{"id":"https://openalex.org/W7124954052","doi":"https://doi.org/10.1109/tcbbio.2026.3655670","title":"scDGCL: A Dual-Level and Graph-Constrained Contrastive Learning Method for Single-Cell RNA Sequencing Data Clustering","display_name":"scDGCL: A Dual-Level and Graph-Constrained Contrastive Learning Method for Single-Cell RNA Sequencing Data Clustering","publication_year":2026,"publication_date":"2026-01-20","ids":{"openalex":"https://openalex.org/W7124954052","doi":"https://doi.org/10.1109/tcbbio.2026.3655670","pmid":"https://pubmed.ncbi.nlm.nih.gov/41557577"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3655670","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3655670","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/A5103160991","display_name":"Kaiwen Tan","orcid":"https://orcid.org/0000-0002-2770-4863"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kaiwen Tan","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123447506","display_name":"Yun Bai","orcid":null},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Bai","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101653272","display_name":"Yongbing Zhang","orcid":"https://orcid.org/0009-0008-1568-3728"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongbing Zhang","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119271895","display_name":"Zhenqiu Shu","orcid":"https://orcid.org/0000-0003-1020-8270"},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenqiu Shu","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China","institution_ids":["https://openalex.org/I10660446"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5123420893","display_name":"Zhengtao Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I10660446","display_name":"Kunming University of Science and Technology","ror":"https://ror.org/00xyeez13","country_code":"CN","type":"education","lineage":["https://openalex.org/I10660446"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhengtao Yu","raw_affiliation_strings":["Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China"],"affiliations":[{"raw_affiliation_string":"Faculty of Information Engineering and Automation, Kunming University of Science and Technology, Kunming, China","institution_ids":["https://openalex.org/I10660446"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5103160991"],"corresponding_institution_ids":["https://openalex.org/I10660446"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.13862298,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"2","first_page":"760","last_page":"773"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9894999861717224,"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":0.9894999861717224,"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":0.004399999976158142,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0007999999797903001,"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/cluster-analysis","display_name":"Cluster analysis","score":0.730400025844574},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5713000297546387},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5392000079154968},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.41600000858306885},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4147000014781952},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.3458000123500824},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.337799996137619},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.3156999945640564}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.730400025844574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6872000098228455},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6233000159263611},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5713000297546387},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5392000079154968},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4943999946117401},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.41600000858306885},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4147000014781952},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3772999942302704},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.3458000123500824},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.337799996137619},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3156999945640564},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.31029999256134033},{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.2994000017642975},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.2897000014781952},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.26499998569488525},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.26429998874664307},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2628999948501587},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.2578999996185303},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.2556999921798706},{"id":"https://openalex.org/C8038995","wikidata":"https://www.wikidata.org/wiki/Q1152135","display_name":"Unsupervised learning","level":2,"score":0.2533000111579895}],"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":"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":"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.2026.3655670","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3655670","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:41557577","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41557577","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":[{"id":"https://metadata.un.org/sdg/12","score":0.41392600536346436,"display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G7506565617","display_name":null,"funder_award_id":"62302201","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8874874764","display_name":null,"funder_award_id":"U23A2038","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"has":[4],"provided":[5],"unprecedented":[6],"insights":[7],"for":[8,25,64],"life":[9],"science":[10],"research.":[11],"In":[12],"scRNA-seq":[13,35,65,141],"data":[14,36,66,142],"analysis,":[15],"clustering":[16,47,133],"is":[17],"a":[18,56,181],"crucial":[19],"step":[20],"that":[21],"lays":[22],"the":[23,29,101,105,135,153,159,174],"foundation":[24],"downstream":[26],"tasks.":[27],"However,":[28],"high":[30],"dimensionality":[31],"and":[32,59,84,89,124,146,158,168],"sparsity":[33],"of":[34,155,162,177],"lead":[37],"to":[38,151],"suboptimal":[39],"representations":[40,79,103],"learned":[41],"by":[42,80],"existing":[43],"methods,":[44,134],"thereby":[45],"limiting":[46],"performance.":[48],"To":[49,113],"address":[50],"these":[51],"issues,":[52],"we":[53,69,93,117],"propose":[54],"scDGCL,":[55,116],"novel":[57],"dual-level":[58],"graph-constrained":[60],"contrastive":[61],"learning":[62],"method":[63,179],"clustering.":[67,143],"Specifically,":[68],"first":[70],"design":[71,94],"Dual-level":[72],"Contrastive":[73,96],"Learning":[74,97],"(DCL),":[75],"which":[76,99],"optimizes":[77],"cell":[78,88,111,169],"simultaneously":[81],"considering":[82],"similarities":[83],"disparities":[85],"at":[86],"both":[87],"cluster":[90],"levels.":[91],"Then,":[92],"Graph-constrained":[95],"(GCL),":[98],"aligns":[100],"DCL-derived":[102],"with":[104,130],"graph's":[106],"relational":[107],"priors,":[108],"further":[109],"enhancing":[110],"representations.":[112],"systematically":[114],"evaluate":[115],"perform":[118],"experiments":[119,145,148],"on":[120],"12":[121],"real":[122],"datasets":[123],"8":[125],"simulated":[126],"datasets.":[127],"Comparing":[128],"scDGCL":[129],"17":[131],"representative":[132],"results":[136],"demonstrate":[137],"it's":[138],"superiority":[139],"in":[140],"Ablation":[144],"hyperparameter":[147],"are":[149],"performed":[150],"verify":[152,173],"effectiveness":[154],"each":[156],"component":[157],"overall":[160],"robustness":[161],"our":[163,178],"method.":[164],"Marker":[165],"gene":[166],"expression":[167],"trajectory":[170],"inference":[171],"analysis":[172],"biological":[175,182],"plausibility":[176],"from":[180],"perspective.":[183]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-21T00:00:00"}