{"id":"https://openalex.org/W7161970460","doi":"https://doi.org/10.1109/tkde.2026.3695648","title":"CIPR: Class Imbalance-Aware Pseudo-Label Regeneration for Single-Cell Multi-Omics Clustering","display_name":"CIPR: Class Imbalance-Aware Pseudo-Label Regeneration for Single-Cell Multi-Omics Clustering","publication_year":2026,"publication_date":"2026-01-01","ids":{"openalex":"https://openalex.org/W7161970460","doi":"https://doi.org/10.1109/tkde.2026.3695648"},"language":"en","primary_location":{"id":"doi:10.1109/tkde.2026.3695648","doi":"https://doi.org/10.1109/tkde.2026.3695648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2026.3695648","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-a","cwts-core","dongbi-a","fnege-3","jufo-3","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","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 Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"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/A5078223155","display_name":"Zixiao Jin","orcid":"https://orcid.org/0009-0009-6366-852X","observed_orcids":["https://orcid.org/0009-0009-6366-852X"]},"institutions":[{"id":"https://openalex.org/I3124059619","display_name":"China University of Geosciences","ror":"https://ror.org/04gcegc37","country_code":"CN","type":"education","lineage":["https://openalex.org/I3124059619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixiao Jin","raw_affiliation_strings":["School of Computer Science, China University of Geosciences, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, China University of Geosciences, Wuhan, China","institution_ids":["https://openalex.org/I3124059619"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103038751","display_name":"Xiao Zheng","orcid":"https://orcid.org/0000-0002-5843-9206","observed_orcids":["https://orcid.org/0000-0002-5843-9206","https://orcid.org/0000-0002-3120-1257"]},"institutions":[{"id":"https://openalex.org/I74525822","display_name":"Hubei University of Technology","ror":"https://ror.org/02d3fj342","country_code":"CN","type":"education","lineage":["https://openalex.org/I74525822"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Zheng","raw_affiliation_strings":["School of Computer Science, Hubei University of Technology, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Hubei University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I74525822"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5151911628","display_name":"Weiqing Yan","orcid":"https://orcid.org/0000-0001-7869-2404","observed_orcids":["https://orcid.org/0000-0001-7869-2404"]},"institutions":[{"id":"https://openalex.org/I18452120","display_name":"Yantai University","ror":"https://ror.org/01rp41m56","country_code":"CN","type":"education","lineage":["https://openalex.org/I18452120"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiqing Yan","raw_affiliation_strings":["School of Computer and Technology, Yantai University, Yantai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer and Technology, Yantai University, Yantai, China","institution_ids":["https://openalex.org/I18452120"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033240507","display_name":"Chang Tang","orcid":"https://orcid.org/0000-0002-6515-7696","observed_orcids":["https://orcid.org/0000-0002-6515-7696"]},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chang Tang","raw_affiliation_strings":["School of Software Engineering, Huazhong University of Science and Technology, Wuhan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Engineering, Huazhong University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I47720641"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2645,"currency":"USD","value_usd":2645},"apc_paid":null,"fwci":2.0668,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.86712846,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"11"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9990000128746033,"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":0.9990000128746033,"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":9.999999747378752e-05,"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/T10637","display_name":"Advanced Clustering Algorithms Research","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/class-imbalance","display_name":"class imbalance","score":0.9950000047683716},{"id":"https://openalex.org/keywords/optimal-transport","display_name":"optimal transport","score":0.7390000224113464},{"id":"https://openalex.org/keywords/rare-cell-populations","display_name":"rare cell populations","score":0.7670000195503235},{"id":"https://openalex.org/keywords/curriculum-learning","display_name":"curriculum learning","score":0.6800000071525574},{"id":"https://openalex.org/keywords/cell-type-identification","display_name":"cell type annotation","score":0.4699999988079071},{"id":"https://openalex.org/keywords/cell-heterogeneity","display_name":"cellular heterogeneity","score":0.5419999957084656}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7634000182151794},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6376000046730042},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.5800999999046326},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40619999170303345},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40209999680519104},{"id":"https://openalex.org/C106516650","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm design","level":2,"score":0.3091999888420105},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.27889999747276306},{"id":"https://openalex.org/C3020028006","wikidata":"https://www.wikidata.org/wiki/Q9158","display_name":"Electronic mail","level":2,"score":0.27480000257492065},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.26829999685287476},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.24369999766349792}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tkde.2026.3695648","doi":"https://doi.org/10.1109/tkde.2026.3695648","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2026.3695648","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","ccf-a","cwts-core","dongbi-a","fnege-3","jufo-3","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","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 Transactions on Knowledge and Data Engineering","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.4000000059604645,"display_name":"Reduced inequalities"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7222835197","https://openalex.org/W7196943465","https://openalex.org/W7202254893","https://openalex.org/W4414110860","https://openalex.org/W4386857837","https://openalex.org/W7126018780","https://openalex.org/W4413278721","https://openalex.org/W4393252672","https://openalex.org/W7148682770","https://openalex.org/W4416955083"],"abstract_inverted_index":{"Single-cell":[0],"multi-omics":[1,103,205],"clustering":[2,69],"has":[3],"emerged":[4],"as":[5,106],"a":[6,77,86,125,131,168,186],"powerful":[7],"paradigm":[8],"for":[9,134],"dissecting":[10],"cellular":[11,91],"heterogeneity":[12],"and":[13,50,95,197,220],"advancing":[14],"precision":[15],"medicine.":[16],"Despite":[17],"recent":[18],"progress,":[19],"most":[20],"existing":[21],"methods":[22],"prioritize":[23],"the":[24,44,52,62,102,153,159],"strict":[25],"alignment":[26,32],"of":[27,46,113,162],"heterogeneous":[28],"modalities.":[29],"However,":[30],"this":[31],"process":[33,105],"is":[34],"often":[35],"dominated":[36],"by":[37,89,147],"majority":[38],"cell":[39,48,136,142,149,218],"populations,":[40],"which":[41],"inadvertently":[42],"suppresses":[43],"representation":[45,133],"rare":[47,141,217],"types":[49],"exacerbates":[51],"long-tail":[53],"effect":[54],"inherent":[55,160],"in":[56,67,215],"biological":[57,121],"data.":[58,164],"This":[59,138],"imbalance":[60,161],"distorts":[61],"latent":[63],"feature":[64],"space,":[65],"resulting":[66],"suboptimal":[68],"performance.":[70],"To":[71],"address":[72],"this,":[73],"we":[74,100,123],"propose":[75],"CIPR,":[76],"Class":[78],"Imbalance-aware":[79],"Pseudo-label":[80],"Regeneration":[81],"framework.":[82],"First,":[83],"CIPR":[84,166,209],"constructs":[85],"unified":[87],"embedding":[88],"integrating":[90],"attributes":[92],"with":[93],"local":[94],"global":[96],"structural":[97],"relationships.":[98],"Crucially,":[99],"formulate":[101],"pseudo-labeling":[104],"an":[107],"imbalanced":[108],"Optimal":[109],"Transport":[110],"problem.":[111],"Instead":[112],"enforcing":[114],"rigid":[115],"equal-sized":[116],"clusters":[117],"that":[118,172,208],"distort":[119],"true":[120],"proportions,":[122],"introduce":[124],"soft":[126],"uniform":[127],"prior":[128],"to":[129,155,158],"guarantee":[130],"baseline":[132],"all":[135],"groups.":[137],"explicitly":[139],"prevents":[140],"populations":[143,219],"from":[144,175],"being":[145],"absorbed":[146],"dominant":[148],"types,":[150],"while":[151],"allowing":[152],"model":[154],"naturally":[156],"adapt":[157],"single-cell":[163],"Furthermore,":[165],"incorporates":[167],"curriculum":[169],"learning":[170],"strategy":[171],"incrementally":[173],"learns":[174],"high-confidence":[176],"samples,":[177],"thereby":[178],"reducing":[179],"noise":[180],"propagation":[181],"during":[182],"pseudo-label":[183],"generation.":[184],"Finally,":[185],"cross-omics":[187],"interaction":[188],"mechanism":[189],"mutually":[190],"guides":[191],"prediction":[192],"distributions,":[193],"minimizing":[194],"inter-modality":[195],"conflicts":[196],"maximizing":[198],"information":[199],"complementarity.":[200],"Extensive":[201],"experiments":[202],"on":[203],"various":[204],"datasets":[206],"demonstrate":[207],"significantly":[210],"outperforms":[211],"state-of-the-art":[212],"methods,":[213],"particularly":[214],"identifying":[216],"handling":[221],"severe":[222],"class":[223],"imbalances.":[224]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-05-22T00:00:00"}
