{"id":"https://openalex.org/W4410639157","doi":"https://doi.org/10.1109/tcbbio.2025.3572783","title":"ZiPo: A Deep Neural Network to De-Noise Single-Cell RNA Sequencing Data","display_name":"ZiPo: A Deep Neural Network to De-Noise Single-Cell RNA Sequencing Data","publication_year":2025,"publication_date":"2025-05-23","ids":{"openalex":"https://openalex.org/W4410639157","doi":"https://doi.org/10.1109/tcbbio.2025.3572783","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811273"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3572783","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3572783","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1109/tcbbio.2025.3572783","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010791936","display_name":"Mohsen Sharifitabar","orcid":"https://orcid.org/0009-0001-2119-0769"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohsen Sharifitabar","raw_affiliation_strings":["Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"],"raw_orcid":"https://orcid.org/0009-0001-2119-0769","affiliations":[{"raw_affiliation_string":"Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079855186","display_name":"Shiva Kazempour Dehkordi","orcid":"https://orcid.org/0000-0003-0349-4360"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shiva Kazempour","raw_affiliation_strings":["Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"],"raw_orcid":"https://orcid.org/0000-0003-0349-4360","affiliations":[{"raw_affiliation_string":"Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017006105","display_name":"Seiied-Mohammad-Javad Razavian","orcid":"https://orcid.org/0000-0002-0222-7570"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Javad Razavian","raw_affiliation_strings":["Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"],"raw_orcid":"https://orcid.org/0000-0002-0222-7570","affiliations":[{"raw_affiliation_string":"Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059258411","display_name":"Sogand Sajedi","orcid":"https://orcid.org/0009-0008-4157-5579"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sogand Sajedi","raw_affiliation_strings":["The University of Texas MD Anderson Cancer Center, Houston, TX, USA","University of Texas MD Anderson Cancer Center, TX, USA"],"raw_orcid":"https://orcid.org/0009-0008-4157-5579","affiliations":[{"raw_affiliation_string":"The University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"University of Texas MD Anderson Cancer Center, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042448754","display_name":"Soroosh Solhjoo","orcid":"https://orcid.org/0000-0002-4908-2479"},"institutions":[{"id":"https://openalex.org/I1299303238","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238"]},{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Soroosh Solhjoo","raw_affiliation_strings":["F. Edward Hébert School of Medicine, Bethesda, MD, USA","Johns Hopkins University School of Medicine, Baltimore, MD, USA"],"raw_orcid":"https://orcid.org/0000-0002-4908-2479","affiliations":[{"raw_affiliation_string":"F. Edward Hébert School of Medicine, Bethesda, MD, USA","institution_ids":["https://openalex.org/I1299303238"]},{"raw_affiliation_string":"Johns Hopkins University School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062228773","display_name":"Habil Zare","orcid":"https://orcid.org/0000-0001-5902-6238"},"institutions":[{"id":"https://openalex.org/I165951966","display_name":"The University of Texas at San Antonio Health Science Center","ror":"https://ror.org/02f6dcw23","country_code":"US","type":"education","lineage":["https://openalex.org/I165951966","https://openalex.org/I45438204"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Habil Zare","raw_affiliation_strings":["Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA"],"raw_orcid":"https://orcid.org/0000-0001-5902-6238","affiliations":[{"raw_affiliation_string":"Department of Cell Systems & Anatomy, The University of Texas Health Science Center, San Antonio, TX, USA","institution_ids":["https://openalex.org/I165951966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"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":0.06749828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2341","last_page":"2352"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9373000264167786,"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":0.9373000264167786,"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/deep-sequencing","display_name":"Deep sequencing","score":0.5271700620651245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5025501251220703},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5025203227996826},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.4751018285751343},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44275978207588196},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3702923655509949},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3336245119571686},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24735021591186523},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10651084780693054},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.08487585186958313}],"concepts":[{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.5271700620651245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5025501251220703},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5025203227996826},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.4751018285751343},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44275978207588196},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3702923655509949},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3336245119571686},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24735021591186523},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10651084780693054},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.08487585186958313},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":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":"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":"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"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},{"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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbbio.2025.3572783","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3572783","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811273","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811273","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},{"id":"pmh:oai:pubmedcentral.nih.gov:12910556","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12910556/","pdf_url":null,"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":"IEEE Trans Comput Biol Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1109/tcbbio.2025.3572783","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3572783","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2662099513","display_name":null,"funder_award_id":"R01AG066524","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G343469054","display_name":null,"funder_award_id":"P30AG066546","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G683723002","display_name":null,"funder_award_id":"R01AG068293","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G7441165371","display_name":null,"funder_award_id":"RF1 AG063507","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1622676895","https://openalex.org/W1966327575","https://openalex.org/W2024391964","https://openalex.org/W2084942072","https://openalex.org/W2107878631","https://openalex.org/W2154431984","https://openalex.org/W2194775991","https://openalex.org/W2311607323","https://openalex.org/W2540833380","https://openalex.org/W2602321039","https://openalex.org/W2606066853","https://openalex.org/W2612502013","https://openalex.org/W2751468300","https://openalex.org/W2783644856","https://openalex.org/W2787894218","https://openalex.org/W2792693509","https://openalex.org/W2794891507","https://openalex.org/W2805619986","https://openalex.org/W2902162324","https://openalex.org/W2935703330","https://openalex.org/W2942678593","https://openalex.org/W2949676527","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2952303649","https://openalex.org/W3019068524","https://openalex.org/W3091376159","https://openalex.org/W3109816533","https://openalex.org/W4200534156","https://openalex.org/W4225981439","https://openalex.org/W4383859620"],"related_works":["https://openalex.org/W2391251536","https://openalex.org/W2362198218","https://openalex.org/W2019521278","https://openalex.org/W1984922432","https://openalex.org/W2375008505","https://openalex.org/W1982750869","https://openalex.org/W2085756966","https://openalex.org/W2350679292","https://openalex.org/W2086348228","https://openalex.org/W4390653028"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq),":[3],"a":[4,51,121],"powerful":[5],"technique":[6],"for":[7,56],"investigating":[8],"the":[9,15,37,72,88,109,118,126,131,145,151,160],"transcriptome":[10],"of":[11,17,39,97,115,120,153,162],"individual":[12],"cells,":[13],"enables":[14],"discovery":[16],"heterogeneous":[18],"cell":[19,22],"populations,":[20],"rare":[21],"types,":[23],"and":[24,59,86,90,104,141,167],"transcriptional":[25],"dynamics":[26],"in":[27,63,71],"separate":[28],"cells.":[29,154],"Yet,":[30],"scRNA-seq":[31,64],"data":[32,65],"analysis":[33],"is":[34,117],"limited":[35],"by":[36,94],"problem":[38],"measurement":[40],"dropouts,":[41],"i.e.,":[42],"genes":[43],"displaying":[44],"zero":[45,69],"expression":[46],"levels.":[47],"We":[48],"introduce":[49],"ZiPo,":[50],"deep":[52,84],"artificial":[53],"neural":[54],"network":[55],"rate":[57],"estimation":[58],"library":[60,101],"size":[61,102],"prediction":[62,103],"that":[66],"incorporates":[67],"adjustable":[68],"inflation":[70],"distribution":[73],"to":[74,107,150],"capture":[75],"dropouts.":[76],"ZiPo":[77,116,136,163],"builds":[78],"upon":[79],"established":[80],"concepts,":[81],"including":[82,100],"using":[83],"autoencoders":[85],"adopting":[87],"Poisson":[89],"negative":[91],"binomial":[92],"distributions,":[93],"taking":[95],"advantage":[96],"novel":[98],"strategies,":[99],"residual":[105],"connections,":[106],"improve":[108],"overall":[110],"performance.":[111],"A":[112],"significant":[113],"innovation":[114],"introduction":[119],"scale-invariant":[122],"loss":[123],"term,":[124],"making":[125],"weights":[127],"sparse":[128],"and,":[129],"hence,":[130],"model":[132],"biologically":[133],"more":[134],"interpretable.":[135],"quickly":[137],"handles":[138],"vast":[139],"singular":[140],"mixed":[142],"datasets,":[143],"with":[144],"processing":[146],"time":[147],"directly":[148],"proportional":[149],"number":[152],"In":[155],"this":[156],"paper,":[157],"we":[158],"demonstrate":[159],"power":[161],"on":[164],"three":[165],"datasets":[166],"show":[168],"its":[169],"advantages":[170],"over":[171],"other":[172],"current":[173],"techniques.":[174]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}