{"id":"https://openalex.org/W4404102546","doi":"https://doi.org/10.1109/tcbb.2024.3492384","title":"Enhancing Single-Cell RNA-Seq Data Completeness With a Graph Learning Framework","display_name":"Enhancing Single-Cell RNA-Seq Data Completeness With a Graph Learning Framework","publication_year":2024,"publication_date":"2024-11-06","ids":{"openalex":"https://openalex.org/W4404102546","doi":"https://doi.org/10.1109/tcbb.2024.3492384","pmid":"https://pubmed.ncbi.nlm.nih.gov/39504287"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3492384","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3492384","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"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/A5060972599","display_name":"Snehalika Lall","orcid":"https://orcid.org/0000-0002-6694-5344"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Snehalika Lall","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal, India","Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India"],"affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal, India","institution_ids":["https://openalex.org/I6498739"]},{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India","institution_ids":["https://openalex.org/I6498739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008522568","display_name":"Sumanta Ray","orcid":"https://orcid.org/0000-0002-3371-8516"},"institutions":[{"id":"https://openalex.org/I180765649","display_name":"Aliah University","ror":"https://ror.org/03rfycd69","country_code":"IN","type":"education","lineage":["https://openalex.org/I180765649"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sumanta Ray","raw_affiliation_strings":["Aliah University, New Town, Kolkata, West Bengal, India","Aliah University, New Town, Kolkata, India"],"affiliations":[{"raw_affiliation_string":"Aliah University, New Town, Kolkata, West Bengal, India","institution_ids":["https://openalex.org/I180765649"]},{"raw_affiliation_string":"Aliah University, New Town, Kolkata, India","institution_ids":["https://openalex.org/I180765649"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036061149","display_name":"Sanghamitra Bandyopadhyay","orcid":"https://orcid.org/0000-0001-6370-2083"},"institutions":[{"id":"https://openalex.org/I6498739","display_name":"Indian Statistical Institute","ror":"https://ror.org/00q2w1j53","country_code":"IN","type":"education","lineage":["https://openalex.org/I6498739"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sanghamitra Bandyopadhyay","raw_affiliation_strings":["Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal, India","Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India"],"affiliations":[{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, Kolkata, West Bengal, India","institution_ids":["https://openalex.org/I6498739"]},{"raw_affiliation_string":"Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India","institution_ids":["https://openalex.org/I6498739"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5060972599"],"corresponding_institution_ids":["https://openalex.org/I6498739"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.17921012,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"1","first_page":"64","last_page":"72"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9341999888420105,"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/completeness","display_name":"Completeness (order theory)","score":0.6437582969665527},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5530275106430054},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5529301166534424},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.49327200651168823},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3364626169204712},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20733395218849182},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17791712284088135},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1026121973991394},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08226528763771057},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08007761836051941},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.0679369866847992}],"concepts":[{"id":"https://openalex.org/C17231256","wikidata":"https://www.wikidata.org/wiki/Q5156540","display_name":"Completeness (order theory)","level":2,"score":0.6437582969665527},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5530275106430054},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5529301166534424},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.49327200651168823},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3364626169204712},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20733395218849182},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17791712284088135},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1026121973991394},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08226528763771057},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08007761836051941},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.0679369866847992},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"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":"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":"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":"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":"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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2024.3492384","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3492384","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"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:39504287","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39504287","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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1967327758","https://openalex.org/W2114104545","https://openalex.org/W2135937351","https://openalex.org/W2151506973","https://openalex.org/W2152239989","https://openalex.org/W2332292689","https://openalex.org/W2564176045","https://openalex.org/W2598326928","https://openalex.org/W2739492614","https://openalex.org/W2747545374","https://openalex.org/W2751468300","https://openalex.org/W2753908609","https://openalex.org/W2755506013","https://openalex.org/W2792693509","https://openalex.org/W2795624730","https://openalex.org/W2799796757","https://openalex.org/W2800392236","https://openalex.org/W2801443765","https://openalex.org/W2805619986","https://openalex.org/W2898718502","https://openalex.org/W2947877009","https://openalex.org/W2949067670","https://openalex.org/W2951217100","https://openalex.org/W2951506174","https://openalex.org/W2956840440","https://openalex.org/W3159332271","https://openalex.org/W3205128056","https://openalex.org/W4221019030","https://openalex.org/W6730084236"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4237277701","https://openalex.org/W2121424666","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W1587028174","https://openalex.org/W2358668433","https://openalex.org/W4301250310"],"abstract_inverted_index":{"Single":[0],"cell":[1,39,142],"RNA":[2,22],"sequencing":[3],"(scRNA-seq)":[4],"is":[5,76,114],"a":[6,18,46,59],"powerful":[7],"tool":[8],"to":[9,78,98,125,134],"capture":[10],"gene":[11],"expression":[12,40,102],"snapshots":[13],"in":[14,23,28,36,91,141],"individual":[15,25],"cells.":[16],"However,":[17],"low":[19],"amount":[20],"of":[21,58,87,104,110],"the":[24,37,55,64,80,85,92,100,105,111],"cells":[26],"results":[27],"dropout":[29],"events,":[30],"which":[31],"introduce":[32],"huge":[33],"zero":[34],"counts":[35],"single":[38],"matrix.":[41],"We":[42,94],"have":[43],"developed":[44],"VAImpute,":[45],"variational":[47],"graph":[48],"autoencoder":[49],"based":[50],"imputation":[51,128],"technique":[52],"that":[53],"learns":[54],"inherent":[56],"distribution":[57],"large":[60],"network/graph":[61],"constructed":[62],"from":[63],"scRNA-seq":[65,121],"data":[66],"leveraging":[67],"copula":[68],"correlation":[69],"($Ccor$)":[70],"among":[71],"cells/genes.":[72],"The":[73,108],"trained":[74],"model":[75,113],"utilized":[77],"predict":[79],"dropouts":[81],"events":[82],"by":[83],"computing":[84],"probability":[86],"all":[88],"non-edges":[89],"(cell-gene)":[90],"network.":[93],"devise":[95],"an":[96],"algorithm":[97],"impute":[99],"missing":[101],"values":[103],"detected":[106],"dropouts.":[107],"performance":[109,140],"proposed":[112],"assessed":[115],"on":[116],"both":[117],"simulated":[118],"and":[119,147],"real":[120],"datasets,":[122],"comparing":[123],"it":[124],"established":[126],"single-cell":[127],"methods.":[129],"VAImpute":[130],"yields":[131],"significant":[132],"improvements":[133],"detect":[135],"dropouts,":[136],"thereby":[137],"achieving":[138],"superior":[139],"clustering,":[143],"detecting":[144],"rare":[145],"cells,":[146],"differential":[148],"expression.":[149]},"counts_by_year":[],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}