","https://openalex.org/W3005970824","https://openalex.org/W3006508031","https://openalex.org/W3012935077","https://openalex.org/W3038662035","https://openalex.org/W3092034553","https://openalex.org/W3094946818","https://openalex.org/W3138771162","https://openalex.org/W4248234957","https://openalex.org/W6682180195","https://openalex.org/W6686420396","https://openalex.org/W6773614549","https://openalex.org/W6773850934","https://openalex.org/W6774165440","https://openalex.org/W6779812169"],"related_works":["https://openalex.org/W4210999218","https://openalex.org/W2963058055","https://openalex.org/W2014069457","https://openalex.org/W3216512054","https://openalex.org/W3113654230","https://openalex.org/W2355108509","https://openalex.org/W3004260451","https://openalex.org/W4286632589","https://openalex.org/W2470825435","https://openalex.org/W4306651466"],"abstract_inverted_index":{"MOTIVATION:":[0],"Emerging":[1],"evidence":[2],"presents":[3],"that":[4],"traditional":[5],"drug":[6,15,27,49,147,163,191,238],"discovery":[7],"experiment":[8],"is":[9,38,43,158,231],"time-consuming":[10],"and":[11,24,29,35,111,142,149,164,186,192,215,244,287,295],"high":[12,55],"costs.":[13],"Computational":[14],"repositioning":[16,239],"plays":[17],"a":[18,44,96,117,125,196,257],"critical":[19],"role":[20],"in":[21,47,86,131,240,279],"saving":[22],"time":[23],"resources":[25],"for":[26,109,221],"research":[28],"discovery.":[30],"Therefore,":[31],"developing":[32],"more":[33,140,174],"accurate":[34],"efficient":[36],"approaches":[37,236],"imperative.":[39],"Heterogeneous":[40],"graph":[41,98,172],"inference":[42,99,173],"classical":[45],"method":[46,66,104,278],"computational":[48],"repositioning,":[50],"which":[51],"not":[52,68,254],"only":[53,255],"has":[54,60,67,263],"convergence":[56,62],"precision,":[57],"but":[58,261],"also":[59,262,272],"fast":[61],"speed.":[63],"However,":[64],"the":[65,71,84,128,162,168,182,204,209,218,225,241,249,274],"fully":[69],"considered":[70],"sparsity":[72],"of":[73,127,170,190,211,227,237,276],"heterogeneous":[74,97,171,198,205],"association":[75,134,213],"network.":[76,151,200],"In":[77,91,268],"addition,":[78,269],"rough":[79],"similarity":[80,177,188],"measure":[81],"can":[82,138],"reduce":[83],"performance":[85,169,226,260],"identifying":[87],"drug-associated":[88],"indications.":[89],"RESULTS:":[90],"this":[92],"article,":[93],"we":[94,115,194],"propose":[95],"with":[100,233],"matrix":[101,119],"completion":[102,120],"(HGIMC)":[103],"to":[105,123,160,207],"predict":[106],"potential":[107],"indications":[108,220],"approved":[110],"novel":[112,197],"drugs.":[113,222],"First,":[114],"use":[116],"bounded":[118],"(BMC)":[121],"model":[122],"prefill":[124],"part":[126],"missing":[129],"entries":[130],"original":[132],"drug-disease":[133,144,184,199],"matrix.":[135],"This":[136],"step":[137],"add":[139],"positive":[141],"formative":[143],"edges":[145],"between":[146],"network":[148,206],"disease":[150,165],"Second,":[152],"Gaussian":[153],"radial":[154],"basis":[155],"function":[156],"(GRB)":[157],"employed":[159],"improve":[161],"similarities":[166],"since":[167],"relies":[175],"on":[176,181],"measures.":[178],"Next,":[179],"based":[180],"updated":[183],"associations":[185],"new":[187],"measures":[189],"disease,":[193],"construct":[195],"Finally,":[201],"HGIMC":[202,230,253,285],"utilizes":[203],"infer":[208],"scores":[210],"unknown":[212],"pairs,":[214],"then":[216],"recommend":[217],"promising":[219],"To":[223],"evaluate":[224],"our":[228,277],"method,":[229],"compared":[232],"five":[234],"state-of-the-art":[235],"10-fold":[242],"cross-validation":[243],"de":[245],"novo":[246],"tests.":[247],"As":[248],"numerical":[250],"results":[251],"shown,":[252],"achieves":[256],"better":[258],"prediction":[259],"an":[264],"excellent":[265],"computation":[266],"efficiency.":[267],"cases":[270],"studies":[271],"confirm":[273],"effectiveness":[275],"practical":[280],"application.":[281],"AVAILABILITYAND":[282],"IMPLEMENTATION:":[283],"The":[284],"software":[286],"data":[288,300],"are":[289,301],"freely":[290],"available":[291,302],"at":[292,303],"https://github.com/BioinformaticsCSU/HGIMC,":[293],"https://hub.docker.com/repository/docker/yangmy84/hgimc":[294],"http://doi.org/10.5281/zenodo.4285640.":[296],"SUPPLEMENTARY":[297],"INFORMATION:":[298],"Supplementary":[299],"Bioinformatics":[304],"online.":[305]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":8}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
