{"id":"https://openalex.org/W4413139867","doi":"https://doi.org/10.1109/tcbbio.2025.3599194","title":"scDVAE:Single-Cell Data Clustering Based on Variational Autoencoder With Disentangled Latent Representations","display_name":"scDVAE:Single-Cell Data Clustering Based on Variational Autoencoder With Disentangled Latent Representations","publication_year":2025,"publication_date":"2025-08-14","ids":{"openalex":"https://openalex.org/W4413139867","doi":"https://doi.org/10.1109/tcbbio.2025.3599194","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811173"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3599194","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3599194","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5083343614","display_name":"Xiaohan Zou","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaohan Zou","raw_affiliation_strings":["School of Information Science and Engineering, Yunnan University, Kunming, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113059708","display_name":"Weihua Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weihua Zheng","raw_affiliation_strings":["School of Information Science and Engineering, Yunnan University, Kunming, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, China","institution_ids":["https://openalex.org/I189210763"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040105964","display_name":"Shunfang Wang","orcid":"https://orcid.org/0000-0002-1927-8753"},"institutions":[{"id":"https://openalex.org/I189210763","display_name":"Yunnan University","ror":"https://ror.org/0040axw97","country_code":"CN","type":"education","lineage":["https://openalex.org/I189210763"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shunfang Wang","raw_affiliation_strings":["School of Information Science and Engineering, Yunnan University, Kunming, China","School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, China","institution_ids":["https://openalex.org/I189210763"]},{"raw_affiliation_string":"School of Information Science and Engineering, Yunnan University, Kunming, Yunnan, China","institution_ids":["https://openalex.org/I189210763"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5083343614"],"corresponding_institution_ids":["https://openalex.org/I189210763"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17953942,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2712","last_page":"2723"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9699000120162964,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9375,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/autoencoder","display_name":"Autoencoder","score":0.8820263147354126},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.8748506307601929},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6805473566055298},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6103278398513794},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.5862464308738708},{"id":"https://openalex.org/keywords/dropout","display_name":"Dropout (neural networks)","score":0.5738416910171509},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4764676094055176},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.44911137223243713},{"id":"https://openalex.org/keywords/clustering-high-dimensional-data","display_name":"Clustering high-dimensional data","score":0.4417073428630829},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.4324776530265808},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.4224204123020172},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4149673879146576},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.30969899892807007}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.8820263147354126},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8748506307601929},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6805473566055298},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6103278398513794},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.5862464308738708},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.5738416910171509},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4764676094055176},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.44911137223243713},{"id":"https://openalex.org/C184509293","wikidata":"https://www.wikidata.org/wiki/Q5136711","display_name":"Clustering high-dimensional data","level":3,"score":0.4417073428630829},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.4324776530265808},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.4224204123020172},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4149673879146576},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.30969899892807007}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3599194","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3599194","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811173","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811173","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4313321071","display_name":null,"funder_award_id":"62462068","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G648225990","display_name":null,"funder_award_id":"62062067","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":42,"referenced_works":["https://openalex.org/W1128809682","https://openalex.org/W1981641790","https://openalex.org/W2007439698","https://openalex.org/W2032054503","https://openalex.org/W2033072655","https://openalex.org/W2051658465","https://openalex.org/W2060446375","https://openalex.org/W2062029454","https://openalex.org/W2069089843","https://openalex.org/W2090984301","https://openalex.org/W2113168077","https://openalex.org/W2120205807","https://openalex.org/W2128728535","https://openalex.org/W2135937351","https://openalex.org/W2137971377","https://openalex.org/W2167823677","https://openalex.org/W2511896561","https://openalex.org/W2523620612","https://openalex.org/W2598326928","https://openalex.org/W2794891507","https://openalex.org/W2800392236","https://openalex.org/W2900411771","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2927507212","https://openalex.org/W2937917790","https://openalex.org/W2949177718","https://openalex.org/W2951506174","https://openalex.org/W2952016241","https://openalex.org/W2953251392","https://openalex.org/W2979464975","https://openalex.org/W3014610125","https://openalex.org/W3024013192","https://openalex.org/W3092253034","https://openalex.org/W3137285774","https://openalex.org/W3185864054","https://openalex.org/W3216990162","https://openalex.org/W4205916264","https://openalex.org/W4235169531","https://openalex.org/W4313561039","https://openalex.org/W4366814680","https://openalex.org/W4380576938"],"related_works":["https://openalex.org/W4310873165","https://openalex.org/W2355395139","https://openalex.org/W4285596704","https://openalex.org/W4394785709","https://openalex.org/W4309969736","https://openalex.org/W2770818364","https://openalex.org/W2953501176","https://openalex.org/W2965095304","https://openalex.org/W2470043383","https://openalex.org/W3034474024"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"technology":[4],"enables":[5],"the":[6,36,42,61,102,115,120,123,129,140,144,149],"analysis":[7],"of":[8,19,38,64,122,151],"gene":[9],"expression":[10],"in":[11,21,32,49,68],"individual":[12],"cells,":[13],"allowing":[14],"for":[15,93,143],"a":[16,29,79,86,135,161],"deeper":[17],"exploration":[18],"heterogeneity":[20],"organisms":[22],"and":[23,46,109],"complex":[24],"diseases.":[25],"Cell":[26],"clustering":[27,57,107,116,124,145,193],"is":[28,104],"crucial":[30],"step":[31],"single-cell":[33,50,94],"analysis,":[34],"enabling":[35],"identification":[37],"cellular":[39],"heterogeneity.":[40],"However,":[41],"high":[43],"dimensionality,":[44],"sparsity,":[45],"dropout":[47,155],"events":[48],"data":[51,163],"have":[52],"brought":[53],"enormous":[54],"challenges":[55],"to":[56,147,166,178,196],"analysis.":[58],"Building":[59],"on":[60,184],"proven":[62],"success":[63],"deep":[65,81],"generative":[66,82,110,130],"models":[67],"learning":[69],"meaningful":[70],"representations":[71,92],"from":[72,128],"low-dimensional":[73],"latent":[74,91,98],"spaces,":[75],"we":[76,133,159],"introduce":[77,160],"scDVAE,":[78],"novel":[80],"approach":[83],"that":[84,189],"leverages":[85],"variational":[87],"autoencoder":[88],"with":[89],"disentangled":[90,105],"clustering.":[95],"First,":[96],"each":[97],"representation":[99],"generated":[100],"by":[101],"encoder":[103],"into":[106],"features":[108,117,146],"features.":[111],"In":[112,157],"this":[113],"way,":[114],"can":[118],"enhance":[119,148],"performance":[121,194],"task":[125],"without":[126],"interference":[127],"task.":[131],"Second,":[132],"employ":[134],"Student's":[136],"t-mixture":[137],"model":[138],"as":[139],"prior":[141],"distribution":[142],"robustness":[150],"our":[152],"method":[153],"against":[154],"events.":[156],"addition,":[158],"hybrid":[162],"augmentation":[164],"strategy":[165],"generate":[167],"augmented":[168],"scRNA-seq":[169],"data,":[170],"which":[171],"enhances":[172],"dataset":[173],"diversity":[174],"while":[175],"also":[176],"helping":[177],"reduce":[179],"noise.":[180],"Our":[181],"experimental":[182],"studies":[183],"10":[185],"real-world":[186],"datasets":[187],"demonstrate":[188],"scDVAE":[190],"significantly":[191],"improves":[192],"compared":[195],"state-of-the-art":[197],"methods.":[198]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
