{"id":"https://openalex.org/W4400519466","doi":"https://doi.org/10.1007/978-981-97-5131-0_10","title":"Accurately Deciphering Novel Cell Type in\u00a0Spatially Resolved Single-Cell Data Through Optimal Transport","display_name":"Accurately Deciphering Novel Cell Type in\u00a0Spatially Resolved Single-Cell Data Through Optimal Transport","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4400519466","doi":"https://doi.org/10.1007/978-981-97-5131-0_10"},"language":"en","primary_location":{"id":"doi:10.1007/978-981-97-5131-0_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-981-97-5131-0_10","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://hdl.handle.net/10072/432231","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002145972","display_name":"Mai Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mai Luo","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088056853","display_name":"Yuansong Zeng","orcid":"https://orcid.org/0000-0002-3145-430X"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuansong Zeng","raw_affiliation_strings":["School of Big Data and Software Engineering, Chongqing University, Chongqing, 400000, China"],"affiliations":[{"raw_affiliation_string":"School of Big Data and Software Engineering, Chongqing University, Chongqing, 400000, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100613502","display_name":"Jianing Chen","orcid":"https://orcid.org/0000-0002-7525-1424"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianing Chen","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094184499","display_name":"Ningyuan Shangguan","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ningyuan Shangguan","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113284784","display_name":"Wenhao Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Zhou","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5023539493","display_name":"Yuedong Yang","orcid":"https://orcid.org/0000-0002-6782-2813"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuedong Yang","raw_affiliation_strings":["School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Sun Yat-Sen University, Guangzhou, 510006, China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5023539493"],"corresponding_institution_ids":["https://openalex.org/I157773358"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25208611,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"107","last_page":"118"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9754999876022339,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.791935920715332},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.45259782671928406}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.791935920715332},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.45259782671928406},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/978-981-97-5131-0_10","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-981-97-5131-0_10","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/432231","is_oa":true,"landing_page_url":"https://hdl.handle.net/10072/432231","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference output"}],"best_oa_location":{"id":"pmh:oai:research-repository.griffith.edu.au:10072/432231","is_oa":true,"landing_page_url":"https://hdl.handle.net/10072/432231","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference output"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2344591493","https://openalex.org/W2510746232","https://openalex.org/W2724892359","https://openalex.org/W2792626041","https://openalex.org/W2923569719","https://openalex.org/W2952383043","https://openalex.org/W3035524453","https://openalex.org/W3042462196","https://openalex.org/W3087998689","https://openalex.org/W3092982430","https://openalex.org/W3108118546","https://openalex.org/W3165120573","https://openalex.org/W3191029526","https://openalex.org/W3196650609","https://openalex.org/W3204015056","https://openalex.org/W3215069361","https://openalex.org/W4214671648","https://openalex.org/W4221095552","https://openalex.org/W4307184360","https://openalex.org/W4311666191","https://openalex.org/W4320489547"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,20,180,189],"spatial":[3,9,35,85,95],"transcriptomics":[4],"enable":[5],"the":[6,59,84,91,99,117,138,141,155,169],"detection":[7],"of":[8,64,140],"heterogeneity":[10],"at":[11,199],"single-cell":[12,74],"resolution.":[13],"However,":[14],"existing":[15],"annotation":[16,194],"methods":[17,179],"are":[18,26,197],"limited":[19],"performance":[21],"due":[22],"to":[23,44,108,116,133,167],"that":[24,56,175],"they":[25,40],"mainly":[27],"designed":[28],"for":[29,34,58,94,164],"scRNA-seq":[30],"data":[31,75,86,115],"without":[32],"accounting":[33,93],"coordinate":[36],"information.":[37,123],"More":[38],"importantly,":[39],"have":[41],"been":[42],"struggling":[43],"identify":[45],"novel":[46,54,68],"cell":[47,69,136,152,190],"types.":[48],"Here,":[49],"we":[50],"introduce":[51],"SPOTAnno,":[52],"a":[53,104],"method":[55],"allows":[57],"simultaneous":[60],"and":[61,67,149,183,193],"accurate":[62],"identification":[63],"both":[65,181],"seen":[66],"types":[70],"within":[71,154],"spatially":[72],"resolved":[73],"using":[76],"Optimal":[77],"Transport":[78],"(OT).":[79],"Concretely,":[80],"SPOTAnno":[81,102,126,176],"first":[82],"embeds":[83],"into":[87],"low-dimensional":[88,100],"embeddings":[89],"through":[90,120],"transformer":[92],"coordinates.":[96],"Based":[97],"on":[98],"embeddings,":[101],"employs":[103],"partial":[105],"alignment":[106],"strategy":[107],"remove":[109],"batch":[110],"effects":[111],"by":[112],"aligning":[113],"target":[114,142,156,165],"reference":[118],"prototypes":[119,139],"OT-based":[121,129],"statistical":[122],"In":[124],"parallel,":[125],"utilizes":[127],"an":[128,159],"representation":[130],"learning":[131],"mechanism":[132],"map":[134],"each":[135],"onto":[137],"data,":[143],"which":[144],"enhances":[145],"global":[146],"cluster":[147],"discrimination":[148],"ensures":[150],"local":[151],"consistency":[153],"dataset.":[157],"Additionally,":[158],"entropy-based":[160],"loss":[161],"is":[162],"applied":[163],"cells":[166],"increase":[168],"prediction":[170],"certainty.":[171],"Comprehensive":[172],"experiments":[173],"demonstrate":[174],"outperforms":[177],"state-of-the-art":[178],"intra-data":[182],"cross-data":[184],"settings,":[185],"showcasing":[186],"its":[187],"effectiveness":[188],"type":[191],"discovery":[192],"accuracy.":[195],"Implementations":[196],"available":[198],"https://github.com/QingJun3/SPOTAnno":[200],".":[201]},"counts_by_year":[],"updated_date":"2026-02-06T02:01:19.302388","created_date":"2025-10-10T00:00:00"}
