{"id":"https://openalex.org/W4200431538","doi":"https://doi.org/10.1093/bib/bbab479","title":"Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey","display_name":"Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey","publication_year":2021,"publication_date":"2021-10-19","ids":{"openalex":"https://openalex.org/W4200431538","doi":"https://doi.org/10.1093/bib/bbab479","pmid":"https://pubmed.ncbi.nlm.nih.gov/34864871"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab479","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab479","pdf_url":null,"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":"review","indexed_in":["crossref","doaj","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/A5030129372","display_name":"Le Ou-Yang","orcid":"https://orcid.org/0000-0003-4007-4568"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210104064","display_name":"Shenzhen Academy of Robotics","ror":"https://ror.org/01h027j09","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210104064"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Le Ou-Yang","raw_affiliation_strings":["Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China","Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen,518172, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China","institution_ids":["https://openalex.org/I180726961"]},{"raw_affiliation_string":"Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen,518172, China","institution_ids":["https://openalex.org/I4210104064"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080310406","display_name":"Fan L\u00fc","orcid":"https://orcid.org/0000-0002-4932-3850"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Lu","raw_affiliation_strings":["Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangdong Key Laboratory of Intelligent Information Processing, Shenzhen Key Laboratory of Media Security, and Guangdong Laboratory of Artificial Intelligence and Digital Economy(SZ), College of Electronics and Information Engineering, Shenzhen University, Shenzhen, 518060, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033278649","display_name":"Zi-Chao Zhang","orcid":"https://orcid.org/0000-0001-5747-3093"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210085920","display_name":"Shanghai Institute for Science of Science","ror":"https://ror.org/004srxn73","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210085920"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zi-Chao Zhang","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I4210085920","https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100340964","display_name":"Min Wu","orcid":"https://orcid.org/0000-0003-0977-3600"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Min Wu","raw_affiliation_strings":["Institute for Infocomm Research (I2R), A*STAR, 138632, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Infocomm Research (I2R), A*STAR, 138632, Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5030129372"],"corresponding_institution_ids":["https://openalex.org/I180726961","https://openalex.org/I4210104064"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.384,"has_fulltext":false,"cited_by_count":20,"citation_normalized_percentile":{"value":0.81527292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969000220298767,"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/matrix-decomposition","display_name":"Matrix decomposition","score":0.757457435131073},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.7567180395126343},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7461323142051697},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5405555963516235},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.5314599275588989},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.459062397480011},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.424483984708786},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.2805677056312561},{"id":"https://openalex.org/keywords/eigenvalues-and-eigenvectors","display_name":"Eigenvalues and eigenvectors","score":0.10930615663528442}],"concepts":[{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.757457435131073},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7567180395126343},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7461323142051697},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5405555963516235},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.5314599275588989},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.459062397480011},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.424483984708786},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.2805677056312561},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.10930615663528442},{"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab479","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab479","pdf_url":null,"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"},{"id":"pmid:34864871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34864871","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":128,"referenced_works":["https://openalex.org/W1466286227","https://openalex.org/W1813068103","https://openalex.org/W1895317372","https://openalex.org/W1976526581","https://openalex.org/W1984883254","https://openalex.org/W2001673920","https://openalex.org/W2017289276","https://openalex.org/W2023887100","https://openalex.org/W2029348196","https://openalex.org/W2033072655","https://openalex.org/W2047071281","https://openalex.org/W2051658465","https://openalex.org/W2058240487","https://openalex.org/W2062451863","https://openalex.org/W2068881679","https://openalex.org/W2069089843","https://openalex.org/W2071010503","https://openalex.org/W2087242711","https://openalex.org/W2087473883","https://openalex.org/W2114104545","https://openalex.org/W2117420919","https://openalex.org/W2118017182","https://openalex.org/W2123688186","https://openalex.org/W2127451705","https://openalex.org/W2128049108","https://openalex.org/W2135007932","https://openalex.org/W2137245235","https://openalex.org/W2153838454","https://openalex.org/W2158135353","https://openalex.org/W2161607603","https://openalex.org/W2163487866","https://openalex.org/W2256553158","https://openalex.org/W2316095770","https://openalex.org/W2343107734","https://openalex.org/W2373831850","https://openalex.org/W2461230718","https://openalex.org/W2508393166","https://openalex.org/W2511896561","https://openalex.org/W2520756084","https://openalex.org/W2522945402","https://openalex.org/W2526724898","https://openalex.org/W2570589864","https://openalex.org/W2576544908","https://openalex.org/W2598326928","https://openalex.org/W2601934706","https://openalex.org/W2624752195","https://openalex.org/W2650688300","https://openalex.org/W2704159227","https://openalex.org/W2750900465","https://openalex.org/W2751468300","https://openalex.org/W2753953057","https://openalex.org/W2757038198","https://openalex.org/W2757764553","https://openalex.org/W2761309784","https://openalex.org/W2766959028","https://openalex.org/W2772618228","https://openalex.org/W2781816753","https://openalex.org/W2792693509","https://openalex.org/W2793951981","https://openalex.org/W2798133167","https://openalex.org/W2801501532","https://openalex.org/W2805619986","https://openalex.org/W2809363952","https://openalex.org/W2809699427","https://openalex.org/W2813324578","https://openalex.org/W2888615663","https://openalex.org/W2900758217","https://openalex.org/W2901039866","https://openalex.org/W2906922052","https://openalex.org/W2907492528","https://openalex.org/W2911932738","https://openalex.org/W2913556077","https://openalex.org/W2926010705","https://openalex.org/W2937762029","https://openalex.org/W2948035163","https://openalex.org/W2949148097","https://openalex.org/W2949755237","https://openalex.org/W2950104637","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2957436444","https://openalex.org/W2963277165","https://openalex.org/W2975498843","https://openalex.org/W2977707586","https://openalex.org/W2988426147","https://openalex.org/W2990747402","https://openalex.org/W2995178483","https://openalex.org/W2999336918","https://openalex.org/W3000082418","https://openalex.org/W3004260451","https://openalex.org/W3005970824","https://openalex.org/W3007573310","https://openalex.org/W3008081001","https://openalex.org/W3009246021","https://openalex.org/W3009302866","https://openalex.org/W3013279271","https://openalex.org/W3013557219","https://openalex.org/W3037489518","https://openalex.org/W3042221936","https://openalex.org/W3045143113","https://openalex.org/W3045879648","https://openalex.org/W3080162757","https://openalex.org/W3092723008","https://openalex.org/W3097857367","https://openalex.org/W3098324794","https://openalex.org/W3108155943","https://openalex.org/W3111467036","https://openalex.org/W3113654230","https://openalex.org/W3117993901","https://openalex.org/W3126763236","https://openalex.org/W3131175301","https://openalex.org/W3138479716","https://openalex.org/W3149361930","https://openalex.org/W3167993868","https://openalex.org/W3176772489","https://openalex.org/W3181518724","https://openalex.org/W6672311006","https://openalex.org/W6680451568","https://openalex.org/W6732210332","https://openalex.org/W6742181258","https://openalex.org/W6752626972","https://openalex.org/W6756634077","https://openalex.org/W6757869429","https://openalex.org/W6787470915","https://openalex.org/W6790018860","https://openalex.org/W6792121546","https://openalex.org/W6792673697","https://openalex.org/W6910505072"],"related_works":["https://openalex.org/W4296209631","https://openalex.org/W4211215373","https://openalex.org/W3217094455","https://openalex.org/W2561617217","https://openalex.org/W2025378473","https://openalex.org/W3119637569","https://openalex.org/W2989589450","https://openalex.org/W2405773734","https://openalex.org/W2355801475","https://openalex.org/W2219450347"],"abstract_inverted_index":{"Advances":[0],"in":[1,27,111],"high-throughput":[2],"experimental":[3,147],"technologies":[4],"promote":[5],"the":[6,41,69,146,173],"accumulation":[7],"of":[8,11,43,58,74],"vast":[9],"number":[10],"biomedical":[12,28,75,112,160,176],"data.":[13],"Biomedical":[14],"link":[15,113,177],"prediction":[16,114,178],"and":[17,37,71,77,108,115,126,164,179],"single-cell":[18],"RNA-sequencing":[19],"(scRNA-seq)":[20],"data":[21,29,79,117,135,181],"imputation":[22],"are":[23],"two":[24],"essential":[25],"tasks":[26,47,163],"analyses,":[30],"which":[31],"can":[32,48],"facilitate":[33],"various":[34,88],"downstream":[35],"studies":[36],"gain":[38],"insights":[39],"into":[40,51],"mechanisms":[42],"complex":[44],"diseases.":[45],"Both":[46],"be":[49],"transformed":[50],"matrix":[52,59,62,89,105,123,155,161],"completion":[53,60,162],"problems.":[54],"For":[55],"a":[56,100,128],"variety":[57],"tasks,":[61],"factorization":[63,90,106,124,156],"has":[64],"shown":[65],"promising":[66],"performance.":[67],"However,":[68],"sparseness":[70],"high":[72],"dimensionality":[73],"networks":[76],"scRNA-seq":[78,116,180],"have":[80,92],"raised":[81],"new":[82],"challenges.":[83],"To":[84],"resolve":[85],"these":[86],"issues,":[87],"methods":[91,107,125,157],"emerged":[93],"recently.":[94],"In":[95],"this":[96],"paper,":[97],"we":[98,120,149],"present":[99],"comprehensive":[101],"review":[102],"on":[103,132],"such":[104],"their":[109,139],"usage":[110],"imputation.":[118,182],"Moreover,":[119],"select":[121],"representative":[122],"conduct":[127],"systematic":[129],"empirical":[130],"comparison":[131],"15":[133],"real":[134],"sets":[136],"to":[137,170],"evaluate":[138],"performance":[140,174],"under":[141],"different":[142,159],"scenarios.":[143],"By":[144],"summarizing":[145],"results,":[148],"provide":[150],"general":[151],"guidelines":[152],"for":[153,158,175],"selecting":[154],"point":[165],"out":[166],"some":[167],"future":[168],"directions":[169],"further":[171],"improve":[172]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}