{"id":"https://openalex.org/W2950118051","doi":"https://doi.org/10.1186/s12859-019-2768-7","title":"L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions","display_name":"L2,1-GRMF: an improved graph regularized matrix factorization method to predict drug-target interactions","publication_year":2019,"publication_date":"2019-06-01","ids":{"openalex":"https://openalex.org/W2950118051","doi":"https://doi.org/10.1186/s12859-019-2768-7","mag":"2950118051"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2768-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2768-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2768-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2768-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5058029547","display_name":"Zhen Cui","orcid":"https://orcid.org/0000-0001-5522-6750"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhen Cui","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026569643","display_name":"Ying-Lian Gao","orcid":"https://orcid.org/0000-0003-0483-5622"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying-Lian Gao","raw_affiliation_strings":["Library of Qufu Normal University, Qufu Normal University, Rizhao, China"],"affiliations":[{"raw_affiliation_string":"Library of Qufu Normal University, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073144090","display_name":"Jin\u2010Xing Liu","orcid":"https://orcid.org/0000-0001-6104-2149"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jin-Xing Liu","raw_affiliation_strings":["Co-Innovation Center for Information Supply & Assurance Technology, Anhui University, Hefei, China","School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"affiliations":[{"raw_affiliation_string":"Co-Innovation Center for Information Supply & Assurance Technology, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100648395","display_name":"Lingyun Dai","orcid":"https://orcid.org/0000-0001-9386-5967"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling-Yun Dai","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011951772","display_name":"Shasha Yuan","orcid":"https://orcid.org/0000-0003-4792-9880"},"institutions":[{"id":"https://openalex.org/I202126657","display_name":"Qufu Normal University","ror":"https://ror.org/03ceheh96","country_code":"CN","type":"education","lineage":["https://openalex.org/I202126657"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sha-Sha Yuan","raw_affiliation_strings":["School of Information Science and Engineering, Qufu Normal University, Rizhao, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Qufu Normal University, Rizhao, China","institution_ids":["https://openalex.org/I202126657"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5058029547"],"corresponding_institution_ids":["https://openalex.org/I202126657"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.9993,"has_fulltext":true,"cited_by_count":24,"citation_normalized_percentile":{"value":0.94332029,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"S8","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":0.9998999834060669,"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":0.9998999834060669,"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":0.9897000193595886,"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/T11440","display_name":"Click Chemistry and Applications","score":0.948199987411499,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5393806099891663},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.5209923386573792},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.505296528339386},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.45474693179130554},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44112205505371094},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3039757013320923},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23467698693275452},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1586851179599762}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5393806099891663},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.5209923386573792},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.505296528339386},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.45474693179130554},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44112205505371094},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3039757013320923},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23467698693275452},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1586851179599762},{"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/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1186/s12859-019-2768-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2768-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2768-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:1f4c3c4fb72c48639e9357be2240aaf0","is_oa":true,"landing_page_url":"https://doaj.org/article/1f4c3c4fb72c48639e9357be2240aaf0","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss S8, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6557743","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6557743","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2768-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2768-7","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2768-7","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G276912340","display_name":null,"funder_award_id":"61701279","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G309252033","display_name":null,"funder_award_id":"61872220, 61572284","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5609717784","display_name":null,"funder_award_id":"61872220","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5860415692","display_name":null,"funder_award_id":"61572284","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","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/W2950118051.pdf","grobid_xml":"https://content.openalex.org/works/W2950118051.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W331119053","https://openalex.org/W1481655810","https://openalex.org/W1968217711","https://openalex.org/W1968691112","https://openalex.org/W1976526581","https://openalex.org/W1978370150","https://openalex.org/W1998121392","https://openalex.org/W2018408116","https://openalex.org/W2019707847","https://openalex.org/W2021979212","https://openalex.org/W2029348196","https://openalex.org/W2096541451","https://openalex.org/W2101940033","https://openalex.org/W2109991441","https://openalex.org/W2125505137","https://openalex.org/W2135007932","https://openalex.org/W2137052779","https://openalex.org/W2153838454","https://openalex.org/W2159822007","https://openalex.org/W2161607603","https://openalex.org/W2162011385","https://openalex.org/W2163835096","https://openalex.org/W2343107734","https://openalex.org/W2543665166","https://openalex.org/W2559588208","https://openalex.org/W2562827486","https://openalex.org/W2572109604","https://openalex.org/W2917352565","https://openalex.org/W4233182706"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2539013788","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W2075222291"],"abstract_inverted_index":{"Predicting":[0],"drug-target":[1,30,53,176],"interactions":[2,54],"is":[3,8,59,126,146],"time-consuming":[4],"and":[5,42,132,157],"expensive.":[6],"It":[7],"important":[9],"to":[10,22,45,55,95,118,128,137,148],"present":[11],"the":[12,15,74,103,113,120,123,167,174],"accuracy":[13,121],"of":[14,27,38,112,122,154],"calculation":[16],"method.":[17,106],"There":[18],"are":[19,76,135,160],"many":[20],"algorithms":[21,49],"predict":[23,51,138,173],"global":[24],"interactions,":[25],"some":[26,52,56,63,152],"which":[28],"use":[29,110],"networks":[31],"for":[32,62],"prediction":[33],"(ie,":[34],"a":[35],"bipartite":[36],"graph":[37],"bound":[39],"drug":[40],"pairs":[41],"targets":[43,67,159],"known":[44,71],"interact).":[46],"Although":[47],"these":[48,97],"can":[50,171],"extent,":[57],"there":[58],"little":[60],"effect":[61],"new":[64,139,155,158],"drugs":[65,156],"or":[66,80],"that":[68],"have":[69],"no":[70],"interaction.":[72],"Since":[73],"datasets":[75],"usually":[77],"located":[78],"at":[79],"near":[81],"low-dimensional":[82],"nonlinear":[83],"manifolds,":[84],"we":[85,109],"propose":[86],"an":[87],"improved":[88,168],"GRMF":[89,169],"(graph":[90],"regularized":[91],"matrix":[92],"factorization)":[93],"method":[94,145,170],"learn":[96],"flow":[98],"patterns":[99],"in":[100],"combination":[101],"with":[102],"previous":[104],"matrix-decomposition":[105],"In":[107,141],"addition,":[108],"one":[111],"pre-processing":[114],"steps":[115],"previously":[116],"proposed":[117],"improve":[119],"prediction.":[124],"Cross-validation":[125],"used":[127,136],"evaluate":[129],"our":[130,144],"method,":[131],"simulation":[133,164],"experiments":[134],"interactions.":[140,177],"most":[142],"cases,":[143],"superior":[147],"other":[149],"methods.":[150],"Finally,":[151],"examples":[153],"predicted":[161],"by":[162],"performing":[163],"experiments.":[165],"And":[166],"better":[172],"remaining":[175]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":11},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}