{"id":"https://openalex.org/W7166889043","doi":"https://doi.org/10.18653/v1/2026.bionlp-1.30","title":"EmCellLLM: Human Peri-Implantation Embryonic Cell Annotation Based on Large Language Models","display_name":"EmCellLLM: Human Peri-Implantation Embryonic Cell Annotation Based on Large Language Models","publication_year":2026,"publication_date":"2026-01-01","ids":{"openalex":"https://openalex.org/W7166889043","doi":"https://doi.org/10.18653/v1/2026.bionlp-1.30"},"language":null,"primary_location":{"id":"doi:10.18653/v1/2026.bionlp-1.30","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2026.bionlp-1.30","pdf_url":"https://aclanthology.org/2026.bionlp-1.30.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":"BioNLP 2026","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2026.bionlp-1.30.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5139753046","display_name":"Xiaorui Guo","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Xiaorui Guo","raw_affiliation_strings":["The University of Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139762333","display_name":"Zhiwei Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zhiwei Liu","raw_affiliation_strings":["The University of Manchester"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Manchester","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139738675","display_name":"Qianqian Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]},{"id":"https://openalex.org/I4210164862","display_name":"Artificial Intelligence in Medicine (Canada)","ror":"https://ror.org/05p590m36","country_code":"CA","type":"company","lineage":["https://openalex.org/I4210164862"]}],"countries":["CA","CN"],"is_corresponding":false,"raw_author_name":"Qianqian Xie","raw_affiliation_strings":["Center for Language and Information Research , Wuhan University","School of Artificial Intelligence , Wuhan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Language and Information Research , Wuhan University","institution_ids":["https://openalex.org/I37461747"]},{"raw_affiliation_string":"School of Artificial Intelligence , Wuhan University","institution_ids":["https://openalex.org/I4210164862"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5139739893","display_name":"Sophia Ananiadou","orcid":null},"institutions":[{"id":"https://openalex.org/I2800979252","display_name":"Elliot Hospital","ror":"https://ror.org/03jachw67","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800979252"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB","US"],"is_corresponding":false,"raw_author_name":"Sophia Ananiadou","raw_affiliation_strings":["ELLIS Manchester","The University of Manchester"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ELLIS Manchester","institution_ids":["https://openalex.org/I2800979252"]},{"raw_affiliation_string":"The University of Manchester","institution_ids":["https://openalex.org/I28407311"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.90411491,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"382","last_page":"391"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10505","display_name":"Pluripotent Stem Cells Research","score":0.09369999915361404,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.09369999915361404,"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/T10775","display_name":"Generative Adversarial Networks and Image Synthesis","score":0.06669999659061432,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13083","display_name":"Advanced Text Analysis Techniques","score":0.03500000014901161,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49070000648498535},{"id":"https://openalex.org/keywords/embryonic-stem-cell","display_name":"Embryonic stem cell","score":0.3799999952316284},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.37560001015663147},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.2728999853134155}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6255000233650208},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4970000088214874},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49070000648498535},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.43050000071525574},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.3799999952316284},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.37560001015663147},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3540000021457672},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3528999984264374},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.25609999895095825}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/2026.bionlp-1.30","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2026.bionlp-1.30","pdf_url":"https://aclanthology.org/2026.bionlp-1.30.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":"BioNLP 2026","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/2026.bionlp-1.30","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2026.bionlp-1.30","pdf_url":"https://aclanthology.org/2026.bionlp-1.30.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":"BioNLP 2026","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5209516035","display_name":"","funder_award_id":"RE/24/130017","funder_id":"https://openalex.org/F4320319992","funder_display_name":"British Heart Foundation"}],"funders":[{"id":"https://openalex.org/F4320316083","display_name":"Tencent","ror":"https://ror.org/00hhjss72"},{"id":"https://openalex.org/F4320319992","display_name":"British Heart Foundation","ror":"https://ror.org/02wdwnk04"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7166889043.pdf","grobid_xml":"https://content.openalex.org/works/W7166889043.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"The":[0],"advent":[1],"of":[2,10,64,69,79,139,147],"single-cell":[3],"RNA":[4],"sequencing":[5],"has":[6],"enabled":[7],"unprecedented":[8],"resolution":[9],"cell":[11,24,72,102,115,135],"fate":[12,37],"decisions":[13],"and":[14,31,38,58,83],"regulatory":[15],"mechanisms":[16],"during":[17],"peri-implantation":[18],"human":[19,70,100,133],"embryogenesis,":[20],"in":[21,48,66],"which":[22],"accurate":[23],"type":[25,103,116,136],"annotation":[26],"is":[27,76],"a":[28,145],"fundamental":[29],"prerequisite":[30],"the":[32,62,67,77,91,112,128],"first":[33,92,113,129],"step":[34],"for":[35,99,131],"subsequent":[36],"mechanism":[39],"inference.Large":[40],"language":[41],"models":[42,143],"(LLMs)":[43],"have":[44,59],"demonstrated":[45],"outstanding":[46],"performance":[47],"various":[49],"fields.However,":[50],"current":[51],"studies":[52],"mostly":[53],"rely":[54],"on":[55,107,149],"traditional":[56],"methods":[57],"not":[60],"explored":[61],"application":[63],"LLMs":[65,95,148,158],"field":[68],"embryonic":[71,101,114,134],"annotation.The":[73],"main":[74],"reason":[75],"lack":[78],"instruction":[80,118,122],"tuning":[81],"datasets":[82],"evaluation":[84],"benchmarks.In":[85],"this":[86],"paper,":[87],"we":[88,124],"proposed":[89],"Em-CellLLM,":[90],"open":[93],"sourced":[94],"that":[96],"are":[97],"specialized":[98],"prediction":[104,117,137],"task":[105],"based":[106],"fine-tuning":[108],"Qwen3-8B":[109],"with":[110,144],"EmCell4Instruction,":[111],"dataset.To":[119],"support":[120],"LLM":[121],"tuning,":[123],"also":[125],"build":[126],"Em-CellBench,":[127],"benchmark":[130],"evaluating":[132],"ability":[138],"LLMs.We":[140],"compare":[141],"our":[142,152],"variety":[146],"EmCellBench,":[150],"where":[151],"model":[153],"outperforms":[154],"all":[155],"other":[156],"open-sourced":[157],"as":[159,161],"well":[160],"DeepSeek.":[162]},"counts_by_year":[],"updated_date":"2026-08-23T07:36:19.812096","created_date":"2026-07-02T00:00:00"}