{"id":"https://openalex.org/W7223571964","doi":"https://doi.org/10.64898/2026.10.20.760373","title":"Multi-scale microenvironment covariance for unsupervised spatial domain identification","display_name":"Multi-scale microenvironment covariance for unsupervised spatial domain identification","publication_year":2026,"publication_date":"2026-10-24","ids":{"openalex":"https://openalex.org/W7223571964","doi":"https://doi.org/10.64898/2026.10.20.760373"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.20.760373","doi":"https://doi.org/10.64898/2026.10.20.760373","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760373","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.20.760373.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.20.760373.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5159508316","display_name":"Bairui Du","orcid":"https://orcid.org/0000-0002-2240-5418","observed_orcids":["https://orcid.org/0000-0002-2240-5418"]},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Bairui Du","raw_affiliation_strings":["Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8563, Chiba, Japan"],"raw_orcid":"https://orcid.org/0000-0002-2240-5418","affiliations":[{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8563, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024402799","display_name":"Hisanori Kiryu","orcid":"https://orcid.org/0000-0003-3554-5353","observed_orcids":["https://orcid.org/0000-0003-3554-5353"]},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hisanori Kiryu","raw_affiliation_strings":["Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8563, Chiba, Japan"],"raw_orcid":"https://orcid.org/0000-0003-3554-5353","affiliations":[{"raw_affiliation_string":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8563, Chiba, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5159508316"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9994999766349792,"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":0.9994999766349792,"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/T10885","display_name":"Gene expression and cancer classification","score":0.00019999999494757503,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0,"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/spatial-domain-identification","display_name":"spatial domain identification","score":0.9860000014305115},{"id":"https://openalex.org/keywords/multiscale-analysis","display_name":"multiscale analysis","score":0.628000020980835},{"id":"https://openalex.org/keywords/cellular-microenvironment","display_name":"cell microenvironment","score":0.5619999766349792},{"id":"https://openalex.org/keywords/unsupervised-clustering","display_name":"unsupervised clustering","score":0.7860000133514404},{"id":"https://openalex.org/keywords/spatial-transcriptomics","display_name":"spatial transcriptomics","score":0.6430000066757202},{"id":"https://openalex.org/keywords/mouse-brain","display_name":"mouse brain","score":0.43299999833106995},{"id":"https://openalex.org/keywords/covet","display_name":"Covet","score":0.48899999260902405}],"concepts":[{"id":"https://openalex.org/C185142706","wikidata":"https://www.wikidata.org/wiki/Q1134404","display_name":"Covariance matrix","level":2,"score":0.6898000240325928},{"id":"https://openalex.org/C178650346","wikidata":"https://www.wikidata.org/wiki/Q201984","display_name":"Covariance","level":2,"score":0.6837000250816345},{"id":"https://openalex.org/C27438332","wikidata":"https://www.wikidata.org/wiki/Q2873","display_name":"Principal component analysis","level":2,"score":0.6577000021934509},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.6468999981880188},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5805000066757202},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5569999814033508},{"id":"https://openalex.org/C137250428","wikidata":"https://www.wikidata.org/wiki/Q5178897","display_name":"Covariance function","level":3,"score":0.5289000272750854},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5142999887466431},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5105000138282776},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.46650001406669617},{"id":"https://openalex.org/C161677786","wikidata":"https://www.wikidata.org/wiki/Q2478475","display_name":"Neighbourhood (mathematics)","level":2,"score":0.460999995470047},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.44830000400543213},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4169999957084656},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.40470001101493835},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C180877172","wikidata":"https://www.wikidata.org/wiki/Q5401390","display_name":"Estimation of covariance matrices","level":3,"score":0.3880999982357025},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.37400001287460327},{"id":"https://openalex.org/C83042196","wikidata":"https://www.wikidata.org/wiki/Q5178898","display_name":"Covariance intersection","level":4,"score":0.36570000648498535},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3547999858856201},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.3531999886035919},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35280001163482666},{"id":"https://openalex.org/C101601086","wikidata":"https://www.wikidata.org/wiki/Q3753228","display_name":"Rank correlation","level":2,"score":0.29910001158714294},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29600000381469727},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.2793999910354614},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C150060386","wikidata":"https://www.wikidata.org/wiki/Q7574054","display_name":"Spatial correlation","level":2,"score":0.2734000086784363},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.27239999175071716},{"id":"https://openalex.org/C119340705","wikidata":"https://www.wikidata.org/wiki/Q1628597","display_name":"Analysis of covariance","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C71176878","wikidata":"https://www.wikidata.org/wiki/Q17014987","display_name":"Functional principal component analysis","level":3,"score":0.257999986410141},{"id":"https://openalex.org/C5349765","wikidata":"https://www.wikidata.org/wiki/Q5282866","display_name":"Distance matrices in phylogeny","level":2,"score":0.2524999976158142},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.2506999969482422}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.20.760373","doi":"https://doi.org/10.64898/2026.10.20.760373","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760373","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.20.760373.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.20.760373","doi":"https://doi.org/10.64898/2026.10.20.760373","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.20.760373","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/24/2026.10.20.760373.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322832","display_name":"University of Tokyo","ror":"https://ror.org/057zh3y96"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223571964.pdf","grobid_xml":"https://content.openalex.org/works/W7223571964.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1942323201","https://openalex.org/W1973370947","https://openalex.org/W2131681506","https://openalex.org/W2570474222","https://openalex.org/W2771365419","https://openalex.org/W2786672974","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W2897249806","https://openalex.org/W2899224111","https://openalex.org/W3013743295","https://openalex.org/W3108118546","https://openalex.org/W3190202966","https://openalex.org/W4229033508","https://openalex.org/W4241727697","https://openalex.org/W4252684946","https://openalex.org/W4285388882","https://openalex.org/W4289745500","https://openalex.org/W4306168059","https://openalex.org/W4317832423","https://openalex.org/W4390615005","https://openalex.org/W4390814844","https://openalex.org/W4392868645","https://openalex.org/W4394927236"],"related_works":["https://openalex.org/W7114895040","https://openalex.org/W4406139326","https://openalex.org/W7127049350","https://openalex.org/W4403512780","https://openalex.org/W4388684677","https://openalex.org/W7155678086","https://openalex.org/W4399488468","https://openalex.org/W7118976976","https://openalex.org/W7168299366","https://openalex.org/W7128902575"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Many":[2],"spatial":[3,35,58,79],"domain":[4,128],"identification":[5],"methods":[6],"describe":[7],"the":[8,18,43,70,75,93],"neighbourhood":[9,59],"of":[10,45,52,56,69,74,124,150],"a":[11,49,109],"cell":[12,47],"by":[13,48],"mean":[14,19],"gene":[15,133],"expression.":[16],"However,":[17],"cannot":[20],"separate":[21],"neighbourhoods":[22],"that":[23,123],"differ":[24],"only":[25],"in":[26],"gene\u2013gene":[27,53],"covariance":[28,54,129],"and":[29,66,114,141,147],"tissue":[30],"is":[31],"organised":[32],"at":[33,60,154,167],"several":[34],"scales.ht":[36],"Results":[37],"We":[38],"propose":[39],"CoSMIM,":[40],"which":[41],"represents":[42],"niche":[44],"each":[46],"weighted":[50],"fusion":[51],"matrices":[55,130],"its":[57,119],"multiple":[61],"scales.":[62],"Principal":[63],"component":[64],"analysis":[65],"Leiden":[67],"clustering":[68],"matrix":[71,77],"square":[72],"root":[73],"fused":[76],"identify":[78],"domains":[80],"without":[81],"model":[82],"training.":[83],"On":[84],"six":[85],"benchmark":[86],"datasets":[87,118],"from":[88],"five":[89],"platforms,":[90],"CoSMIM":[91,151],"attains":[92],"best":[94],"overall":[95],"rank":[96],"over":[97],"eight":[98],"evaluation":[99],"metrics":[100],"among":[101],"16":[102],"methods.":[103],"It":[104],"also":[105,131],"ranks":[106],"first":[107],"on":[108,115],"Xenium":[110],"mouse":[111],"brain":[112],"dataset,":[113],"all":[116],"seven":[117],"median":[120],"NMI":[121],"exceeds":[122],"single-scale":[125],"COVET.":[126],"The":[127,143],"show":[132],"pairs":[134],"whose":[135],"correlation":[136],"differs":[137],"between":[138],"domains.":[139],"Availability":[140],"implementation":[142],"source":[144],"code,":[145],"documentation":[146],"test":[148],"data":[149,164],"are":[152,165],"available":[153,166],"GitHub":[155],"(":[156],"https://github.com/barondu/cosmim":[157],").":[158],"Contact":[159],"du_bairui_24@stu-cbms.k.u-tokyo.ac.jp":[160],"Supplementary":[161,163],"information":[162],"Bioinformatics":[168],"online.":[169]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-10-26T00:00:00"}
