{"id":"https://openalex.org/W4317480129","doi":"https://doi.org/10.1093/bioinformatics/btad006","title":"Prediction of drug side effects with transductive matrix co-completion","display_name":"Prediction of drug side effects with transductive matrix co-completion","publication_year":2023,"publication_date":"2023-01-01","ids":{"openalex":"https://openalex.org/W4317480129","doi":"https://doi.org/10.1093/bioinformatics/btad006","pmid":"https://pubmed.ncbi.nlm.nih.gov/36655793"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad006/48829712/btad006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad006/48829712/btad006.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020544678","display_name":"Xujun Liang","orcid":"https://orcid.org/0000-0003-1698-5193"},"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/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xujun Liang","raw_affiliation_strings":["NHC Key Laboratory of Cancer Proteomics, Department of Oncology","National Clinical Research Center for Gerontology, Xiangya Hospital, Central South University , Changsha 410008, China"],"raw_orcid":"https://orcid.org/0000-0003-1698-5193","affiliations":[{"raw_affiliation_string":"NHC Key Laboratory of Cancer Proteomics, Department of Oncology","institution_ids":[]},{"raw_affiliation_string":"National Clinical Research Center for Gerontology, Xiangya Hospital, Central South University , Changsha 410008, China","institution_ids":["https://openalex.org/I4210159865","https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004429108","display_name":"Ying Fu","orcid":"https://orcid.org/0000-0002-8196-6493"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ying Fu","raw_affiliation_strings":["NHC Key Laboratory of Cancer Proteomics, Department of Oncology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NHC Key Laboratory of Cancer Proteomics, Department of Oncology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054904663","display_name":"Lingzhi Qu","orcid":"https://orcid.org/0000-0002-8212-6605"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lingzhi Qu","raw_affiliation_strings":["NHC Key Laboratory of Cancer Proteomics, Department of Oncology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NHC Key Laboratory of Cancer Proteomics, Department of Oncology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100426136","display_name":"Pengfei Zhang","orcid":"https://orcid.org/0000-0003-3470-085X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pengfei Zhang","raw_affiliation_strings":["NHC Key Laboratory of Cancer Proteomics, Department of Oncology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NHC Key Laboratory of Cancer Proteomics, Department of Oncology","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002430973","display_name":"Yongheng Chen","orcid":"https://orcid.org/0000-0001-8139-6892"},"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/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yongheng Chen","raw_affiliation_strings":["NHC Key Laboratory of Cancer Proteomics, Department of Oncology","National Clinical Research Center for Gerontology, Xiangya Hospital, Central South University , Changsha 410008, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NHC Key Laboratory of Cancer Proteomics, Department of Oncology","institution_ids":[]},{"raw_affiliation_string":"National Clinical Research Center for Gerontology, Xiangya Hospital, Central South University , Changsha 410008, China","institution_ids":["https://openalex.org/I4210159865","https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002430973","https://openalex.org/A5020544678"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I4210159865"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8971,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.87477919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"39","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":0.9602000117301941,"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":0.9602000117301941,"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":0.010200000368058681,"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":0.0038999998942017555,"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/leverage","display_name":"Leverage (statistics)","score":0.7287461757659912},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6960204839706421},{"id":"https://openalex.org/keywords/side-effect","display_name":"Side effect (computer science)","score":0.6607679724693298},{"id":"https://openalex.org/keywords/matrix-completion","display_name":"Matrix completion","score":0.6543336510658264},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.577393651008606},{"id":"https://openalex.org/keywords/regularization","display_name":"Regularization (linguistics)","score":0.49163156747817993},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.49034547805786133},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.46851846575737},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42631810903549194},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40310969948768616},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1349169909954071},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.11690887808799744},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10809996724128723}],"concepts":[{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.7287461757659912},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6960204839706421},{"id":"https://openalex.org/C3454156","wikidata":"https://www.wikidata.org/wiki/Q1144241","display_name":"Side effect (computer science)","level":2,"score":0.6607679724693298},{"id":"https://openalex.org/C2778459887","wikidata":"https://www.wikidata.org/wiki/Q6787865","display_name":"Matrix completion","level":3,"score":0.6543336510658264},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.577393651008606},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.49163156747817993},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.49034547805786133},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46851846575737},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42631810903549194},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40310969948768616},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1349169909954071},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.11690887808799744},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10809996724128723},{"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/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000076722","descriptor_name":"Drug Development","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad006/48829712/btad006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36655793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36655793","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:pubmedcentral.nih.gov:9869719","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9869719","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9869719/pdf/btad006.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad006","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btad006/48829712/btad006.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6600000262260437,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G131854829","display_name":null,"funder_award_id":"82073008","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G327906417","display_name":null,"funder_award_id":"2018JJ3807","funder_id":"https://openalex.org/F4320322866","funder_display_name":"Natural Science Foundation of Hainan Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322866","display_name":"Natural Science Foundation of Hainan Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4317480129.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W82560133","https://openalex.org/W846728699","https://openalex.org/W1663154925","https://openalex.org/W1862448690","https://openalex.org/W1955951250","https://openalex.org/W1999010280","https://openalex.org/W2017479556","https://openalex.org/W2027982384","https://openalex.org/W2049946556","https://openalex.org/W2070789802","https://openalex.org/W2136127280","https://openalex.org/W2145578524","https://openalex.org/W2148679377","https://openalex.org/W2152454589","https://openalex.org/W2154896031","https://openalex.org/W2294516783","https://openalex.org/W2481699501","https://openalex.org/W2746873727","https://openalex.org/W2767891136","https://openalex.org/W2789789321","https://openalex.org/W2902773418","https://openalex.org/W2994625500","https://openalex.org/W2995517528","https://openalex.org/W3017652999","https://openalex.org/W3170148256","https://openalex.org/W3174291985","https://openalex.org/W4243639900","https://openalex.org/W6603246417","https://openalex.org/W6797244631"],"related_works":["https://openalex.org/W3024870410","https://openalex.org/W2410652950","https://openalex.org/W4380150146","https://openalex.org/W4283773154","https://openalex.org/W3139174110","https://openalex.org/W4289597203","https://openalex.org/W1977098485","https://openalex.org/W2085630472","https://openalex.org/W4285201053","https://openalex.org/W3152273675"],"abstract_inverted_index":{"MOTIVATION:":[0],"Side":[1],"effects":[2,102,194],"of":[3,13,39,57,78,117,195,204],"drugs":[4,40,196],"could":[5,45,188,199],"cause":[6],"severe":[7],"health":[8],"problems":[9],"and":[10,25,72,94,103,146,154,180,211],"the":[11,19,33,36,52,69,76,96,100,111,115,127,137,185,192,201,212,215],"failure":[12],"drug":[14,128,142,147],"development.":[15],"Drug-target":[16],"interactions":[17],"are":[18,26,64,218,226],"basis":[20],"for":[21,28,131,158,214],"side":[22,29,54,79,101,132,140,159,193],"effect":[23,30,55,80,133,160],"production":[24],"important":[27],"prediction.":[31,81,134,161],"However,":[32],"information":[34,130],"on":[35,90,139],"known":[37],"targets":[38,203],"is":[41,108],"incomplete.":[42],"Furthermore,":[43],"there":[44],"be":[46],"also":[47,121,198],"some":[48],"missing":[49,70,73,202],"data":[50,138,210,225],"in":[51,75,99],"existing":[53],"profile":[56],"drugs.":[58,205],"As":[59],"a":[60,85],"result,":[61],"new":[62],"methods":[63,173],"needed":[65],"to":[66,113,125,150],"deal":[67],"with":[68],"features":[71],"labels":[74],"problem":[77],"RESULTS:":[82],"We":[83,120,135],"propose":[84],"novel":[86],"computational":[87],"method":[88,168,187,217],"based":[89],"transductive":[91],"matrix":[92],"co-completion":[93],"leverage":[95],"low-rank":[97],"structure":[98],"drug-target":[104],"data.":[105,119],"Positive-unlabelled":[106],"learning":[107],"incorporated":[109],"into":[110],"model":[112,153],"handle":[114],"impact":[116],"unobserved":[118],"introduce":[122],"graph":[123],"regularization":[124],"integrate":[126],"chemical":[129,148],"collect":[136],"effects,":[141],"targets,":[143],"drug-associated":[144],"proteins":[145],"structures":[149],"train":[151],"our":[152,167],"test":[155],"its":[156],"performance":[157],"The":[162,177,209],"experiment":[163],"results":[164],"show":[165],"that":[166,184],"outperforms":[169],"several":[170],"other":[171],"state-of-the-art":[172],"under":[174],"different":[175],"scenarios.":[176],"case":[178],"study":[179],"additional":[181],"analysis":[182],"illustrate":[183],"proposed":[186,216],"not":[189],"only":[190],"predict":[191],"but":[197],"infer":[200],"AVAILABILITY":[206],"AND":[207],"IMPLEMENTATION:":[208],"code":[213],"available":[219,227],"at":[220,228],"https://github.com/LiangXujun/GTMCC.":[221],"SUPPLEMENTARY":[222],"INFORMATION:":[223],"Supplementary":[224],"Bioinformatics":[229],"online.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}