{"id":"https://openalex.org/W4412945491","doi":"https://doi.org/10.18653/v1/2025.acl-long.455","title":"Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models","display_name":"Identifying Cellular Niches in Spatial Transcriptomics: An Investigation into the Capabilities of Large Language Models","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4412945491","doi":"https://doi.org/10.18653/v1/2025.acl-long.455"},"language":"en","primary_location":{"id":"doi:10.18653/v1/2025.acl-long.455","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.acl-long.455","pdf_url":"https://aclanthology.org/2025.acl-long.455.pdf","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 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2025.acl-long.455.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101855397","display_name":"Huanhuan Wei","orcid":"https://orcid.org/0000-0002-6481-5407"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huanhuan Wei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082738053","display_name":"Xiao Luo","orcid":"https://orcid.org/0000-0002-2561-6114"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiao Luo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102825711","display_name":"Hongliang Yu","orcid":"https://orcid.org/0000-0003-2404-4158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hongyi Yu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102341708","display_name":"Jinping Liang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jinping Liang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052691413","display_name":"Luning Yang","orcid":"https://orcid.org/0000-0001-7863-6605"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luning Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025103802","display_name":"Lin Li","orcid":"https://orcid.org/0009-0007-4737-4500"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lixing Lin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057981704","display_name":"Alexandra Popa","orcid":"https://orcid.org/0000-0001-7156-272X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alexandra Popa","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5079068469","display_name":"Xiting Yan","orcid":"https://orcid.org/0000-0001-8688-9004"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiting Yan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"9275","last_page":"9289"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8198000192642212,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8198000192642212,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7591999769210815,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.7211999893188477,"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":0.6740680932998657},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.44767865538597107},{"id":"https://openalex.org/keywords/ecological-niche","display_name":"Ecological niche","score":0.4300961494445801},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1573980748653412},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.12393510341644287}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6740680932998657},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.44767865538597107},{"id":"https://openalex.org/C102715595","wikidata":"https://www.wikidata.org/wiki/Q172861","display_name":"Ecological niche","level":3,"score":0.4300961494445801},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1573980748653412},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.12393510341644287},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185933670","wikidata":"https://www.wikidata.org/wiki/Q52105","display_name":"Habitat","level":2,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/2025.acl-long.455","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.acl-long.455","pdf_url":"https://aclanthology.org/2025.acl-long.455.pdf","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 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/2025.acl-long.455","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.acl-long.455","pdf_url":"https://aclanthology.org/2025.acl-long.455.pdf","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 63rd Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers)","raw_type":"proceedings-article"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4412945491.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2399513595","https://openalex.org/W4308922319","https://openalex.org/W4388386498","https://openalex.org/W3127999365","https://openalex.org/W2390279801","https://openalex.org/W2028462563","https://openalex.org/W2982720988"],"abstract_inverted_index":{"Huanhuan":[0],"Wei,":[1],"Xiao":[2],"Luo,":[3],"Hongyi":[4],"Yu,":[5],"Jinping":[6],"Liang,":[7],"Luning":[8],"Yang,":[9],"Lixing":[10],"Lin,":[11],"Alexandra":[12],"Popa,":[13],"Xiting":[14],"Yan.":[15],"Proceedings":[16],"of":[17,22],"the":[18,23],"63rd":[19],"Annual":[20],"Meeting":[21],"Association":[24],"for":[25],"Computational":[26],"Linguistics":[27],"(Volume":[28],"1:":[29],"Long":[30],"Papers).":[31],"2025.":[32]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
