{"id":"https://openalex.org/W4390970083","doi":"https://doi.org/10.1109/bibm58861.2023.10385561","title":"scSRL: Siamese Representation Learning-based method for analyzing single-cell RNA-seq data","display_name":"scSRL: Siamese Representation Learning-based method for analyzing single-cell RNA-seq data","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390970083","doi":"https://doi.org/10.1109/bibm58861.2023.10385561"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385561","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385561","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5065254777","display_name":"Zhaoyang Sun","orcid":"https://orcid.org/0000-0001-5119-7091"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoyang Sun","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100414459","display_name":"Ying Liu","orcid":"https://orcid.org/0000-0003-3672-9621"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101442903","display_name":"Pei Liu","orcid":"https://orcid.org/0000-0002-2828-8179"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pei Liu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114859464","display_name":"Wanwan Shi","orcid":"https://orcid.org/0000-0003-4730-4610"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanwan Shi","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101750544","display_name":"Jiawei Luo","orcid":"https://orcid.org/0000-0003-4737-9014"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiawei Luo","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China,410083","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25391154,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":null,"first_page":"636","last_page":"641"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.98089998960495,"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9689000248908997,"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/computer-science","display_name":"Computer science","score":0.7860280275344849},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6571205854415894},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6242814660072327},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6031879186630249},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5474210977554321},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5408397912979126},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.48690807819366455},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4831649661064148},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46016523241996765},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.457547128200531},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.43075430393218994},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4296726584434509},{"id":"https://openalex.org/keywords/external-data-representation","display_name":"External Data Representation","score":0.4206867516040802},{"id":"https://openalex.org/keywords/skyline","display_name":"Skyline","score":0.4149993360042572},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.41386252641677856},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.16883888840675354}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7860280275344849},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6571205854415894},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6242814660072327},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6031879186630249},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5474210977554321},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5408397912979126},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.48690807819366455},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4831649661064148},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46016523241996765},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.457547128200531},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.43075430393218994},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4296726584434509},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.4206867516040802},{"id":"https://openalex.org/C2780757406","wikidata":"https://www.wikidata.org/wiki/Q465837","display_name":"Skyline","level":2,"score":0.4149993360042572},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.41386252641677856},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.16883888840675354},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385561","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm58861.2023.10385561","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320330944","display_name":"Nature","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W2007439698","https://openalex.org/W2023887100","https://openalex.org/W2051658465","https://openalex.org/W2066617774","https://openalex.org/W2068881679","https://openalex.org/W2069089843","https://openalex.org/W2089468765","https://openalex.org/W2135937351","https://openalex.org/W2195294260","https://openalex.org/W2307567449","https://openalex.org/W2467604901","https://openalex.org/W2526262591","https://openalex.org/W2562003322","https://openalex.org/W2743416243","https://openalex.org/W2747877289","https://openalex.org/W2800392236","https://openalex.org/W2801803962","https://openalex.org/W2901677030","https://openalex.org/W2902652978","https://openalex.org/W2907783748","https://openalex.org/W2951381561","https://openalex.org/W2952350893","https://openalex.org/W2960029024","https://openalex.org/W3035060554","https://openalex.org/W3035524453","https://openalex.org/W3092295864","https://openalex.org/W3171007011","https://openalex.org/W3173463846","https://openalex.org/W3179857518","https://openalex.org/W3203731429","https://openalex.org/W4235169531","https://openalex.org/W4295717668","https://openalex.org/W4315621823","https://openalex.org/W6720208624","https://openalex.org/W6779326418"],"related_works":["https://openalex.org/W4313443867","https://openalex.org/W2952512863","https://openalex.org/W1994605287","https://openalex.org/W3134504629","https://openalex.org/W1996424025","https://openalex.org/W2938696877","https://openalex.org/W4323911413","https://openalex.org/W1982536061","https://openalex.org/W2329521575","https://openalex.org/W4286796787"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"technology":[4],"is":[5,28,113,190],"utilized":[6],"to":[7,37,87,105],"analyze":[8],"cellular":[9,21],"heterogeneity,":[10],"perform":[11],"cellular-level":[12],"biological":[13],"research":[14],"and":[15,42,92,151,153,175,184],"derive":[16],"novel":[17],"insights":[18],"from":[19],"complex":[20],"systems.":[22],"However,":[23],"the":[24,65,72,109,117,176],"raw":[25],"scRNA-seq":[26],"data":[27,84,90],"not":[29],"directly":[30],"suitable":[31],"for":[32,144],"downstream":[33,145],"task":[34],"analysis":[35],"due":[36],"its":[38],"high":[39],"variability,":[40],"sparsity":[41],"dimensionality.":[43],"Therefore,":[44],"in":[45,108,159,170],"this":[46],"study,":[47],"we":[48,165],"propose":[49],"a":[50,101],"new":[51],"self-supervised":[52],"framework":[53],"based":[54],"on":[55,120,140],"siamese":[56,110],"representation":[57],"learning,":[58],"named":[59],"scSRL":[60,118,139,177,189],"which":[61,130],"can":[62,131,179],"fully":[63],"explore":[64],"intrinsic":[66],"properties":[67],"of":[68],"cells":[69,122],"by":[70,82],"maximizing":[71],"similarity":[73],"between":[74],"positive":[75,78],"pairs.":[76],"These":[77],"pairs":[79],"are":[80],"constructed":[81],"multiple":[83],"augmentation":[85],"operations":[86],"further":[88],"increase":[89],"diversity":[91],"better":[93],"learn":[94],"latent":[95],"representation.":[96],"Moreover,":[97],"our":[98],"method":[99],"employs":[100],"gradient":[102],"stopping":[103],"strategy":[104],"mitigate":[106],"collapsing":[107],"network.":[111],"It":[112],"worth":[114],"noting":[115],"that":[116],"focuses":[119],"aggregating":[121],"with":[123],"similar":[124],"functions":[125],"without":[126],"introducing":[127],"negative":[128],"samples,":[129],"avoid":[132],"additional":[133],"computational":[134],"cost.":[135],"Finally,":[136],"We":[137],"evaluated":[138],"10":[141],"real":[142],"datasets":[143],"tasks":[146],"such":[147],"as":[148],"clustering,":[149],"classification":[150],"visualization,":[152],"it":[154],"consistently":[155],"exhibited":[156],"outstanding":[157],"performance":[158],"all":[160],"these":[161],"fundamental":[162],"tasks.":[163],"Meanwhile,":[164],"did":[166],"pseudotime":[167],"inference":[168],"experiments":[169],"two":[171],"embryonic":[172],"development":[173],"datasets,":[174],"model":[178],"accurately":[180],"reconstruct":[181],"cell":[182,186],"trajectory":[183],"describe":[185],"developmental":[187],"process.":[188],"currently":[191],"an":[192],"open-source":[193],"method,":[194],"available":[195],"at":[196],"https://github.com/zysun17/scSRL.":[197]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}