{"id":"https://openalex.org/W4415934814","doi":"https://doi.org/10.1109/tcbbio.2025.3629161","title":"scGCRC: Graph and Contrastive-Based Representation Learning for Single-Cell RNA-Seq Data Clustering","display_name":"scGCRC: Graph and Contrastive-Based Representation Learning for Single-Cell RNA-Seq Data Clustering","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4415934814","doi":"https://doi.org/10.1109/tcbbio.2025.3629161","pmid":"https://pubmed.ncbi.nlm.nih.gov/41191468"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3629161","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3629161","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/A5060868822","display_name":"Yuchen Shi","orcid":"https://orcid.org/0009-0007-2790-9678"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuchen Shi","raw_affiliation_strings":["School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","institution_ids":["https://openalex.org/I50760025"]},{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101964066","display_name":"Jian Wan","orcid":"https://orcid.org/0000-0003-0775-4254"},"institutions":[{"id":"https://openalex.org/I168879160","display_name":"Zhejiang University of Science and Technology","ror":"https://ror.org/05mx0wr29","country_code":"CN","type":"education","lineage":["https://openalex.org/I168879160"]},{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wan","raw_affiliation_strings":["School of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, China","School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China"],"affiliations":[{"raw_affiliation_string":"School of Information and Electronic Engineering, Zhejiang University of Science and Technology, Hangzhou, China","institution_ids":["https://openalex.org/I168879160"]},{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100327604","display_name":"Xin Zhang","orcid":"https://orcid.org/0000-0003-3416-839X"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","institution_ids":["https://openalex.org/I50760025"]},{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070185855","display_name":"Yuyu Yin","orcid":"https://orcid.org/0000-0001-7565-4111"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuyu Yin","raw_affiliation_strings":["School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, China","institution_ids":["https://openalex.org/I50760025"]},{"raw_affiliation_string":"School of Computer Science and Technology, Hangzhou Dianzi University, Hangzhou, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5060868822"],"corresponding_institution_ids":["https://openalex.org/I50760025"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29255294,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"3513","last_page":"3523"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9800000190734863,"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":0.9800000190734863,"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":0.007499999832361937,"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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.006399999838322401,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/cluster-analysis","display_name":"Cluster analysis","score":0.7720000147819519},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.598800003528595},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5281000137329102},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5030999779701233},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42340001463890076},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.40529999136924744},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3847000002861023},{"id":"https://openalex.org/keywords/feature-vector","display_name":"Feature vector","score":0.35760000348091125}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7720000147819519},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6650000214576721},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6606000065803528},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.598800003528595},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5281000137329102},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5030999779701233},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.47530001401901245},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42340001463890076},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.40529999136924744},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3847000002861023},{"id":"https://openalex.org/C83665646","wikidata":"https://www.wikidata.org/wiki/Q42139305","display_name":"Feature vector","level":2,"score":0.35760000348091125},{"id":"https://openalex.org/C39235581","wikidata":"https://www.wikidata.org/wiki/Q5158434","display_name":"Conceptual clustering","level":5,"score":0.35749998688697815},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.33820000290870667},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2957000136375427},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.2824000120162964},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.273499995470047},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.2721000015735626},{"id":"https://openalex.org/C58973888","wikidata":"https://www.wikidata.org/wiki/Q1041418","display_name":"Semi-supervised learning","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C105611402","wikidata":"https://www.wikidata.org/wiki/Q2976589","display_name":"Spectral clustering","level":3,"score":0.26080000400543213},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2531000077724457}],"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"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":"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},{"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.2025.3629161","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3629161","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:41191468","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41191468","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":38,"referenced_works":["https://openalex.org/W2010653277","https://openalex.org/W2078904484","https://openalex.org/W2100495367","https://openalex.org/W2102212449","https://openalex.org/W2194775991","https://openalex.org/W2572662684","https://openalex.org/W2598326928","https://openalex.org/W2605810679","https://openalex.org/W2774307122","https://openalex.org/W2794480084","https://openalex.org/W2894687190","https://openalex.org/W2897249806","https://openalex.org/W2937917790","https://openalex.org/W2947877009","https://openalex.org/W2951506174","https://openalex.org/W2952303649","https://openalex.org/W2997470228","https://openalex.org/W3021272327","https://openalex.org/W3034363127","https://openalex.org/W3049679592","https://openalex.org/W3087124270","https://openalex.org/W3091988478","https://openalex.org/W3110446398","https://openalex.org/W3127011314","https://openalex.org/W3132757822","https://openalex.org/W3138479716","https://openalex.org/W3157644645","https://openalex.org/W3163972593","https://openalex.org/W3185430726","https://openalex.org/W3211499194","https://openalex.org/W4205281625","https://openalex.org/W4210840193","https://openalex.org/W4213136259","https://openalex.org/W4214510096","https://openalex.org/W4235169531","https://openalex.org/W4295717668","https://openalex.org/W4315621823","https://openalex.org/W4321748573"],"related_works":[],"abstract_inverted_index":{"The":[0,132],"advent":[1],"of":[2,20,30,50,63,109,214,219,231],"single-cell":[3],"RNA-sequencing":[4],"(scRNA-seq)":[5],"technology":[6,39],"promotes":[7],"biological":[8],"analysis":[9],"at":[10,139,152],"the":[11,18,31,47,59,66,71,125,140,144,153,157,228,232],"cellular":[12],"level.":[13,155],"Clustering":[14],"cells":[15,51,110,137,148],"to":[16,45,57,149,184],"identify":[17],"type":[19],"cell":[21,81,114,126,175,178,187,215],"is":[22,86,163],"an":[23,42,201],"important":[24],"step":[25],"in":[26,128,189],"scRNA-seq":[27,97],"analysis.":[28],"Most":[29],"existing":[32],"clustering":[33,60,166],"methods":[34],"based":[35,87,111,167],"on":[36,88,112,168,207],"deep":[37],"learning":[38,68,83,95,121,183],"first":[40],"adopt":[41],"autoencoder-decoder":[43,202],"module":[44,122,134,146],"learn":[46,58,186],"low-dimensional":[48,191],"features":[49,62],"and":[52,93,117,130,180,222],"then":[53],"apply":[54],"other":[55],"modules":[56],"relationship":[61,115],"cells.":[64],"However,":[65],"two-stage":[67],"process":[69],"makes":[70,135],"model":[72],"training":[73],"more":[74],"difficult.":[75],"Here":[76],"we":[77,173],"propose":[78],"a":[79,89,101,113,118,190],"novel":[80],"representation":[82,127],"method":[84,234],"that":[85],"local":[90,102,196],"self-attention":[91,103],"network":[92,104],"contrastive":[94,120,182],"for":[96,165],"clustering.":[98],"In":[99,171],"particular,":[100],"automatically":[105],"aggregates":[106],"potential":[107],"information":[108],"graph,":[116],"dual":[119],"simultaneously":[123],"optimizes":[124],"cell-":[129],"cluster-level.":[131],"cell-level":[133],"related":[136],"similar":[138],"feature":[141],"level,":[142],"whereas":[143],"cluster-level":[145],"enables":[147],"form":[150],"clusters":[151],"cluster":[154],"Finally,":[156],"powerful":[158],"Leiden":[159],"community":[160],"discovery":[161],"algorithm":[162],"used":[164],"learned":[169],"representation.":[170],"brief,":[172],"construct":[174],"pairs":[176],"through":[177],"relationships":[179,198],"utilize":[181],"directly":[185],"representations":[188],"space":[192],"while":[193],"preserving":[194],"their":[195],"structural":[197],"without":[199],"pretraining":[200],"module.":[203],"Three":[204],"benchmark":[205],"experiments":[206],"160":[208],"subsample":[209],"datasets":[210,218,226],"with":[211,236],"different":[212,220],"numbers":[213],"types,":[216],"3":[217],"protocols,":[221],"9":[223],"real":[224],"public":[225],"demonstrate":[227],"superior":[229],"performance":[230],"proposed":[233],"compared":[235],"baseline":[237],"methods.":[238]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-11-05T00:00:00"}
