{"id":"https://openalex.org/W4321748573","doi":"https://doi.org/10.1093/bioinformatics/btad098","title":"scGCL: an imputation method for scRNA-seq data based on graph contrastive learning","display_name":"scGCL: an imputation method for scRNA-seq data based on graph contrastive learning","publication_year":2023,"publication_date":"2023-02-24","ids":{"openalex":"https://openalex.org/W4321748573","doi":"https://doi.org/10.1093/bioinformatics/btad098","pmid":"https://pubmed.ncbi.nlm.nih.gov/36825817"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad098","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad098/49447251/btad098.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad098/49447251/btad098.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077277630","display_name":"Zehao Xiong","orcid":"https://orcid.org/0000-0002-6549-9610"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zehao Xiong","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-6549-9610","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026469278","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-2385-8272"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114859464","display_name":"Wanwan Shi","orcid":"https://orcid.org/0000-0003-4730-4610"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanwan Shi","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100414459","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0003-3672-9621"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101498383","display_name":"XU Zhong-yuan","orcid":"https://orcid.org/0000-0003-1759-9665"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhongyuan Xu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":"https://orcid.org/0000-0003-1759-9665","affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100408160","display_name":"Bo Wang","orcid":"https://orcid.org/0000-0002-9620-3413"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Wang","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University , Changsha 410083, China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5026469278"],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.4334,"has_fulltext":true,"cited_by_count":37,"citation_normalized_percentile":{"value":0.93871702,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"39","issue":"3","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":0.9976999759674072,"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":0.9976999759674072,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00039999998989515007,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7323943376541138},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.732245683670044},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6436970233917236},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6156013607978821},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48450157046318054},{"id":"https://openalex.org/keywords/dropout","display_name":"Dropout (neural networks)","score":0.46979841589927673},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4670874774456024},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45055699348449707},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3779827356338501},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32836011052131653},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.2665252387523651},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.20438936352729797},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.13412702083587646}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7323943376541138},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.732245683670044},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6436970233917236},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6156013607978821},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48450157046318054},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.46979841589927673},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4670874774456024},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45055699348449707},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3779827356338501},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32836011052131653},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.2665252387523651},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.20438936352729797},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.13412702083587646}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","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":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad098","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad098/49447251/btad098.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36825817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36825817","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9991516","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9991516","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9991516/pdf/btad098.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad098","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad098","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/3/btad098/49447251/btad098.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4321748573.pdf"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1580018887","https://openalex.org/W1979283544","https://openalex.org/W1981641790","https://openalex.org/W2033403400","https://openalex.org/W2102212449","https://openalex.org/W2135937351","https://openalex.org/W2526262591","https://openalex.org/W2735067671","https://openalex.org/W2747877289","https://openalex.org/W2751468300","https://openalex.org/W2752378502","https://openalex.org/W2791142331","https://openalex.org/W2800392236","https://openalex.org/W2801175520","https://openalex.org/W2805619986","https://openalex.org/W2885499809","https://openalex.org/W2887326710","https://openalex.org/W2894687190","https://openalex.org/W2898718502","https://openalex.org/W2900144939","https://openalex.org/W2901677030","https://openalex.org/W2907783748","https://openalex.org/W2924067995","https://openalex.org/W2980495984","https://openalex.org/W2991414673","https://openalex.org/W3037216933","https://openalex.org/W3080162757","https://openalex.org/W3138479716","https://openalex.org/W3140605903","https://openalex.org/W3163972593","https://openalex.org/W3198255086","https://openalex.org/W4205916264","https://openalex.org/W4225579877","https://openalex.org/W4226408593","https://openalex.org/W6743835438","https://openalex.org/W6787157338","https://openalex.org/W6792121546"],"related_works":["https://openalex.org/W4287995534","https://openalex.org/W2998168123","https://openalex.org/W2897995864","https://openalex.org/W2292254049","https://openalex.org/W2592385986","https://openalex.org/W4281924768","https://openalex.org/W3099179464","https://openalex.org/W2772780115","https://openalex.org/W4309838615","https://openalex.org/W4214881770"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA-sequencing":[2],"(scRNA-seq)":[3],"is":[4,52],"widely":[5],"used":[6],"to":[7,19,111,129],"reveal":[8],"cellular":[9],"heterogeneity,":[10],"complex":[11,23],"disease":[12,198],"mechanisms":[13],"and":[14,22,43,58,76,105,118,125,176,205],"cell":[15,41],"differentiation":[16],"processes.":[17],"Due":[18],"high":[20],"sparsity":[21],"gene":[24,177],"expression":[25,48,191],"patterns,":[26],"scRNA-seq":[27,64,74,95,154,181],"data":[28,65,75,96,155,206,217],"present":[29],"a":[30,88],"large":[31],"number":[32],"of":[33,50,73,133,193,207],"dropout":[34,113],"events,":[35],"affecting":[36],"downstream":[37,60],"tasks":[38],"such":[39],"as":[40],"clustering":[42,174],"pseudo-time":[44],"analysis.":[45,61],"Restoring":[46],"the":[47,69,80,131,138,148,153,158,190],"levels":[49],"genes":[51,195],"essential":[53],"for":[54,94],"reducing":[55],"technical":[56],"noise":[57],"facilitating":[59],"However,":[62],"existing":[63,169],"imputation":[66,171,178],"methods":[67,172],"ignore":[68],"topological":[70],"structure":[71],"information":[72,121],"cannot":[77],"comprehensively":[78],"utilize":[79],"relationships":[81],"between":[82],"cells.":[83],"RESULTS:":[84],"Here,":[85],"we":[86,164,184],"propose":[87],"single-cell":[89],"Graph":[90],"Contrastive":[91],"Learning":[92],"method":[93],"imputation,":[97],"named":[98],"scGCL,":[99],"which":[100,151],"integrates":[101],"graph":[102],"contrastive":[103,123],"learning":[104,124],"Zero-inflated":[106],"Negative":[107],"Binomial":[108],"(ZINB)":[109],"distribution":[110],"estimate":[112],"values.":[114],"scGCL":[115,142,167,187,208],"summarizes":[116],"global":[117,139],"local":[119],"semantic":[120],"through":[122],"selects":[126],"positive":[127],"samples":[128],"enhance":[130,189],"representation":[132],"target":[134],"nodes.":[135],"To":[136],"capture":[137],"probability":[140],"distribution,":[141,150],"introduces":[143],"an":[144],"autoencoder":[145],"based":[146,156],"on":[147,157,179,211],"ZINB":[149],"reconstructs":[152],"prior":[159],"distribution.":[160],"Through":[161],"extensive":[162],"experiments,":[163],"verify":[165],"that":[166,186],"outperforms":[168],"state-of-the-art":[170],"in":[173,196],"performance":[175],"14":[180],"datasets.":[182,199],"Further,":[183],"find":[185],"can":[188],"patterns":[192],"specific":[194],"Alzheimer's":[197],"AVAILABILITY":[200],"AND":[201],"IMPLEMENTATION:":[202],"The":[203],"code":[204],"are":[209,218],"available":[210,219],"Github:":[212],"https://github.com/zehaoxiong123/scGCL.":[213],"SUPPLEMENTARY":[214],"INFORMATION:":[215],"Supplementary":[216],"at":[220],"Bioinformatics":[221],"online.":[222]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":3}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}