{"id":"https://openalex.org/W7171510697","doi":"https://doi.org/10.1145/3807503.3819485","title":"Cross-batch concordant clustering for comprehensive single-cell transcriptomic stratification","display_name":"Cross-batch concordant clustering for comprehensive single-cell transcriptomic stratification","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171510697","doi":"https://doi.org/10.1145/3807503.3819485"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819485","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819485","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819485","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5143777927","display_name":"Jiayu Zhao","orcid":"https://orcid.org/0009-0009-3707-1965"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiayu Zhao","raw_affiliation_strings":["Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0009-3707-1965","affiliations":[{"raw_affiliation_string":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065348694","display_name":"Xinzhu Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinzhu Jiang","raw_affiliation_strings":["Global College, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0001-6379-9759","affiliations":[{"raw_affiliation_string":"Global College, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015764172","display_name":"\u6bdb\u51b2\u9704","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chongxiao Mao","raw_affiliation_strings":["Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0008-7294-7160","affiliations":[{"raw_affiliation_string":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087925176","display_name":"Hongyi Xin","orcid":"https://orcid.org/0000-0003-2864-7386"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongyi Xin","raw_affiliation_strings":["Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-2864-7386","affiliations":[{"raw_affiliation_string":"Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5964000225067139},{"id":"https://openalex.org/keywords/stratification","display_name":"Stratification (seeds)","score":0.3880000114440918},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.3788999915122986},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.2802000045776367}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5964000225067139},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45320001244544983},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40709999203681946},{"id":"https://openalex.org/C192943249","wikidata":"https://www.wikidata.org/wiki/Q1893382","display_name":"Stratification (seeds)","level":5,"score":0.3880000114440918},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3855000138282776},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.3788999915122986},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3336000144481659},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.28870001435279846},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2802000045776367},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.2547999918460846}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819485","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819485","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819485","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819485","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2069089843","https://openalex.org/W2131681506","https://openalex.org/W2555892463","https://openalex.org/W2605810679","https://openalex.org/W2612519453","https://openalex.org/W2766959028","https://openalex.org/W2794480084","https://openalex.org/W2897249806","https://openalex.org/W2901677030","https://openalex.org/W2949177718","https://openalex.org/W2949237386","https://openalex.org/W2967177832","https://openalex.org/W2978169711","https://openalex.org/W2984472267","https://openalex.org/W2996998709","https://openalex.org/W3107142041","https://openalex.org/W3163661434","https://openalex.org/W3164692211","https://openalex.org/W4220939068","https://openalex.org/W4225598893","https://openalex.org/W4235169531","https://openalex.org/W4296767449","https://openalex.org/W4385290032","https://openalex.org/W4390064086"],"related_works":[],"abstract_inverted_index":{"Coordinated":[0],"stratification":[1,56],"of":[2,23,79,129,162,171,203],"cells":[3,27,100],"across":[4,46,166],"batches":[5,47,204],"is":[6,69],"essential":[7],"for":[8,16,214],"constructing":[9],"a":[10,29,90,114,119,155,176,212],"comprehensive":[11],"transcriptomic":[12],"landscape.":[13],"Current":[14],"strategies":[15],"establishing":[17],"cell":[18],"identities":[19],"generally":[20],"follow":[21],"one":[22],"two":[24],"paradigms:":[25],"clustering":[26,84,93,164,187],"in":[28,43,138,175],"shared":[30,156,177],"latent":[31,157],"space":[32],"after":[33],"cross-batch":[34],"data":[35,221],"integration":[36],"(integration-first)":[37],"or":[38],"harmonizing":[39],"clusters":[40,77],"identified":[41],"independently":[42],"individual":[44],"datasets":[45],"(clustering-first).":[48],"Both":[49],"are":[50],"limited:":[51],"the":[52,130,148,159,169,201],"former":[53],"often":[54],"compromises":[55],"resolution,":[57,188],"as":[58,200,211],"subtle":[59],"subtype":[60],"differences":[61],"may":[62],"be":[63],"obscured":[64],"during":[65],"integration.":[66],"The":[67],"latter":[68],"prone":[70],"to":[71],"enforcing":[72],"correspondence":[73],"between":[74,126,135,173],"inherently":[75],"incompatible":[76],"because":[78],"discordant":[80],"and":[81,97,118,133,168,193],"ad":[82],"hoc":[83],"criteria.":[85],"Here,":[86],"we":[87],"present":[88],"ConcordanSC,":[89],"multi-batch":[91],"concordant":[92],"framework":[94,213],"that":[95,183],"accurately":[96],"coherently":[98],"partitions":[99],"into":[101,154],"fine-grained":[102],"subtypes":[103],"by":[104],"leveraging":[105],"data-driven,":[106],"cross-batch-coherent":[107],"marker-gene":[108,116,141,191],"expression":[109],"patterns.":[110],"ConcordanSC":[111,146,184,210],"jointly":[112],"learns":[113],"parameterized":[115],"matrix":[117],"cross-batch-aligned":[120],"membership":[121],"matrix,":[122],"while":[123],"maximizing":[124],"correlations":[125],"pseudo-bulk":[127],"profiles":[128],"same":[131],"stratum":[132],"anti-correlations":[134],"opposing":[136],"strata":[137],"their":[139],"respective":[140],"subspaces.":[142],"In":[143],"doing":[144],"so,":[145],"avoids":[147],"resolution":[149],"loss":[150,170],"associated":[151],"with":[152,196],"projection":[153],"space,":[158],"futile":[160],"alignment":[161],"irreconcilable":[163],"schemes":[165],"datasets,":[167],"contrast":[172],"subpopulations":[174],"global":[178],"gene":[179],"space.":[180],"Benchmarks":[181],"show":[182],"achieves":[185],"higher":[186],"more":[189],"accurate":[190],"characterization,":[192],"excellent":[194],"scalability,":[195],"minimal":[197],"performance":[198],"degradation":[199],"number":[202],"increases.":[205],"Together,":[206],"these":[207],"results":[208],"establish":[209],"future":[215],"high-resolution,":[216],"fully":[217],"inclusive,":[218],"atlas-scale":[219],"single-cell":[220],"consolidation.":[222]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}