{"id":"https://openalex.org/W4378348563","doi":"https://doi.org/10.1093/bioinformatics/btad342","title":"Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning","display_name":"Deep single-cell RNA-seq data clustering with graph prototypical contrastive learning","publication_year":2023,"publication_date":"2023-05-25","ids":{"openalex":"https://openalex.org/W4378348563","doi":"https://doi.org/10.1093/bioinformatics/btad342","pmid":"https://pubmed.ncbi.nlm.nih.gov/37233193","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/10246584"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad342","doi":"https://doi.org/10.1093/bioinformatics/btad342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad342","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad342/50457178/btad342.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad342/50457178/btad342.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100765319","display_name":"Junseok Lee","orcid":"https://orcid.org/0000-0003-3874-1667","observed_orcids":["https://orcid.org/0000-0003-3874-1667"]},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Junseok Lee","raw_affiliation_strings":["Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0003-3874-1667","affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046600148","display_name":"Sungwon Kim","orcid":"https://orcid.org/0000-0001-8605-2618","observed_orcids":["https://orcid.org/0000-0001-8605-2618"]},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sungwon Kim","raw_affiliation_strings":["Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064840324","display_name":"Dongmin Hyun","orcid":"https://orcid.org/0000-0001-7757-3227","observed_orcids":["https://orcid.org/0000-0001-7757-3227"]},"institutions":[{"id":"https://openalex.org/I123900574","display_name":"Pohang University of Science and Technology","ror":"https://ror.org/04xysgw12","country_code":"KR","type":"education","lineage":["https://openalex.org/I123900574"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Dongmin Hyun","raw_affiliation_strings":["Institute of Artificial Intelligence, POSTECH , Pohang 37673, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence, POSTECH , Pohang 37673, Republic of Korea","institution_ids":["https://openalex.org/I123900574"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085288448","display_name":"Namkyeong Lee","orcid":"https://orcid.org/0000-0003-3995-1148","observed_orcids":["https://orcid.org/0000-0003-3995-1148"]},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Namkyeong Lee","raw_affiliation_strings":["Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea","institution_ids":["https://openalex.org/I157485424"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100358135","display_name":"Yejin Kim","orcid":"https://orcid.org/0000-0001-7815-6310","observed_orcids":["https://orcid.org/0000-0001-7815-6310"]},"institutions":[{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yejin Kim","raw_affiliation_strings":["Center for Safe Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030, United States"],"raw_orcid":"https://orcid.org/0000-0001-7815-6310","affiliations":[{"raw_affiliation_string":"Center for Safe Artificial Intelligence for Healthcare, School of Biomedical Informatics, University of Texas Health Science Center at Houston , Houston, TX 77030, United States","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101629748","display_name":"Chanyoung Park","orcid":"https://orcid.org/0000-0002-5957-5816","observed_orcids":["https://orcid.org/0000-0002-5957-5816"]},"institutions":[{"id":"https://openalex.org/I157485424","display_name":"Korea Advanced Institute of Science and Technology","ror":"https://ror.org/05apxxy63","country_code":"KR","type":"education","lineage":["https://openalex.org/I157485424"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Chanyoung Park","raw_affiliation_strings":["Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Industrial and Systems Engineering, KAIST , Daejeon 34141, Republic of Korea","institution_ids":["https://openalex.org/I157485424"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5101629748"],"corresponding_institution_ids":["https://openalex.org/I157485424"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7669,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.92384976,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":93,"max":100},"biblio":{"volume":"39","issue":"6","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":1.0,"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":1.0,"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":0.0,"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":0.0,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.8679999709129333},{"id":"https://openalex.org/keywords/cell-type-clustering","display_name":"cell type clustering","score":0.7829999923706055},{"id":"https://openalex.org/keywords/graph-neural-networks","display_name":"graph neural networks","score":0.6639999747276306},{"id":"https://openalex.org/keywords/prototypical-contrastive-learning","display_name":"prototypical contrastive learning","score":0.9160000085830688},{"id":"https://openalex.org/keywords/graph-clustering","display_name":"graph clustering","score":0.4339999854564667}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7915025949478149},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7019635438919067},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5342501997947693},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4978506565093994},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4861299991607666},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.43151095509529114},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4076700508594513},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3780677318572998},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3041006028652191},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"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":"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}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad342","doi":"https://doi.org/10.1093/bioinformatics/btad342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad342","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad342/50457178/btad342.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":"pmh:oai:pubmedcentral.nih.gov:10246584","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10246584","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10246584/pdf/btad342.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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmid:37233193","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37233193","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,"listed_in":[],"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":"Journal Article"},{"id":"pmh:oai:digitalcommons.library.tmc.edu:uthshis_docs-1247","doi":null,"is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthshis_docs/251","pdf_url":null,"source":{"id":"https://openalex.org/S4377196655","display_name":"Digital Commons-TMC (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1337852284","host_organization_name":"Texas Medical Center","host_organization_lineage":["https://openalex.org/I1337852284"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad342","doi":"https://doi.org/10.1093/bioinformatics/btad342","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad342","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad342/50457178/btad342.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,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"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":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3373663135","display_name":null,"funder_award_id":"2022-0-00157","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G4323383363","display_name":null,"funder_award_id":"2021R1C1C1009081","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G4700831490","display_name":null,"funder_award_id":"2022-","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4378348563.pdf","grobid_xml":"https://content.openalex.org/works/W4378348563.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W1580018887","https://openalex.org/W2107680358","https://openalex.org/W2109890799","https://openalex.org/W2187089797","https://openalex.org/W2624431344","https://openalex.org/W2741943936","https://openalex.org/W2800392236","https://openalex.org/W2937917790","https://openalex.org/W2949067670","https://openalex.org/W2949272108","https://openalex.org/W2951381561","https://openalex.org/W2952303649","https://openalex.org/W2953251392","https://openalex.org/W3029148360","https://openalex.org/W3039465721","https://openalex.org/W3098903006","https://openalex.org/W3138479716","https://openalex.org/W3163972593","https://openalex.org/W4205281625","https://openalex.org/W4205916264"],"related_works":["https://openalex.org/W4413374944","https://openalex.org/W7124954052","https://openalex.org/W4412523591","https://openalex.org/W4403972624","https://openalex.org/W7147583754","https://openalex.org/W7121244592","https://openalex.org/W4415934814","https://openalex.org/W7204092208","https://openalex.org/W7139099545","https://openalex.org/W7133607513"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"enables":[4],"researchers":[5],"to":[6,50,119],"study":[7],"cellular":[8],"heterogeneity":[9],"at":[10,158],"single-cell":[11],"level.":[12],"To":[13],"this":[14],"end,":[15],"identifying":[16],"cell":[17,96,121],"types":[18],"of":[19,33,57,150],"cells":[20],"with":[21],"clustering":[22,44],"techniques":[23],"becomes":[24],"an":[25],"important":[26],"task":[27],"for":[28],"downstream":[29],"analysis.":[30],"However,":[31],"challenges":[32],"scRNA-seq":[34,112,142],"data":[35,74,113],"such":[36],"as":[37],"pervasive":[38],"dropout":[39],"phenomena":[40],"hinder":[41],"obtaining":[42],"robust":[43],"outputs.":[45],"Although":[46],"existing":[47],"studies":[48],"try":[49],"alleviate":[51],"these":[52],"problems,":[53],"they":[54],"fall":[55],"short":[56],"fully":[58],"leveraging":[59],"the":[60,73,95,107,146],"relationship":[61],"information":[62,109],"and":[63,114,129,140,148],"mainly":[64],"rely":[65],"on":[66,72,102,137],"reconstruction-based":[67],"losses":[68],"that":[69,105],"highly":[70],"depend":[71],"quality,":[75],"which":[76],"is":[77,156],"sometimes":[78],"noisy.":[79],"RESULTS:":[80],"This":[81],"work":[82],"proposes":[83],"a":[84],"graph-based":[85],"prototypical":[86,116],"contrastive":[87,117],"learning":[88,118],"method,":[89],"named":[90],"scGPCL.":[91,151],"Specifically,":[92],"scGPCL":[93],"encodes":[94],"representations":[97,122],"using":[98],"Graph":[99],"Neural":[100],"Networks":[101],"cell-gene":[103],"graph":[104],"captures":[106],"relational":[108],"inherent":[110],"in":[111],"introduces":[115],"learn":[120],"by":[123],"pushing":[124],"apart":[125],"semantically":[126],"dissimilar":[127],"pairs":[128],"pulling":[130],"together":[131],"similar":[132],"ones.":[133],"Through":[134],"extensive":[135],"experiments":[136],"both":[138],"simulated":[139],"real":[141],"data,":[143],"we":[144],"demonstrate":[145],"effectiveness":[147],"efficiency":[149],"AVAILABILITY":[152],"AND":[153],"IMPLEMENTATION:":[154],"Code":[155],"available":[157],"https://github.com/Junseok0207/scGPCL.":[159]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2023-05-27T00:00:00"}