{"id":"https://openalex.org/W2953544853","doi":"https://doi.org/10.1021/acs.jcim.9b00408","title":"Improved Prediction of Drug\u2013Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization","display_name":"Improved Prediction of Drug\u2013Target Interactions Using Self-Paced Learning with Collaborative Matrix Factorization","publication_year":2019,"publication_date":"2019-07-01","ids":{"openalex":"https://openalex.org/W2953544853","doi":"https://doi.org/10.1021/acs.jcim.9b00408","mag":"2953544853","pmid":"https://pubmed.ncbi.nlm.nih.gov/31260620"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00408","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00408","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5018295220","display_name":"Liang-Yong Xia","orcid":"https://orcid.org/0000-0003-1015-7127"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Liang-Yong Xia","raw_affiliation_strings":["Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078","institution_ids":["https://openalex.org/I111950717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085127108","display_name":"Ziyi Yang","orcid":"https://orcid.org/0000-0002-3550-9283"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Zi-Yi Yang","raw_affiliation_strings":["Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078","institution_ids":["https://openalex.org/I111950717"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100323532","display_name":"Hui Zhang","orcid":"https://orcid.org/0000-0003-1715-4332"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Hui Zhang","raw_affiliation_strings":["Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078","institution_ids":["https://openalex.org/I111950717"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100760226","display_name":"Yong Liang","orcid":"https://orcid.org/0000-0002-1449-4182"},"institutions":[{"id":"https://openalex.org/I111950717","display_name":"Macau University of Science and Technology","ror":"https://ror.org/03jqs2n27","country_code":"MO","type":"education","lineage":["https://openalex.org/I111950717","https://openalex.org/I4391767947"]}],"countries":["MO"],"is_corresponding":true,"raw_author_name":"Yong Liang","raw_affiliation_strings":["Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078","State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China 999078"],"raw_orcid":"https://orcid.org/0000-0002-1449-4182","affiliations":[{"raw_affiliation_string":"Faculty of Information Technology, Macau University of Science and Technology, Macau, China 999078","institution_ids":["https://openalex.org/I111950717"]},{"raw_affiliation_string":"State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Macau, China 999078","institution_ids":["https://openalex.org/I111950717"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100760226"],"corresponding_institution_ids":["https://openalex.org/I111950717"],"apc_list":null,"apc_paid":null,"fwci":3.4706,"has_fulltext":false,"cited_by_count":36,"citation_normalized_percentile":{"value":0.93307741,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"59","issue":"7","first_page":"3340","last_page":"3351"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9603000283241272,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.955299973487854,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7459955215454102},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.7166308760643005},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6286754608154297},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6102370619773865},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6068059206008911},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5509914755821228},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.5505663156509399},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.45944344997406006},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.45452630519866943},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35643506050109863},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.22194579243659973},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16386952996253967}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7459955215454102},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.7166308760643005},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6286754608154297},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6102370619773865},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6068059206008911},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5509914755821228},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.5505663156509399},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.45944344997406006},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.45452630519866943},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35643506050109863},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.22194579243659973},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16386952996253967},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"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/C118552586","wikidata":"https://www.wikidata.org/wiki/Q7867","display_name":"Psychiatry","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C126838900","wikidata":"https://www.wikidata.org/wiki/Q77604","display_name":"Radiology","level":1,"score":0.0},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","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},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00408","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00408","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:31260620","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31260620","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2500687236","display_name":null,"funder_award_id":"0055/2018/A2","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"},{"id":"https://openalex.org/G685587733","display_name":null,"funder_award_id":"003/2016/AFJ","funder_id":"https://openalex.org/F4320323893","funder_display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320323893","display_name":"Fundo para o Desenvolvimento das Ci\u00eancias e da Tecnologia","ror":"https://ror.org/05vna4324"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W363319864","https://openalex.org/W1466286227","https://openalex.org/W1974095883","https://openalex.org/W1976526581","https://openalex.org/W1984014392","https://openalex.org/W1984084871","https://openalex.org/W2018408116","https://openalex.org/W2029348196","https://openalex.org/W2048565304","https://openalex.org/W2055147198","https://openalex.org/W2066201825","https://openalex.org/W2070789802","https://openalex.org/W2076430826","https://openalex.org/W2079745490","https://openalex.org/W2093117046","https://openalex.org/W2097998348","https://openalex.org/W2100672820","https://openalex.org/W2106029302","https://openalex.org/W2109991441","https://openalex.org/W2127132032","https://openalex.org/W2128137143","https://openalex.org/W2135007932","https://openalex.org/W2139736926","https://openalex.org/W2153838454","https://openalex.org/W2155958387","https://openalex.org/W2162011385","https://openalex.org/W2167212630","https://openalex.org/W2256553158","https://openalex.org/W2259538443","https://openalex.org/W2343107734","https://openalex.org/W2399392834","https://openalex.org/W2513494919","https://openalex.org/W2576544908","https://openalex.org/W2753953057","https://openalex.org/W2770663710","https://openalex.org/W2789789321","https://openalex.org/W2793951981","https://openalex.org/W2803500509","https://openalex.org/W2885883357","https://openalex.org/W2896646632","https://openalex.org/W2906922052","https://openalex.org/W2945444034","https://openalex.org/W2949419207"],"related_works":["https://openalex.org/W2180954594","https://openalex.org/W2052835778","https://openalex.org/W2049003611","https://openalex.org/W2108418243","https://openalex.org/W2127804977","https://openalex.org/W164103134","https://openalex.org/W3010058077","https://openalex.org/W2920569584","https://openalex.org/W2951512731","https://openalex.org/W4392354878"],"abstract_inverted_index":{"Identifying":[0],"drug-target":[1],"interactions":[2],"(DTIs)":[3],"plays":[4],"an":[5],"important":[6],"role":[7],"in":[8,20,36,141],"the":[9,66,136],"field":[10],"of":[11,111,139],"drug":[12,14,17,185,187],"discovery,":[13,186],"side-effects,":[15],"and":[16,33,52,98,103,148,190],"repositioning.":[18],"However,":[19],"vivo":[21],"or":[22,38],"biochemical":[23],"experimental":[24],"methods":[25,41,59],"for":[26,45,69,88],"identifying":[27,71],"new":[28,182],"DTIs":[29],"are":[30],"extremely":[31],"expensive":[32],"time-consuming.":[34],"Recently,":[35],"silico":[37],"various":[39],"computational":[40,58],"have":[42,60],"been":[43],"developed":[44],"DTI":[46,73,89],"prediction,":[47,90,189],"such":[48],"as":[49],"ligand-based":[50],"approaches":[51,68],"docking":[53],"approaches,":[54],"but":[55],"these":[56],"traditional":[57],"several":[61],"limitations.":[62],"This":[63],"work":[64],"utilizes":[65],"chemogenomic-based":[67],"efficiently":[70],"potential":[72],"candidates,":[74],"namely,":[75],"self-paced":[76],"learning":[77,106],"with":[78],"collaborative":[79],"matrix":[80],"factorization":[81],"based":[82],"on":[83,105,145],"weighted":[84],"low-rank":[85],"approximation":[86],"(SPLCMF)":[87],"which":[91,129,179],"integrates":[92],"multiple":[93],"networks":[94],"related":[95],"to":[96,121,132,175],"drugs":[97],"targets":[99],"into":[100,123,184],"regularized":[101],"least-squares":[102],"focuses":[104],"a":[107,172],"low-dimensional":[108],"vector":[109],"representation":[110],"features.":[112],"The":[113],"SPLCMF":[114,157,169],"framework":[115],"can":[116,170],"select":[117],"samples":[118,140],"from":[119],"easy":[120],"complex":[122],"training":[124],"by":[125],"using":[126],"soft":[127],"weighting,":[128],"is":[130],"inclined":[131],"more":[133],"faithfully":[134],"reflect":[135],"latent":[137],"importance":[138],"training.":[142],"Experimental":[143],"results":[144,164],"synthetic":[146],"data":[147,151],"five":[149],"benchmark":[150],"sets":[152],"show":[153],"that":[154,166],"our":[155,167],"proposed":[156,168],"outperforms":[158],"other":[159],"existing":[160,192],"state-of-the-art":[161],"approaches.":[162],"These":[163],"indicate":[165],"provide":[171,181],"useful":[173],"tool":[174],"predict":[176],"unknown":[177],"DTIs,":[178],"may":[180],"insights":[183],"side-effect":[188],"repositioning":[191],"drug.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
