{"id":"https://openalex.org/W4414359778","doi":"https://doi.org/10.24963/ijcai.2025/875","title":"scSiameseClu: A Siamese Clustering Framework for Interpreting Single-cell RNA Sequencing Data","display_name":"scSiameseClu: A Siamese Clustering Framework for Interpreting Single-cell RNA Sequencing Data","publication_year":2025,"publication_date":"2025-09-01","ids":{"openalex":"https://openalex.org/W4414359778","doi":"https://doi.org/10.24963/ijcai.2025/875"},"language":"en","primary_location":{"id":"doi:10.24963/ijcai.2025/875","is_oa":false,"landing_page_url":"https://doi.org/10.24963/ijcai.2025/875","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Fourth International Joint Conference on Artificial Intelligence","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/A5101480265","display_name":"Ping Xu","orcid":"https://orcid.org/0009-0001-9927-134X"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ping Xu","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017565499","display_name":"Zhiyuan Ning","orcid":"https://orcid.org/0009-0000-4718-1564"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyuan Ning","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007615104","display_name":"Pengjiang Li","orcid":"https://orcid.org/0000-0003-1115-0664"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengjiang Li","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100520467","display_name":"Wenhao Liu","orcid":"https://orcid.org/0000-0002-2385-2172"},"institutions":[{"id":"https://openalex.org/I169572211","display_name":"Northeast Agricultural University","ror":"https://ror.org/0515nd386","country_code":"CN","type":"education","lineage":["https://openalex.org/I169572211"]},{"id":"https://openalex.org/I2802805919","display_name":"Science North","ror":"https://ror.org/028k36c88","country_code":"CA","type":"archive","lineage":["https://openalex.org/I2802805919"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Wenhao Liu","raw_affiliation_strings":["College of Life Science, Northeast Agricultural University, Harbin"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Northeast Agricultural University, Harbin","institution_ids":["https://openalex.org/I169572211","https://openalex.org/I2802805919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036270316","display_name":"Pengyang Wang","orcid":"https://orcid.org/0000-0003-3961-5523"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I6469544","display_name":"City University of Macau","ror":"https://ror.org/04gpd4q15","country_code":"MO","type":"education","lineage":["https://openalex.org/I6469544"]}],"countries":["CN","MO"],"is_corresponding":false,"raw_author_name":"Pengyang Wang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","SKL-IOTSC and Department of CIS, University of Macau, Macau","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"SKL-IOTSC and Department of CIS, University of Macau, Macau","institution_ids":["https://openalex.org/I204512498","https://openalex.org/I6469544"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065331390","display_name":"Jiaxu Cui","orcid":"https://orcid.org/0000-0002-4922-0915"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxu Cui","raw_affiliation_strings":["Jilin University, Changchun"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jilin University, Changchun","institution_ids":["https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065865669","display_name":"Yuanchun Zhou","orcid":"https://orcid.org/0000-0003-2144-1131"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanchun Zhou","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100399600","display_name":"Pengfei Wang","orcid":"https://orcid.org/0009-0002-2900-5561"},"institutions":[{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]},{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I6469544","display_name":"City University of Macau","ror":"https://ror.org/04gpd4q15","country_code":"MO","type":"education","lineage":["https://openalex.org/I6469544"]}],"countries":["CN","MO"],"is_corresponding":false,"raw_author_name":"Pengfei Wang","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","SKL-IOTSC and Department of CIS, University of Macau, Macau","University of Chinese Academy of Sciences, Beijing\uff1b"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210108629"]},{"raw_affiliation_string":"SKL-IOTSC and Department of CIS, University of Macau, Macau","institution_ids":["https://openalex.org/I204512498","https://openalex.org/I6469544"]},{"raw_affiliation_string":"University of Chinese Academy of Sciences, Beijing\uff1b","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"7867","last_page":"7875"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9973000288009644,"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":0.9973000288009644,"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":0.9441999793052673,"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/T11482","display_name":"RNA modifications and cancer","score":0.9304999709129333,"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":0.7389000058174133},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.5127999782562256},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.4927000105381012},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4909000098705292},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.47620001435279846},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4131999909877777},{"id":"https://openalex.org/keywords/consensus-clustering","display_name":"Consensus clustering","score":0.3702000081539154},{"id":"https://openalex.org/keywords/rand-index","display_name":"Rand index","score":0.3434000015258789}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7389000058174133},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6661999821662903},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.5127999782562256},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.4927000105381012},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4909000098705292},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.47620001435279846},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46630001068115234},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46399998664855957},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4196000099182129},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4131999909877777},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.3702000081539154},{"id":"https://openalex.org/C111442797","wikidata":"https://www.wikidata.org/wiki/Q7291446","display_name":"Rand index","level":3,"score":0.3434000015258789},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.33899998664855957},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.3352999985218048},{"id":"https://openalex.org/C116409475","wikidata":"https://www.wikidata.org/wiki/Q1385056","display_name":"External Data Representation","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3102000057697296},{"id":"https://openalex.org/C105611402","wikidata":"https://www.wikidata.org/wiki/Q2976589","display_name":"Spectral clustering","level":3,"score":0.3043999969959259},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.28839999437332153},{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.28369998931884766},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.275299996137619},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.2752000093460083},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.27219998836517334},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.2712000012397766},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.26429998874664307}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.24963/ijcai.2025/875","is_oa":false,"landing_page_url":"https://doi.org/10.24963/ijcai.2025/875","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the Thirty-Fourth International Joint Conference on Artificial Intelligence","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"reveals":[4],"cell":[5,8,16,100,162,166],"heterogeneity,":[6],"with":[7,141],"clustering":[9,32],"playing":[10],"a":[11,70,170],"key":[12,83],"role":[13],"in":[14,159],"identifying":[15],"types":[17],"and":[18,46,99,115,127,165],"marker":[19],"genes.":[20],"Recent":[21],"advances,":[22],"especially":[23],"graph":[24,101],"neural":[25],"networks":[26],"(GNNs)-based":[27],"methods,":[28],"have":[29],"significantly":[30],"improved":[31],"performance.":[33],"However,":[34],"the":[35,95],"analysis":[36],"of":[37,81],"scRNA-seq":[38,174],"data":[39,175],"remains":[40],"challenging":[41],"due":[42],"to":[43,60,94,103,119,136],"noise,":[44],"sparsity,":[45],"high":[47],"dimensionality.":[48],"Compounding":[49],"these":[50],"challenges,":[51],"GNNs":[52],"often":[53],"suffer":[54],"from":[55],"over-smoothing,":[56],"limiting":[57],"their":[58],"ability":[59],"capture":[61,120],"complex":[62,121],"biological":[63],"information.":[64],"In":[65],"response,":[66],"we":[67],"propose":[68],"scSiameseClu,":[69],"novel":[71],"Siamese":[72,108],"Clustering":[73],"framework":[74],"for":[75,173],"interpreting":[76],"single-cell":[77,160],"RNA-seq":[78],"data,":[79],"comprising":[80],"3":[82],"steps:":[84],"(1)":[85],"Dual":[86],"Augmentation":[87],"Module,":[88,110],"which":[89,111,132],"applies":[90],"biologically":[91],"informed":[92],"perturbations":[93],"gene":[96],"expression":[97],"matrix":[98],"relationships":[102,123],"enhance":[104],"representation":[105],"robustness;":[106],"(2)":[107],"Fusion":[109],"combines":[112],"cross-correlation":[113],"refinement":[114],"adaptive":[116],"information":[117],"fusion":[118],"cellular":[122],"while":[124,144],"mitigating":[125],"over-smoothing;":[126],"(3)":[128],"Optimal":[129],"Transport":[130],"Clustering,":[131],"utilizes":[133],"Sinkhorn":[134],"distance":[135],"efficiently":[137],"align":[138],"cluster":[139],"assignments":[140],"predefined":[142],"proportions":[143],"maintaining":[145],"balance.":[146],"Comprehensive":[147],"evaluations":[148],"on":[149],"seven":[150],"real-world":[151],"datasets":[152],"demonstrate":[153],"that":[154],"scSiameseClu":[155],"outperforms":[156],"state-of-the-art":[157],"methods":[158],"clustering,":[161],"type":[163,167],"annotation,":[164],"classification,":[168],"providing":[169],"powerful":[171],"tool":[172],"interpretation.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
