{"id":"https://openalex.org/W7136368864","doi":"https://doi.org/10.1109/tcbbio.2026.3674362","title":"SAD: Sparse-Aware Diffusion Model for Single-Cell Gene Expression Completion","display_name":"SAD: Sparse-Aware Diffusion Model for Single-Cell Gene Expression Completion","publication_year":2026,"publication_date":"2026-03-16","ids":{"openalex":"https://openalex.org/W7136368864","doi":"https://doi.org/10.1109/tcbbio.2026.3674362","pmid":"https://pubmed.ncbi.nlm.nih.gov/41838515"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3674362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3674362","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 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/A5129581626","display_name":"Tianhao Li","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianhao Li","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, Chengdu, China"],"raw_orcid":"https://orcid.org/0009-0007-2952-7788","affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073433244","display_name":"Yi Xiang","orcid":"https://orcid.org/0000-0002-0724-6359"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixin Xiang","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China"],"raw_orcid":"https://orcid.org/0009-0008-6759-7194","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129629123","display_name":"Zixuan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]},{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zixuan Wang","raw_affiliation_strings":["College of Electronics and Information Engineering, Sichuan University, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engineering, Sichuan University, Chengdu, China","institution_ids":["https://openalex.org/I24185976","https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129529025","display_name":"Mengwen Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mengwen Liu","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129606563","display_name":"Quan Zou","orcid":null},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-6406-1142","affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129407796","display_name":"Yongqing Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I24201400","display_name":"Chengdu University of Information Technology","ror":"https://ror.org/01yxwrh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I24201400"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongqing Zhang","raw_affiliation_strings":["School of Computer Science, Chengdu University of Information Technology, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0003-3422-8305","affiliations":[{"raw_affiliation_string":"School of Computer Science, Chengdu University of Information Technology, Chengdu, China","institution_ids":["https://openalex.org/I24201400"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.23189112,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"3","first_page":"1200","last_page":"1213"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9071000218391418,"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":0.9071000218391418,"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":0.05429999902844429,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.0031999999191612005,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4887999892234802},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4052000045776367},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.3361000120639801},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2919999957084656}],"concepts":[{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4887999892234802},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4052000045776367},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3831000030040741},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.3361000120639801},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2962000072002411},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.29280000925064087},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2922999858856201},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2919999957084656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29159998893737793},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2720000147819519},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.26739999651908875},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.25859999656677246}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2026.3674362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3674362","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"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 Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41838515","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41838515","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/G5133105583","display_name":null,"funder_award_id":"62131004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8617958116","display_name":null,"funder_award_id":"62272067","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1966327575","https://openalex.org/W2020541351","https://openalex.org/W2133665775","https://openalex.org/W2165446840","https://openalex.org/W2616922646","https://openalex.org/W2792693509","https://openalex.org/W2805619986","https://openalex.org/W2900510132","https://openalex.org/W2901292166","https://openalex.org/W2945823867","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W3013135635","https://openalex.org/W3015461837","https://openalex.org/W3180669414","https://openalex.org/W3196572827","https://openalex.org/W3196650609","https://openalex.org/W3212516020","https://openalex.org/W4253759977","https://openalex.org/W4296371910","https://openalex.org/W4297243391","https://openalex.org/W4368359332","https://openalex.org/W4377029825","https://openalex.org/W4378838672","https://openalex.org/W4386890586","https://openalex.org/W4387195417","https://openalex.org/W4390946179","https://openalex.org/W4391576548","https://openalex.org/W4392168151","https://openalex.org/W4394011009","https://openalex.org/W4394870153","https://openalex.org/W4399387478","https://openalex.org/W4399498407","https://openalex.org/W4401093660","https://openalex.org/W4401415776","https://openalex.org/W4401794004","https://openalex.org/W4404328656","https://openalex.org/W4408223389","https://openalex.org/W4410026608","https://openalex.org/W4410255551","https://openalex.org/W4410521040","https://openalex.org/W4413146684","https://openalex.org/W4413147517","https://openalex.org/W4415536730","https://openalex.org/W7127046274"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"is":[4],"entering":[5],"an":[6],"era":[7],"of":[8,37,65,102,115],"foundation":[9,109,147],"models":[10,39,110],"that":[11,81,124],"accept":[12],"the":[13,35,48,84,97],"complete":[14],"gene":[15,92],"atlas":[16],"as":[17],"input,":[18],"yet":[19],"most":[20],"current":[21],"datasets":[22],"cover":[23],"only":[24],"10-12":[25],"k":[26,119],"genes":[27,67],"and":[28,53,68,103,107,153],"contain":[29],"numerous":[30],"technical":[31],"zeros,":[32],"severely":[33],"limiting":[34],"generalization":[36],"these":[38],"in":[40,135],"downstream":[41],"tasks.":[42],"To":[43],"address":[44],"this,":[45],"we":[46],"pioneer":[47],"gene-completion":[49],"task":[50],"for":[51,148,154],"scRNA-seq":[52,151],"present":[54],"SAD,":[55],"a":[56,145],"diffusion-based":[57],"framework":[58],"tailored":[59],"to":[60],"extremely":[61],"sparse":[62],"data,":[63],"capable":[64],"completing":[66],"correcting":[69],"sparsity":[70],"bias":[71],"under":[72],"high":[73],"missing":[74,139,150],"rates.":[75],"Unlike":[76],"imputation":[77],"or":[78],"reconstruction":[79],"methods":[80,129],"rely":[82],"on":[83],"i.i.d.":[85],"assumption,":[86],"SAD's":[87],"completion":[88,132],"paradigm":[89],"can":[90],"generate":[91],"entries":[93],"originally":[94],"absent":[95],"from":[96],"expression":[98],"profile,":[99],"be":[100],"aware":[101],"rectify":[104],"sparsity-distribution":[105],"bias,":[106],"supply":[108],"with":[111,138],"consistent,":[112],"reliable":[113],"inputs":[114],"more":[116],"than":[117],"30":[118],"genes.":[120],"Extensive":[121],"benchmarks":[122],"show":[123],"SAD":[125],"significantly":[126],"outperforms":[127],"existing":[128],"across":[130],"multiple":[131],"metrics,":[133],"particularly":[134],"extreme":[136],"scenarios":[137],"rates":[140],"above":[141],"80%.":[142],"This":[143],"provides":[144],"data":[146],"reusing":[149],"information":[152],"precision-medicine":[155],"applications.":[156]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-03-17T00:00:00"}
