{"id":"https://openalex.org/W4405666966","doi":"https://doi.org/10.1093/bib/bbae662","title":"scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning","display_name":"scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405666966","doi":"https://doi.org/10.1093/bib/bbae662","pmid":"https://pubmed.ncbi.nlm.nih.gov/39708840"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae662","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae662","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae662/61251510/bbae662.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/bib/article-pdf/26/1/bbae662/61251510/bbae662.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101924090","display_name":"Lin Yuan","orcid":"https://orcid.org/0000-0002-9694-8191"},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210142748","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210142748"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Lin Yuan","raw_affiliation_strings":["Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,"],"raw_orcid":"https://orcid.org/0000-0002-9694-8191","affiliations":[{"raw_affiliation_string":"Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I152269853","https://openalex.org/I4210142748"]},{"raw_affiliation_string":"Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I4210142748","https://openalex.org/I152269853"]},{"raw_affiliation_string":"Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100518074","display_name":"Shengguo Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210142748","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210142748"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shengguo Sun","raw_affiliation_strings":["Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I152269853","https://openalex.org/I4210142748"]},{"raw_affiliation_string":"Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I4210142748","https://openalex.org/I152269853"]},{"raw_affiliation_string":"Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051199839","display_name":"Yufeng Jiang","orcid":"https://orcid.org/0000-0003-4553-4834"},"institutions":[{"id":"https://openalex.org/I152269853","display_name":"Qilu University of Technology","ror":"https://ror.org/04hyzq608","country_code":"CN","type":"education","lineage":["https://openalex.org/I152269853"]},{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210142748","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210142748"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yufeng Jiang","raw_affiliation_strings":["Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Computing Power Network and Information Security, Ministry of Education, Shandong Computer Science Center, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I152269853","https://openalex.org/I4210142748"]},{"raw_affiliation_string":"Shandong Engineering Research Center of Big Data Applied Technology, Faculty of Computer Science and Technology, Qilu University of Technology (Shandong Academy of Sciences) , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I4210142748","https://openalex.org/I152269853"]},{"raw_affiliation_string":"Shandong Provincial Key Laboratory of Industrial Network and Information System Security, Shandong Fundamental Research Center for Computer Science , 3501 Daxue Road, 250353, Shandong ,","institution_ids":["https://openalex.org/I154099455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062540383","display_name":"Qinhu Zhang","orcid":"https://orcid.org/0000-0002-4232-7736"},"institutions":[{"id":"https://openalex.org/I127108677","display_name":"Eastern Institute of Technology","ror":"https://ror.org/00ct9cz38","country_code":"NZ","type":"education","lineage":["https://openalex.org/I127108677","https://openalex.org/I4387152882"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Qinhu Zhang","raw_affiliation_strings":["Ningbo Institute of Digital Twin, Eastern Institute of Technology , 568 Tongxin Road, 315201, Zhejiang ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , 568 Tongxin Road, 315201, Zhejiang ,","institution_ids":["https://openalex.org/I127108677"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090447371","display_name":"Lan Ye","orcid":"https://orcid.org/0000-0003-3735-5844"},"institutions":[{"id":"https://openalex.org/I4210103957","display_name":"Second Hospital of Shandong University","ror":"https://ror.org/01fd86n56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210103957"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lan Ye","raw_affiliation_strings":["Cancer Center, The Second Hospital of Shandong University , 247 Beiyuan Street, 250033, Shandong ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cancer Center, The Second Hospital of Shandong University , 247 Beiyuan Street, 250033, Shandong ,","institution_ids":["https://openalex.org/I4210103957"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113323469","display_name":"Chun-Hou Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chun-Hou Zheng","raw_affiliation_strings":["Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , 111 Jiulong Road, 230601, Anhui ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Lab of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University , 111 Jiulong Road, 230601, Anhui ,","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060381913","display_name":"De-Shuang Huang","orcid":"https://orcid.org/0000-0002-6759-2691"},"institutions":[{"id":"https://openalex.org/I127108677","display_name":"Eastern Institute of Technology","ror":"https://ror.org/00ct9cz38","country_code":"NZ","type":"education","lineage":["https://openalex.org/I127108677","https://openalex.org/I4387152882"]},{"id":"https://openalex.org/I4210128175","display_name":"Shanghai East Hospital","ror":"https://ror.org/038xmzj21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128175"]}],"countries":["CN","NZ"],"is_corresponding":false,"raw_author_name":"De-Shuang Huang","raw_affiliation_strings":["Institute for Regenerative Medicine, Medical Innovation Center and State Key Laboratory of Cardiology , Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, 200123, Shanghai,","Ningbo Institute of Digital Twin, Eastern Institute of Technology , 568 Tongxin Road, 315201, Zhejiang ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Regenerative Medicine, Medical Innovation Center and State Key Laboratory of Cardiology , Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, 200123, Shanghai,","institution_ids":["https://openalex.org/I4210128175"]},{"raw_affiliation_string":"Ningbo Institute of Digital Twin, Eastern Institute of Technology , 568 Tongxin Road, 315201, Zhejiang ,","institution_ids":["https://openalex.org/I127108677"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5101924090"],"corresponding_institution_ids":["https://openalex.org/I152269853","https://openalex.org/I154099455","https://openalex.org/I4210142748"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":9.6481,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.98852176,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"26","issue":"1","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":0.9998000264167786,"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":0.9998000264167786,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9955000281333923,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9948999881744385,"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/overfitting","display_name":"Overfitting","score":0.7964474558830261},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7661287784576416},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7437496781349182},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6366171836853027},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6218809485435486},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5871420502662659},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5266730189323425},{"id":"https://openalex.org/keywords/residual","display_name":"Residual","score":0.5259347558021545},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3904363512992859},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36281707882881165},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3321722745895386},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.14823374152183533},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.10885107517242432}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.7964474558830261},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7661287784576416},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7437496781349182},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6366171836853027},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6218809485435486},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5871420502662659},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5266730189323425},{"id":"https://openalex.org/C155512373","wikidata":"https://www.wikidata.org/wiki/Q287450","display_name":"Residual","level":2,"score":0.5259347558021545},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3904363512992859},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36281707882881165},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3321722745895386},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.14823374152183533},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.10885107517242432}],"mesh":[{"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":"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":"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":"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":"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":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"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":3,"locations":[{"id":"doi:10.1093/bib/bbae662","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae662","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae662/61251510/bbae662.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39708840","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39708840","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11663015","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11663015","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11663015/pdf/bbae662.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae662","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae662","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae662/61251510/bbae662.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1141093333","display_name":null,"funder_award_id":"2021JJA170199","funder_id":"https://openalex.org/F4320322768","funder_display_name":"Natural Science Foundation of Guangxi Province"},{"id":"https://openalex.org/G173893127","display_name":null,"funder_award_id":"ZR2024MF011","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G1857610291","display_name":null,"funder_award_id":"62073231","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2151120206","display_name":null,"funder_award_id":"W2412087","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5774277518","display_name":null,"funder_award_id":"62472239","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6332332648","display_name":null,"funder_award_id":"62002189","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G643023014","display_name":null,"funder_award_id":"62372255","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6915093697","display_name":null,"funder_award_id":"ZR2020QF038","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G6940641828","display_name":null,"funder_award_id":"ZR2021MH104","funder_id":"https://openalex.org/F4320324174","funder_display_name":"Natural Science Foundation of Shandong Province"},{"id":"https://openalex.org/G7699868062","display_name":null,"funder_award_id":"2021JJA170204","funder_id":"https://openalex.org/F4320322768","funder_display_name":"Natural Science Foundation of Guangxi Province"},{"id":"https://openalex.org/G7894669521","display_name":null,"funder_award_id":"U22A2039","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7969017031","display_name":null,"funder_award_id":"2023J199","funder_id":"https://openalex.org/F4320332587","funder_display_name":"Natural Science Foundation of Ningbo"},{"id":"https://openalex.org/G906490537","display_name":null,"funder_award_id":"62333018","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320308724","display_name":"Texas Space Grant Consortium","ror":"https://ror.org/05k1jx057"},{"id":"https://openalex.org/F4320311026","display_name":"Shandong University","ror":"https://ror.org/0207yh398"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322768","display_name":"Natural Science Foundation of Guangxi Province","ror":null},{"id":"https://openalex.org/F4320324099","display_name":"Russian Science Foundation","ror":"https://ror.org/03y2gwe85"},{"id":"https://openalex.org/F4320324174","display_name":"Natural Science Foundation of Shandong Province","ror":null},{"id":"https://openalex.org/F4320332587","display_name":"Natural Science Foundation of Ningbo","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405666966.pdf","grobid_xml":"https://content.openalex.org/works/W4405666966.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1689711448","https://openalex.org/W2053757129","https://openalex.org/W2068767807","https://openalex.org/W2128728535","https://openalex.org/W2138470019","https://openalex.org/W2522417827","https://openalex.org/W2523369352","https://openalex.org/W2523419694","https://openalex.org/W2523620612","https://openalex.org/W2526262591","https://openalex.org/W2809000676","https://openalex.org/W2894687190","https://openalex.org/W2898120081","https://openalex.org/W2907514116","https://openalex.org/W2939422961","https://openalex.org/W2946348245","https://openalex.org/W2950891712","https://openalex.org/W2951914955","https://openalex.org/W2963263347","https://openalex.org/W2964643116","https://openalex.org/W3006566541","https://openalex.org/W3013151148","https://openalex.org/W3016360824","https://openalex.org/W3022072135","https://openalex.org/W3022968840","https://openalex.org/W3111222208","https://openalex.org/W3128182147","https://openalex.org/W3164129446","https://openalex.org/W3165190053","https://openalex.org/W3174864715","https://openalex.org/W3198628780","https://openalex.org/W3202393418","https://openalex.org/W3211778832","https://openalex.org/W4205921232","https://openalex.org/W4223893712","https://openalex.org/W4223992851","https://openalex.org/W4225568512","https://openalex.org/W4236965008","https://openalex.org/W4287812705","https://openalex.org/W4294558607","https://openalex.org/W4308834893","https://openalex.org/W4311144837","https://openalex.org/W4316096017","https://openalex.org/W4377029825","https://openalex.org/W4380551045","https://openalex.org/W4399829001","https://openalex.org/W6727363061","https://openalex.org/W6728500052","https://openalex.org/W6738964360","https://openalex.org/W6756043290","https://openalex.org/W6775667395","https://openalex.org/W6776700526","https://openalex.org/W6847117328"],"related_works":["https://openalex.org/W4362597605","https://openalex.org/W1574414179","https://openalex.org/W4297676672","https://openalex.org/W3009056573","https://openalex.org/W3099765033","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2990636717","https://openalex.org/W2951211570","https://openalex.org/W3103566983"],"abstract_inverted_index":{"Cell":[0],"type":[1,96,124,189,247],"annotation":[2,97,125],"is":[3,151,250],"a":[4,91,134],"critical":[5],"step":[6],"in":[7,66,70,82,222,226],"analyzing":[8],"single-cell":[9,99,127,215],"RNA":[10],"sequencing":[11],"(scRNA-seq)":[12],"data.":[13,72,129,159],"A":[14,145],"large":[15],"number":[16],"of":[17,29,64,98,126,133,183,195,243],"deep":[18],"learning":[19,110,121,161,206],"(DL)-based":[20],"methods":[21,203,237],"have":[22,33],"been":[23],"proposed":[24],"to":[25,42,80,153],"annotate":[26],"cell":[27,95,123,188,246],"types":[28],"scRNA-seq":[30],"data":[31,101],"and":[32,62,119,142,176,208,224],"achieved":[34],"impressive":[35],"results.":[36],"However,":[37],"there":[38],"are":[39,56],"several":[40],"limitations":[41],"these":[43],"methods.":[44],"First,":[45],"they":[46,55],"do":[47],"not":[48,230],"fully":[49],"exploit":[50],"cell-to-cell":[51,168],"differential":[52,169],"features.":[53,170],"Second,":[54],"developed":[57],"based":[58,112],"on":[59,113,187,213],"shallow":[60,205],"features":[61,69,77,157],"lack":[63],"flexibility":[65],"integrating":[67],"high-order":[68,156],"the":[71,74,164,178,181,193,241],"Finally,":[73],"low-dimensional":[75],"gene":[76,185],"may":[78],"lead":[79],"overfitting":[81,175],"neural":[83,106,117,138,149],"networks.":[84],"To":[85,191],"overcome":[86],"those":[87],"limitations,":[88],"we":[89,197],"propose":[90],"novel":[92],"DL-based":[93,211],"model,":[94],"RNA-seq":[100,128],"using":[102],"residual":[103,114,135,146],"graph":[104,115,136,147],"convolutional":[105,116,137,148],"network":[107,118,150],"with":[108,201],"contrastive":[109,120,140],"(scRGCL),":[111],"for":[122,245],"scRGCL":[130,234,244,249],"mainly":[131],"consists":[132],"network,":[139],"learning,":[141],"weight":[143],"freezing.":[144],"utilized":[152],"extract":[154],"complex":[155],"from":[158,218],"Contrastive":[160],"can":[162,173],"help":[163,177],"model":[165,179],"learn":[166],"meaningful":[167],"Weight":[171],"freezing":[172],"avoid":[174],"discover":[180],"impact":[182],"specific":[184],"expression":[186],"annotation.":[190,248],"verify":[192],"effectiveness":[194],"scRGCL,":[196],"compared":[198],"its":[199],"performance":[200],"six":[202],"(three":[204],"algorithms":[207],"three":[209],"state-of-the-art":[210],"methods)":[212],"eight":[214],"benchmark":[216],"datasets":[217],"two":[219],"species":[220],"(seven":[221],"human":[223],"one":[225],"mouse).":[227],"Experimental":[228],"results":[229],"only":[231],"show":[232],"that":[233],"outperforms":[235],"competing":[236],"but":[238],"also":[239],"demonstrate":[240],"generalizability":[242],"available":[251],"at":[252],"https://github.com/nathanyl/scRGCL.":[253]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":36}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}