{"id":"https://openalex.org/W7139064881","doi":"https://doi.org/10.1186/s12859-026-06422-2","title":"scZiva: imputation method for single-cell RNA-seq data with zero-inflated variational autoencoder","display_name":"scZiva: imputation method for single-cell RNA-seq data with zero-inflated variational autoencoder","publication_year":2026,"publication_date":"2026-03-19","ids":{"openalex":"https://openalex.org/W7139064881","doi":"https://doi.org/10.1186/s12859-026-06422-2","pmid":"https://pubmed.ncbi.nlm.nih.gov/41857511"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06422-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06422-2","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-026-06422-2.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1186/s12859-026-06422-2.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5130158171","display_name":"Long Tuan Vo","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148201","display_name":"Ho Chi Minh City University of Technology and Engineering","ror":"https://ror.org/05hzn5427","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210148201"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Long Tuan Vo","raw_affiliation_strings":["Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam","institution_ids":["https://openalex.org/I4210148201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129850956","display_name":"Va\u0306n Th\u01a1m Le\u0302","orcid":null},"institutions":[{"id":"https://openalex.org/I23582244","display_name":"Ho Chi Minh City University of Science","ror":"https://ror.org/05jfbgm49","country_code":"VN","type":"education","lineage":["https://openalex.org/I123565023","https://openalex.org/I23582244"]},{"id":"https://openalex.org/I4210148201","display_name":"Ho Chi Minh City University of Technology and Engineering","ror":"https://ror.org/05hzn5427","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210148201"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Van Vinh Le","raw_affiliation_strings":["Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam. vinhlv@hcmute.edu.vn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam. vinhlv@hcmute.edu.vn","institution_ids":["https://openalex.org/I23582244","https://openalex.org/I4210148201"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130140393","display_name":"Quoc Toan Ha","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148201","display_name":"Ho Chi Minh City University of Technology and Engineering","ror":"https://ror.org/05hzn5427","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210148201"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Quoc Toan Ha","raw_affiliation_strings":["Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam","institution_ids":["https://openalex.org/I4210148201"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129965528","display_name":"Nguyen, Anh H. G.;Sheen, Gwo-Ji","orcid":null},"institutions":[{"id":"https://openalex.org/I4210148201","display_name":"Ho Chi Minh City University of Technology and Engineering","ror":"https://ror.org/05hzn5427","country_code":"VN","type":"education","lineage":["https://openalex.org/I4210148201"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Anh Quoc Nguyen","raw_affiliation_strings":["Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ho Chi Minh City University of Technology and Engineering, Vo Van Ngan Street, Ho Chi Minh City, 700000, Vietnam","institution_ids":["https://openalex.org/I4210148201"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5129850956"],"corresponding_institution_ids":["https://openalex.org/I23582244","https://openalex.org/I4210148201"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":9.3661,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.97962641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"27","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":0.9993000030517578,"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":0.9993000030517578,"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/T10773","display_name":"Extracellular vesicles in disease","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/T11287","display_name":"Cancer Genomics and Diagnostics","score":9.999999747378752e-05,"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/autoencoder","display_name":"Autoencoder","score":0.765500009059906},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.4941999912261963},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.47519999742507935},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.3176000118255615},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.2935999929904938}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.765500009059906},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6182000041007996},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5231999754905701},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.4941999912261963},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.47519999742507935},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4424000084400177},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3643999993801117},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.3176000118255615},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.2935999929904938},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.26510000228881836},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26339998841285706},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25760000944137573}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":4,"locations":[{"id":"doi:10.1186/s12859-026-06422-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06422-2","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-026-06422-2.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41857511","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41857511","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13122936","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13122936/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13122936/pdf/12859_2026_Article_6422.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:af3079876fac4514a13d8dc12019311c","is_oa":true,"landing_page_url":"https://doaj.org/article/af3079876fac4514a13d8dc12019311c","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06422-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06422-2","pdf_url":"https://link.springer.com/content/pdf/10.1186/s12859-026-06422-2.pdf","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.48220810294151306}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323346","display_name":"B\u1ed9 Gi\u00e1o d\u1ee5c v\u00e0 \u00d0\u00e0o t\u1ea1o","ror":"https://ror.org/00drv3378"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7139064881.pdf","grobid_xml":"https://content.openalex.org/works/W7139064881.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1546952499","https://openalex.org/W1984883254","https://openalex.org/W2084706776","https://openalex.org/W2128728535","https://openalex.org/W2149573463","https://openalex.org/W2150593711","https://openalex.org/W2511896561","https://openalex.org/W2522775671","https://openalex.org/W2792693509","https://openalex.org/W2794891507","https://openalex.org/W2805619986","https://openalex.org/W2927507212","https://openalex.org/W2949067670","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2951638683","https://openalex.org/W3003185417","https://openalex.org/W3007573310","https://openalex.org/W3009560560","https://openalex.org/W3080162757","https://openalex.org/W4235169531","https://openalex.org/W4312195190","https://openalex.org/W4364352246","https://openalex.org/W4386221015","https://openalex.org/W4388035146","https://openalex.org/W4391262644","https://openalex.org/W4391886418","https://openalex.org/W4393034417","https://openalex.org/W4401173640","https://openalex.org/W4401553158","https://openalex.org/W4403046430","https://openalex.org/W4406464712","https://openalex.org/W4408245148","https://openalex.org/W4410517693"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"is":[5,156,219],"considered":[6],"a":[7,26,105,121,139,159,166,220],"revolution":[8],"in":[9,32,70,81,86,93,198,208],"gene":[10,67,134,211],"expression":[11,51,68,212],"studies":[12],"and":[13,39,53,89,130,176,195,214],"offers":[14],"significant":[15],"benefits":[16],"across":[17],"various":[18],"fields":[19],"of":[20,29,43,182],"biomedical":[21],"or":[22],"clinical":[23],"applications.":[24],"However,":[25],"high":[27],"proportion":[28],"technical":[30,95,147],"dropouts":[31,148],"scRNA-seq":[33,71,87,110,225],"data":[34,88],"leads":[35],"to":[36,64,144,203],"increased":[37],"noise":[38],"reduces":[40],"the":[41,74,91,180],"performance":[42,197],"downstream":[44,216],"analyses":[45],"such":[46],"as":[47],"cell":[48,54],"clustering,":[49],"differential":[50],"analysis,":[52],"trajectory":[55],"inference.":[56],"Numerous":[57],"recent":[58],"imputation":[59,107,142],"methods":[60,78],"utilize":[61],"deep":[62],"learning":[63],"recover":[65,145],"missing":[66,210],"values":[69,213],"data.":[72,226],"Despite":[73],"research":[75],"efforts,":[76],"existing":[77],"have":[79],"limitations":[80],"capturing":[82],"local":[83,133],"co-expression":[84],"patterns":[85],"handling":[90],"uncertainty":[92,129],"distinguishing":[94],"zeros":[96],"from":[97],"true":[98],"biological":[99],"zeros.":[100,153],"RESULTS:":[101],"This":[102],"work":[103],"proposes":[104],"novel":[106],"method":[108,192],"for":[109,223],"data,":[111],"called":[112],"scZiva,":[113],"based":[114],"on":[115,173],"Variational":[116],"Autoencoder":[117],"(VAE).":[118],"It":[119,218],"introduces":[120],"structured":[122],"probabilistic":[123],"framework":[124,155],"that":[125],"jointly":[126],"models":[127],"dropout":[128],"statistically":[131],"induced":[132],"dependencies.":[135],"scZiva":[136,183],"also":[137],"adopts":[138],"probability-guided":[140],"selective":[141],"mechanism":[143],"likely":[146],"while":[149],"preserving":[150],"biologically":[151],"meaningful":[152],"The":[154,190],"implemented":[157],"using":[158],"Zero-Inflated":[160],"Negative":[161],"Binomial":[162],"(ZINB)":[163],"likelihood":[164],"with":[165,185],"convolution-enhanced":[167],"encoder":[168],"architecture.":[169],"Comprehensive":[170],"experiments":[171],"conducted":[172],"both":[174],"simulated":[175],"real":[177],"datasets":[178],"demonstrate":[179],"strength":[181],"compared":[184,202],"other":[186],"baseline":[187,205],"methods.":[188],"CONCLUSION:":[189],"proposed":[191],"demonstrates":[193],"strong":[194],"stable":[196],"most":[199],"evaluation":[200],"settings":[201],"five":[204],"methods,":[206],"particularly":[207],"recovering":[209],"supporting":[215],"analyses.":[217],"promising":[221],"approach":[222],"analyzing":[224]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2026-03-20T00:00:00"}
