{"id":"https://openalex.org/W4319999819","doi":"https://doi.org/10.1109/tcbb.2023.3240253","title":"Deep Multi-Constraint Soft Clustering Analysis for Single-Cell RNA-Seq Data via Zero-Inflated Autoencoder Embedding","display_name":"Deep Multi-Constraint Soft Clustering Analysis for Single-Cell RNA-Seq Data via Zero-Inflated Autoencoder Embedding","publication_year":2023,"publication_date":"2023-01-27","ids":{"openalex":"https://openalex.org/W4319999819","doi":"https://doi.org/10.1109/tcbb.2023.3240253","pmid":"https://pubmed.ncbi.nlm.nih.gov/37022218"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3240253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3240253","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM 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/A5045589663","display_name":"Yezi He","orcid":"https://orcid.org/0000-0002-4505-4120"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yezi He","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0002-4505-4120","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020334528","display_name":"Xiangtao Chen","orcid":"https://orcid.org/0000-0002-5102-1472"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangtao Chen","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0002-5102-1472","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103096012","display_name":"Nguyen Hoang Tu","orcid":"https://orcid.org/0000-0002-4973-2400"},"institutions":[{"id":"https://openalex.org/I45756140","display_name":"Hanoi University of Industry","ror":"https://ror.org/05hhz4s12","country_code":"VN","type":"education","lineage":["https://openalex.org/I45756140"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Nguyen Hoang Tu","raw_affiliation_strings":["Center for Information Technology and Faculty of Information and Technology, Hanoi University of Industry, Hanoi, Vietnam"],"raw_orcid":"https://orcid.org/0000-0002-4973-2400","affiliations":[{"raw_affiliation_string":"Center for Information Technology and Faculty of Information and Technology, Hanoi University of Industry, Hanoi, Vietnam","institution_ids":["https://openalex.org/I45756140"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026469278","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-2385-8272"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China"],"raw_orcid":"https://orcid.org/0000-0003-2385-8272","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":2.5677,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.89462165,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"20","issue":"3","first_page":"2254","last_page":"2265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.9732999801635742,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9319000244140625,"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/cluster-analysis","display_name":"Cluster analysis","score":0.8023475408554077},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5968265533447266},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.5652502179145813},{"id":"https://openalex.org/keywords/compact-space","display_name":"Compact space","score":0.5431675910949707},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5237417221069336},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.4370366036891937},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.43256309628486633},{"id":"https://openalex.org/keywords/rand-index","display_name":"Rand index","score":0.42959505319595337},{"id":"https://openalex.org/keywords/constrained-clustering","display_name":"Constrained clustering","score":0.4203697741031647},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.4203358292579651},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41804271936416626},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.416159987449646},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4138537347316742},{"id":"https://openalex.org/keywords/correlation-clustering","display_name":"Correlation clustering","score":0.373504638671875},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.29367268085479736},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.2158166766166687},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.14682060480117798},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07822543382644653}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8023475408554077},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5968265533447266},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.5652502179145813},{"id":"https://openalex.org/C18648836","wikidata":"https://www.wikidata.org/wiki/Q381892","display_name":"Compact space","level":2,"score":0.5431675910949707},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5237417221069336},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4370366036891937},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.43256309628486633},{"id":"https://openalex.org/C111442797","wikidata":"https://www.wikidata.org/wiki/Q7291446","display_name":"Rand index","level":3,"score":0.42959505319595337},{"id":"https://openalex.org/C27964816","wikidata":"https://www.wikidata.org/wiki/Q5164359","display_name":"Constrained clustering","level":5,"score":0.4203697741031647},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.4203358292579651},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41804271936416626},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.416159987449646},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4138537347316742},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.373504638671875},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29367268085479736},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.2158166766166687},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.14682060480117798},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07822543382644653},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"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/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"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":"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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"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":"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":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","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":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3240253","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3240253","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37022218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37022218","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6549098544","display_name":null,"funder_award_id":"62032007","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":59,"referenced_works":["https://openalex.org/W6908809","https://openalex.org/W1522301498","https://openalex.org/W1523794535","https://openalex.org/W1580018887","https://openalex.org/W1985867823","https://openalex.org/W2025768430","https://openalex.org/W2030006812","https://openalex.org/W2030017878","https://openalex.org/W2069089843","https://openalex.org/W2100495367","https://openalex.org/W2102212449","https://openalex.org/W2107680358","https://openalex.org/W2109890799","https://openalex.org/W2133811295","https://openalex.org/W2135937351","https://openalex.org/W2152692691","https://openalex.org/W2162833336","https://openalex.org/W2187089797","https://openalex.org/W2205138079","https://openalex.org/W2510746232","https://openalex.org/W2611831635","https://openalex.org/W2616922646","https://openalex.org/W2735067671","https://openalex.org/W2739492614","https://openalex.org/W2741943936","https://openalex.org/W2783644856","https://openalex.org/W2785523195","https://openalex.org/W2788348358","https://openalex.org/W2800392236","https://openalex.org/W2898718502","https://openalex.org/W2901677030","https://openalex.org/W2907783748","https://openalex.org/W2919115771","https://openalex.org/W2935703330","https://openalex.org/W2937917790","https://openalex.org/W2949272108","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2952016241","https://openalex.org/W2952303649","https://openalex.org/W2952350893","https://openalex.org/W2953251392","https://openalex.org/W2959295202","https://openalex.org/W3001485171","https://openalex.org/W3021272327","https://openalex.org/W3029148360","https://openalex.org/W3044164214","https://openalex.org/W3122205983","https://openalex.org/W3137285774","https://openalex.org/W3196454481","https://openalex.org/W4235169531","https://openalex.org/W4244030505","https://openalex.org/W4283573809","https://openalex.org/W4319069334","https://openalex.org/W6600284362","https://openalex.org/W6631190155","https://openalex.org/W6685380521","https://openalex.org/W6687888912","https://openalex.org/W6747620207"],"related_works":["https://openalex.org/W3146523624","https://openalex.org/W2951567704","https://openalex.org/W4300978037","https://openalex.org/W2086579450","https://openalex.org/W4312142847","https://openalex.org/W2969974905","https://openalex.org/W2515532987","https://openalex.org/W2535986621","https://openalex.org/W2186905933","https://openalex.org/W3011266291"],"abstract_inverted_index":{"Clustering":[0],"cells":[1],"into":[2],"subgroups":[3],"plays":[4],"a":[5,47,65,95],"critical":[6],"role":[7],"in":[8],"single":[9],"cell-based":[10],"analyses,":[11],"which":[12,107,147],"facilitates":[13],"to":[14,21,35,76,91,102,129,173],"reveal":[15],"cell":[16,105],"heterogeneity":[17],"and":[18,26,38,116,133],"diversity.":[19],"Due":[20],"the":[22,78,104,109,130,141,166,174],"ever-increasing":[23],"scRNA-seq":[24,40,122],"data":[25,115],"low":[27],"RNA":[28],"capture":[29],"rate,":[30],"it":[31],"has":[32],"become":[33],"challenging":[34],"cluster":[36,136],"high-dimensional":[37],"sparse":[39],"data.":[41],"In":[42],"this":[43],"study,":[44],"we":[45,139],"propose":[46],"single-cell":[48],"Multi-Constraint":[49],"deep":[50],"soft":[51,97],"K-means":[52,98],"Clustering(scMCKC)":[53],"framework.":[54],"Based":[55],"on":[56,112,120,143,155,161],"zero-inflated":[57],"negative":[58],"binomial":[59],"(ZINB)":[60],"model-based":[61],"autoencoder,":[62],"scMCKC":[63,83,126,150],"constructs":[64],"novel":[66,167],"cell-level":[67,168],"compactness":[68,79,169],"constraint":[69,86,170],"by":[70,88],"considering":[71],"association":[72],"between":[73,80,114],"similar":[74],"cell,":[75],"emphasize":[77],"clusters.":[81],"Besides,":[82],"utilizes":[84],"pairwise":[85],"encoded":[87],"prior":[89],"information":[90],"guide":[92],"clustering.":[93],"Meanwhile,":[94],"weighted":[96],"algorithm":[99],"is":[100,127,171],"leveraged":[101],"determine":[103],"populations,":[106],"assigns":[108],"label":[110],"based":[111],"affinity":[113],"clustering":[117,156,175],"center.":[118],"Experiments":[119],"eleven":[121,162],"datasets":[123,163],"demonstrate":[124],"that":[125,149,165],"superior":[128],"state-of-the-art":[131],"methods":[132],"notably":[134],"improves":[135],"performance.":[137],"Moreover,":[138],"validate":[140],"robustness":[142],"human":[144],"kidney":[145],"dataset,":[146],"demonstrates":[148],"exhibits":[151],"comprehensively":[152],"excellent":[153],"performance":[154],"analysis.":[157],"The":[158],"ablation":[159],"study":[160],"proves":[164],"conductive":[172],"results.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
