{"id":"https://openalex.org/W4310601440","doi":"https://doi.org/10.1021/acs.jcim.2c01305","title":"Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering","display_name":"Robust Graph Regularized NMF with Dissimilarity and Similarity Constraints for ScRNA-seq Data Clustering","publication_year":2022,"publication_date":"2022-12-02","ids":{"openalex":"https://openalex.org/W4310601440","doi":"https://doi.org/10.1021/acs.jcim.2c01305","pmid":"https://pubmed.ncbi.nlm.nih.gov/36459053"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01305","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01305","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/A5083569726","display_name":"Zhenqiu Shu","orcid":"https://orcid.org/0000-0001-5737-3383"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhenqiu Shu","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079493077","display_name":"Qinghan Long","orcid":null},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinghan Long","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100748604","display_name":"Luping Zhang","orcid":"https://orcid.org/0000-0002-9998-1798"},"institutions":[{"id":"https://openalex.org/I26080491","display_name":"Kunming Medical University","ror":"https://ror.org/038c3w259","country_code":"CN","type":"education","lineage":["https://openalex.org/I26080491"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Luping Zhang","raw_affiliation_strings":["Library of Kunming Medical University, Kunming 650031, China"],"affiliations":[{"raw_affiliation_string":"Library of Kunming Medical University, Kunming 650031, China","institution_ids":["https://openalex.org/I26080491"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619287","display_name":"Zhengtao Yu","orcid":"https://orcid.org/0000-0002-4012-461X"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengtao Yu","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming 650093, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087450445","display_name":"Xiao\u2010Jun Wu","orcid":"https://orcid.org/0000-0002-0310-5778"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao-Jun Wu","raw_affiliation_strings":["Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Jiangnan University, Wuxi 214122, China"],"affiliations":[{"raw_affiliation_string":"Jiangsu Provincial Engineering Laboratory of Pattern Recognition and Computational Intelligence, Jiangnan University, Wuxi 214122, China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083569726","https://openalex.org/A5100748604"],"corresponding_institution_ids":["https://openalex.org/I10660446","https://openalex.org/I26080491"],"apc_list":null,"apc_paid":null,"fwci":1.8014,"has_fulltext":false,"cited_by_count":21,"citation_normalized_percentile":{"value":0.85719833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"62","issue":"23","first_page":"6271","last_page":"6286"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9937000274658203,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/cluster-analysis","display_name":"Cluster analysis","score":0.7783605456352234},{"id":"https://openalex.org/keywords/non-negative-matrix-factorization","display_name":"Non-negative matrix factorization","score":0.7257898449897766},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5848244428634644},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5781572461128235},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5625574588775635},{"id":"https://openalex.org/keywords/matrix-decomposition","display_name":"Matrix decomposition","score":0.526362955570221},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5028855204582214},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.47653159499168396},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.44479626417160034},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4306285083293915},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3249998092651367},{"id":"https://openalex.org/keywords/eigenvalues-and-eigenvectors","display_name":"Eigenvalues and eigenvectors","score":0.17771175503730774},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.08897954225540161}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7783605456352234},{"id":"https://openalex.org/C152671427","wikidata":"https://www.wikidata.org/wiki/Q10843505","display_name":"Non-negative matrix factorization","level":4,"score":0.7257898449897766},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5848244428634644},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5781572461128235},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5625574588775635},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.526362955570221},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5028855204582214},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.47653159499168396},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.44479626417160034},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4306285083293915},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3249998092651367},{"id":"https://openalex.org/C158693339","wikidata":"https://www.wikidata.org/wiki/Q190524","display_name":"Eigenvalues and eigenvectors","level":2,"score":0.17771175503730774},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.08897954225540161},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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:10.1021/acs.jcim.2c01305","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01305","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:36459053","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36459053","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/G5513235841","display_name":null,"funder_award_id":"62162033","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8212330373","display_name":null,"funder_award_id":"61603159","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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1754857113","https://openalex.org/W1902027874","https://openalex.org/W1968970305","https://openalex.org/W1997201895","https://openalex.org/W2002469984","https://openalex.org/W2007439698","https://openalex.org/W2049633694","https://openalex.org/W2060245619","https://openalex.org/W2088851040","https://openalex.org/W2108119513","https://openalex.org/W2121690903","https://openalex.org/W2128040385","https://openalex.org/W2132914434","https://openalex.org/W2137874965","https://openalex.org/W2145567933","https://openalex.org/W2150593711","https://openalex.org/W2165685007","https://openalex.org/W2169658215","https://openalex.org/W2222512263","https://openalex.org/W2239077479","https://openalex.org/W2279323413","https://openalex.org/W2522945402","https://openalex.org/W2548889510","https://openalex.org/W2571012312","https://openalex.org/W2610509384","https://openalex.org/W2626990934","https://openalex.org/W2733002388","https://openalex.org/W2750900465","https://openalex.org/W2794480084","https://openalex.org/W2794521141","https://openalex.org/W2894687190","https://openalex.org/W2918882492","https://openalex.org/W2923396414","https://openalex.org/W2923950283","https://openalex.org/W2951444558","https://openalex.org/W2953251392","https://openalex.org/W2982114105","https://openalex.org/W2999905431","https://openalex.org/W3008534764","https://openalex.org/W3091988478","https://openalex.org/W3093217784","https://openalex.org/W3105146463","https://openalex.org/W3211499194","https://openalex.org/W3212838933","https://openalex.org/W4225760234","https://openalex.org/W4235169531","https://openalex.org/W4280579662","https://openalex.org/W4293187222"],"related_works":["https://openalex.org/W2127243424","https://openalex.org/W4390394189","https://openalex.org/W2037504162","https://openalex.org/W2539013788","https://openalex.org/W2792706544","https://openalex.org/W1568451138","https://openalex.org/W2156699640","https://openalex.org/W2045265907","https://openalex.org/W2972997031","https://openalex.org/W34555840"],"abstract_inverted_index":{"The":[0],"notable":[1],"progress":[2],"in":[3,126,170],"single-cell":[4],"RNA":[5],"sequencing":[6],"(ScRNA-seq)":[7],"technology":[8],"is":[9,21],"beneficial":[10],"to":[11,43,108,119,134,150],"accurately":[12,79],"discover":[13,120],"the":[14,27,81,85,89,93,121,132,136,143,146,151],"heterogeneity":[15],"and":[16,47,70,88,105,139],"diversity":[17],"of":[18,84,100,145],"cells.":[19],"Clustering":[20],"an":[22],"extremely":[23],"important":[24],"step":[25],"during":[26],"ScRNA-seq":[28,40,57,75,127,157],"data":[29,41,58,76],"analysis.":[30],"However,":[31],"it":[32],"cannot":[33],"achieve":[34],"satisfactory":[35],"performances":[36],"by":[37],"directly":[38],"clustering":[39],"due":[42],"its":[44],"high":[45],"dimensionality":[46],"noise.":[48],"To":[49,78],"address":[50],"these":[51],"issues,":[52],"we":[53,114,130],"propose":[54],"a":[55,98,116],"novel":[56],"representation":[59],"model,":[60],"termed":[61],"Robust":[62],"Graph":[63],"regularized":[64],"Non-Negative":[65],"Matrix":[66],"Factorization":[67],"with":[68],"Dissimilarity":[69],"Similarity":[71],"constraints":[72],"(RGNMF-DS),":[73],"for":[74],"clustering.":[77,171],"characterize":[80],"structure":[82,124],"information":[83],"labeled":[86],"samples":[87],"unlabeled":[90],"samples,":[91],"respectively,":[92],"proposed":[94,147,163],"RGNMF-DS":[95,148,164],"model":[96,149,165],"adopts":[97],"couple":[99],"complementary":[101],"regularizers":[102],"(i.e.,":[103],"similarity":[104],"dissimilar":[106],"regularizers)":[107],"guide":[109],"matrix":[110],"decomposition.":[111],"In":[112],"addition,":[113],"construct":[115],"graph":[117],"regularizer":[118],"local":[122],"geometric":[123],"hidden":[125],"data.":[128],"Moreover,":[129],"adopt":[131],"<i>l</i><sub>2,1</sub>-norm":[133],"measure":[135],"reconstruction":[137],"error":[138],"thereby":[140],"effectively":[141],"improve":[142],"robustness":[144],"noises.":[152],"Experimental":[153],"results":[154],"on":[155],"several":[156],"datasets":[158],"have":[159],"demonstrated":[160],"that":[161],"our":[162],"outperforms":[166],"other":[167],"state-of-the-art":[168],"competitors":[169]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}