{"id":"https://openalex.org/W4410359280","doi":"https://doi.org/10.1109/jbhi.2025.3570265","title":"scSTD: A Swin Transformer-Based Diffusion Model for Recovering scRNA-Seq Data","display_name":"scSTD: A Swin Transformer-Based Diffusion Model for Recovering scRNA-Seq Data","publication_year":2025,"publication_date":"2025-05-14","ids":{"openalex":"https://openalex.org/W4410359280","doi":"https://doi.org/10.1109/jbhi.2025.3570265","pmid":"https://pubmed.ncbi.nlm.nih.gov/40366848"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3570265","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3570265","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5100421418","display_name":"Yang Li","orcid":"https://orcid.org/0000-0002-0736-251X"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Li","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026553094","display_name":"Furui Liu","orcid":"https://orcid.org/0000-0003-3997-3822"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Furui Liu","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011001187","display_name":"Junlei Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junlei Zhou","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065978622","display_name":"Fangyuan Shi","orcid":"https://orcid.org/0000-0003-4185-8129"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangyuan Shi","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"raw_orcid":"https://orcid.org/0000-0003-4185-8129","affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000095054","display_name":"Zhenhua Yu","orcid":"https://orcid.org/0000-0001-6526-6991"},"institutions":[{"id":"https://openalex.org/I21642278","display_name":"Ningxia University","ror":"https://ror.org/04j7b2v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I21642278"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenhua Yu","raw_affiliation_strings":["School of Information Engineering, Ningxia University, Yinchuan, China"],"raw_orcid":"https://orcid.org/0000-0001-6526-6991","affiliations":[{"raw_affiliation_string":"School of Information Engineering, Ningxia University, Yinchuan, China","institution_ids":["https://openalex.org/I21642278"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I21642278"],"apc_list":null,"apc_paid":null,"fwci":0.5926,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.67446319,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"29","issue":"10","first_page":"7763","last_page":"7775"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9613000154495239,"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"}},"topics":[{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9613000154495239,"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"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9162999987602234,"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":0.9122999906539917,"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/computer-science","display_name":"Computer science","score":0.5579071640968323},{"id":"https://openalex.org/keywords/data-modeling","display_name":"Data modeling","score":0.5041776895523071},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.42101380228996277},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.17412632703781128},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1187620460987091},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.10609591007232666},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.08860203623771667}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5579071640968323},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.5041776895523071},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.42101380228996277},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.17412632703781128},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1187620460987091},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.10609591007232666},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.08860203623771667}],"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":"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":"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":"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":"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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3570265","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3570265","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40366848","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40366848","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4047386877","display_name":null,"funder_award_id":"2023BEG02009","funder_id":"https://openalex.org/F4320334010","funder_display_name":"Key Research and Development Program of Ningxia"},{"id":"https://openalex.org/G5103070055","display_name":null,"funder_award_id":"2023AAC05006","funder_id":"https://openalex.org/F4320322877","funder_display_name":"Natural Science Foundation of Ningxia Province"},{"id":"https://openalex.org/G8815381927","display_name":null,"funder_award_id":"2023AAC03030","funder_id":"https://openalex.org/F4320322877","funder_display_name":"Natural Science Foundation of Ningxia Province"}],"funders":[{"id":"https://openalex.org/F4320322877","display_name":"Natural Science Foundation of Ningxia Province","ror":null},{"id":"https://openalex.org/F4320334010","display_name":"Key Research and Development Program of Ningxia","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W1988391018","https://openalex.org/W2069089843","https://openalex.org/W2107680358","https://openalex.org/W2511896561","https://openalex.org/W2523369352","https://openalex.org/W2743416243","https://openalex.org/W2751468300","https://openalex.org/W2792693509","https://openalex.org/W2805619986","https://openalex.org/W2902652978","https://openalex.org/W2907783748","https://openalex.org/W2947877009","https://openalex.org/W2951217100","https://openalex.org/W2951271761","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2952303649","https://openalex.org/W2977512847","https://openalex.org/W2980495984","https://openalex.org/W3001485171","https://openalex.org/W3003185417","https://openalex.org/W3007573310","https://openalex.org/W3008081001","https://openalex.org/W3009560560","https://openalex.org/W3037216933","https://openalex.org/W3089871235","https://openalex.org/W3138479716","https://openalex.org/W3140605903","https://openalex.org/W3162113604","https://openalex.org/W3164852867","https://openalex.org/W3205959358","https://openalex.org/W3216759837","https://openalex.org/W4205559708","https://openalex.org/W4220905914","https://openalex.org/W4225138617","https://openalex.org/W4225579877","https://openalex.org/W4288384137","https://openalex.org/W4289335819","https://openalex.org/W4294990955","https://openalex.org/W4312933868","https://openalex.org/W4319049324","https://openalex.org/W4321748573","https://openalex.org/W4385638791","https://openalex.org/W4386047807","https://openalex.org/W4386890586","https://openalex.org/W4388035146","https://openalex.org/W4389220058","https://openalex.org/W4390872297","https://openalex.org/W4391576548","https://openalex.org/W4393906055","https://openalex.org/W4394870153","https://openalex.org/W4396663708","https://openalex.org/W4401247064","https://openalex.org/W4401415776","https://openalex.org/W4401794004","https://openalex.org/W4404122385"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Dropout":[0],"events":[1],"and":[2,20,29,40,61,134,143,150,167],"technical":[3],"noise":[4],"are":[5],"pervasive":[6],"challenges":[7],"in":[8,161],"single-cell":[9],"RNA":[10],"sequencing":[11],"(scRNA-seq)":[12],"data,":[13],"often":[14],"obscuring":[15],"true":[16,163],"gene":[17,118,164],"expression":[18,119,165],"profiles":[19,120,166],"undermining":[21],"the":[22,45,67,104,169],"reliability":[23],"of":[24,48,108,172],"downstream":[25],"analyses.":[26],"Existing":[27],"imputation":[28,60,142],"denoising":[30,62],"methods":[31,160],"offer":[32],"partial":[33],"relief":[34],"but":[35],"frequently":[36],"struggle":[37],"with":[38,72],"over-smoothing":[39],"fail":[41],"to":[42,102,115],"fully":[43],"capture":[44],"complex":[46],"heterogeneity":[47],"cellular":[49,173],"states.":[50],"To":[51],"address":[52],"these":[53],"limitations,":[54],"we":[55],"introduce":[56],"scSTD,":[57,78],"a":[58,73,79,87,96],"novel":[59],"framework":[63],"that":[64,155],"uniquely":[65],"combines":[66],"Swin":[68],"Transformer":[69],"(SwinT)":[70],"architecture":[71],"latent":[74,89,98,129],"diffusion":[75,99],"model.":[76],"In":[77],"deep":[80],"autoencoder":[81],"first":[82],"encodes":[83],"each":[84,132],"cell":[85,133],"into":[86],"compact":[88],"embedding,":[90],"which":[91],"is":[92],"then":[93],"modeled":[94],"via":[95],"SwinT-based":[97],"process":[100],"designed":[101],"learn":[103],"rich,":[105],"multimodal":[106],"distribution":[107],"scRNA-seq":[109,152],"data.":[110],"This":[111],"integration":[112],"enables":[113],"scSTD":[114,139,156],"accurately":[116],"recover":[117],"while":[121],"preserving":[122],"subtle":[123],"biological":[124],"variation.":[125],"By":[126],"synthesizing":[127],"realistic":[128],"neighbors":[130],"for":[131],"aggregating":[135],"their":[136],"decoded":[137],"outputs,":[138],"achieves":[140],"high-fidelity":[141],"denoising.":[144],"Comprehensive":[145],"evaluations":[146],"on":[147],"both":[148],"synthetic":[149],"real":[151],"datasets":[153],"demonstrate":[154],"significantly":[157],"outperforms":[158],"existing":[159],"recovering":[162],"maintaining":[168],"topological":[170],"integrity":[171],"landscapes.":[174]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}