{"id":"https://openalex.org/W4414422436","doi":"https://doi.org/10.1093/bib/bbaf485","title":"scHSC: enhancing single-cell RNA-seq clustering via hard sample contrastive learning","display_name":"scHSC: enhancing single-cell RNA-seq clustering via hard sample contrastive learning","publication_year":2025,"publication_date":"2025-08-29","ids":{"openalex":"https://openalex.org/W4414422436","doi":"https://doi.org/10.1093/bib/bbaf485","pmid":"https://pubmed.ncbi.nlm.nih.gov/40977264"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf485","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf485/64339201/bbaf485.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","license_id":"https://openalex.org/licenses/cc-by","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/26/5/bbaf485/64339201/bbaf485.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088110322","display_name":"Sheng Fang","orcid":"https://orcid.org/0000-0002-1917-3281"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Sheng Fang","raw_affiliation_strings":["Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China"],"affiliations":[{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","institution_ids":["https://openalex.org/I78988378"]},{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032553168","display_name":"Xiaokang Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xiaokang Yu","raw_affiliation_strings":["Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania , Philadelphia, PA 19104 ,","Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States","Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China"],"affiliations":[{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","institution_ids":["https://openalex.org/I78988378"]},{"raw_affiliation_string":"Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania , Philadelphia, PA 19104 ,","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104, United States","institution_ids":["https://openalex.org/I79576946"]},{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063711785","display_name":"Xinyi Xu","orcid":"https://orcid.org/0000-0001-5081-625X"},"institutions":[{"id":"https://openalex.org/I137867983","display_name":"Central University of Finance and Economics","ror":"https://ror.org/008e3hf02","country_code":"CN","type":"education","lineage":["https://openalex.org/I137867983"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyi Xu","raw_affiliation_strings":["School of Statistics and Mathematics, Central University of Finance and Economics , Beijing 100081 ,","School of Statistics and Mathematics, Central University of Finance and Economics, Beijing 100081, China"],"affiliations":[{"raw_affiliation_string":"School of Statistics and Mathematics, Central University of Finance and Economics , Beijing 100081 ,","institution_ids":["https://openalex.org/I137867983"]},{"raw_affiliation_string":"School of Statistics and Mathematics, Central University of Finance and Economics, Beijing 100081, China","institution_ids":["https://openalex.org/I137867983"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046940971","display_name":"Jingxiao Zhang","orcid":"https://orcid.org/0000-0002-0857-6835"},"institutions":[{"id":"https://openalex.org/I78988378","display_name":"Renmin University of China","ror":"https://ror.org/041pakw92","country_code":"CN","type":"education","lineage":["https://openalex.org/I78988378"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingxiao Zhang","raw_affiliation_strings":["Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China"],"affiliations":[{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China , Beijing 100872 ,","institution_ids":["https://openalex.org/I78988378"]},{"raw_affiliation_string":"Center for Applied Statistics, School of Statistics, Renmin University of China, Beijing 100872, China","institution_ids":["https://openalex.org/I78988378"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012206667","display_name":"Xiangjie Li","orcid":"https://orcid.org/0000-0002-9600-8984"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210161896","display_name":"Fu Wai Hospital","ror":"https://ror.org/0590dnz19","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161896"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangjie Li","raw_affiliation_strings":["National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100037 ,","National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China"],"affiliations":[{"raw_affiliation_string":"National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , Beijing 100037 ,","institution_ids":["https://openalex.org/I4210161896","https://openalex.org/I200296433"]},{"raw_affiliation_string":"National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100037, China","institution_ids":["https://openalex.org/I200296433"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5088110322"],"corresponding_institution_ids":["https://openalex.org/I78988378"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.8425,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.77506769,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"26","issue":"5","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":0.9958000183105469,"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":0.9958000183105469,"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":0.9664999842643738,"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":0.9472000002861023,"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":0.8136000037193298},{"id":"https://openalex.org/keywords/weighting","display_name":"Weighting","score":0.5676000118255615},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5511999726295471},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.435699999332428},{"id":"https://openalex.org/keywords/dropout","display_name":"Dropout (neural networks)","score":0.420199990272522},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.3853999972343445},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3817000091075897},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.3677000105381012}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.8136000037193298},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7738999724388123},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6604999899864197},{"id":"https://openalex.org/C183115368","wikidata":"https://www.wikidata.org/wiki/Q856577","display_name":"Weighting","level":2,"score":0.5676000118255615},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5511999726295471},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.435699999332428},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.426800012588501},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4237000048160553},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.420199990272522},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.3853999972343445},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3817000091075897},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.3677000105381012},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.36559998989105225},{"id":"https://openalex.org/C111442797","wikidata":"https://www.wikidata.org/wiki/Q7291446","display_name":"Rand index","level":3,"score":0.3587000072002411},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3544999957084656},{"id":"https://openalex.org/C184509293","wikidata":"https://www.wikidata.org/wiki/Q5136711","display_name":"Clustering high-dimensional data","level":3,"score":0.3456000089645386},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.3411000072956085},{"id":"https://openalex.org/C17212007","wikidata":"https://www.wikidata.org/wiki/Q5511111","display_name":"Fuzzy clustering","level":3,"score":0.30730000138282776},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2667999863624573},{"id":"https://openalex.org/C8038995","wikidata":"https://www.wikidata.org/wiki/Q1152135","display_name":"Unsupervised learning","level":2,"score":0.2506999969482422}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep 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":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep 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":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":"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":"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":"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":"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":"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":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":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf485","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf485/64339201/bbaf485.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40977264","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40977264","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:europepmc.org:11260550","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12451106","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12451106","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12451106/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf485","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf485","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf485/64339201/bbaf485.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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322724","display_name":"Ministry of Education, India","ror":"https://ror.org/048xjjh50"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414422436.pdf","grobid_xml":"https://content.openalex.org/works/W4414422436.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1580018887","https://openalex.org/W1981641790","https://openalex.org/W1987111416","https://openalex.org/W1998871699","https://openalex.org/W2066617774","https://openalex.org/W2102212449","https://openalex.org/W2571662414","https://openalex.org/W2598326928","https://openalex.org/W2604983939","https://openalex.org/W2735067671","https://openalex.org/W2907783748","https://openalex.org/W2937917790","https://openalex.org/W2951381561","https://openalex.org/W2952303649","https://openalex.org/W2953251392","https://openalex.org/W3021272327","https://openalex.org/W3029148360","https://openalex.org/W3040213512","https://openalex.org/W3084428275","https://openalex.org/W3137285774","https://openalex.org/W3163972593","https://openalex.org/W3173463846","https://openalex.org/W3202332579","https://openalex.org/W4205281625","https://openalex.org/W4283815719","https://openalex.org/W4293237882","https://openalex.org/W4315621823","https://openalex.org/W4317888741","https://openalex.org/W4382466430","https://openalex.org/W4389937732","https://openalex.org/W4390946179","https://openalex.org/W4394743912","https://openalex.org/W4405516441"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"provides":[4],"high-throughput":[5],"information":[6,81],"about":[7],"the":[8,14,22,28,34,90,100,153],"genome-wide":[9],"gene":[10,76],"expression":[11,77],"levels":[12],"at":[13],"single-cell":[15,119,126],"resolution,":[16],"bringing":[17],"a":[18,51,115],"precise":[19],"understanding":[20],"on":[21,69,124,152],"transcriptome":[23],"of":[24,36,92],"individual":[25],"cells.":[26],"Unfortunately,":[27],"rapidly":[29],"growing":[30],"scRNA-seq":[31,66],"data":[32],"and":[33,44,78,95,159],"prevalence":[35],"dropout":[37],"events":[38],"pose":[39],"substantial":[40],"challenges":[41],"for":[42,64,118],"clustering":[43,65,86,120,137,144],"cell":[45],"type":[46],"annotation.":[47],"Here,":[48],"we":[49],"propose":[50],"deep":[52,142],"learning":[53,63,113],"method,":[54],"scHSC,":[55],"that":[56,131],"employs":[57,105],"hard":[58,70,93,96],"sample":[59],"mining":[60],"through":[61],"contrastive":[62,112],"data.":[67],"Focusing":[68],"samples,":[71],"this":[72],"approach":[73],"simultaneously":[74],"integrates":[75],"topological":[79],"structure":[80],"between":[82],"cells":[83],"to":[84,110,140],"improve":[85],"accuracy.":[87],"By":[88],"adjusting":[89],"weights":[91],"positive":[94],"negative":[97],"samples":[98],"during":[99],"iterative":[101],"training":[102],"process,":[103],"scHSC":[104,132,146],"an":[106],"adaptive":[107],"weighting":[108],"strategy":[109],"integrate":[111],"with":[114],"ZINB":[116],"model":[117],"tasks.":[121],"Extensive":[122],"experiments":[123],"18":[125],"RNA-seq":[127],"real":[128],"datasets":[129,160],"demonstrate":[130],"exhibits":[133],"significant":[134],"superiority":[135],"in":[136,149],"performance":[138],"compared":[139],"existing":[141],"learning-based":[143],"methods.":[145],"is":[147],"implemented":[148],"Python":[150],"based":[151],"PyTorch":[154],"framework.":[155],"The":[156],"source":[157],"code":[158],"are":[161],"available":[162],"via":[163],"https://github.com/fangs25/scHSC.":[164]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
