{"id":"https://openalex.org/W7126122784","doi":"https://doi.org/10.1109/bibm66473.2025.11357050","title":"A Unified Biomedical Named Entity Recognition Framework With Large Language Models","display_name":"A Unified Biomedical Named Entity Recognition Framework With Large Language Models","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126122784","doi":"https://doi.org/10.1109/bibm66473.2025.11357050"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11357050","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11357050","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5116560980","display_name":"Tengxiao Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tengxiao Lv","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124173863","display_name":"Ling Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100741725","display_name":"Junjian Li","orcid":"https://orcid.org/0000-0003-0336-8452"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Juntao Li","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yanhua Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4402554061","display_name":"Air Force Communication NCO Academy","ror":"https://ror.org/02n6w8087","country_code":null,"type":"education","lineage":["https://openalex.org/I4210160531","https://openalex.org/I4402554004","https://openalex.org/I4402554061"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanhua Wang","raw_affiliation_strings":["Air Force Communications NCO Academy,Dalian,China","College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"Air Force Communications NCO Academy,Dalian,China","institution_ids":["https://openalex.org/I4402554061"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124247911","display_name":"Yuchen Pan","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuchen Pan","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124175482","display_name":"Chao Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Liu","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124286780","display_name":"Yanan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4402554061","display_name":"Air Force Communication NCO Academy","ror":"https://ror.org/02n6w8087","country_code":null,"type":"education","lineage":["https://openalex.org/I4210160531","https://openalex.org/I4402554004","https://openalex.org/I4402554061"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanan Wang","raw_affiliation_strings":["Air Force Communications NCO Academy,Dalian,China","College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"Air Force Communications NCO Academy,Dalian,China","institution_ids":["https://openalex.org/I4402554061"]},{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124278983","display_name":"Yan Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]},{"id":"https://openalex.org/I4210100868","display_name":"Second Affiliated Hospital of Dalian Medical University","ror":"https://ror.org/012f2cn18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210100868"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Jiang","raw_affiliation_strings":["Second Affiliated Hospital of Dalian Medical University,Department of Pharmacy,Dalian,China"],"affiliations":[{"raw_affiliation_string":"Second Affiliated Hospital of Dalian Medical University,Department of Pharmacy,Dalian,China","institution_ids":["https://openalex.org/I191996457","https://openalex.org/I4210100868"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112254465","display_name":"Huiyi LV","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]},{"id":"https://openalex.org/I4210100868","display_name":"Second Affiliated Hospital of Dalian Medical University","ror":"https://ror.org/012f2cn18","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210100868"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiyi Lv","raw_affiliation_strings":["Second Affiliated Hospital of Dalian Medical University,Department of Pharmacy,Dalian,China"],"affiliations":[{"raw_affiliation_string":"Second Affiliated Hospital of Dalian Medical University,Department of Pharmacy,Dalian,China","institution_ids":["https://openalex.org/I191996457","https://openalex.org/I4210100868"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124157098","display_name":"Yuanyuan Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Sun","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108047889","display_name":"Y\u00ec W\u00e1ng","orcid":"https://orcid.org/0000-0001-5697-0717"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124158791","display_name":"Hongfei Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Lin","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology,Dalian,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5116560980"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.83709003,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3913","last_page":"3916"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.7789999842643738,"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"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.7789999842643738,"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"}},{"id":"https://openalex.org/T13702","display_name":"Machine Learning in Healthcare","score":0.10909999907016754,"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"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.03840000182390213,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.7605000138282776},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.6949999928474426},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.6169999837875366},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5320000052452087},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5214999914169312},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.48660001158714294},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.47450000047683716},{"id":"https://openalex.org/keywords/joint","display_name":"Joint (building)","score":0.45489999651908875}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8600999712944031},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.7605000138282776},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.6949999928474426},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6761000156402588},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6377999782562256},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.6169999837875366},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5320000052452087},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5214999914169312},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.48660001158714294},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.47450000047683716},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.45489999651908875},{"id":"https://openalex.org/C62354387","wikidata":"https://www.wikidata.org/wiki/Q875399","display_name":"Boundary (topology)","level":2,"score":0.453900009393692},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.397599995136261},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.36079999804496765},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.3467999994754791},{"id":"https://openalex.org/C22367795","wikidata":"https://www.wikidata.org/wiki/Q7625208","display_name":"Structured prediction","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C45493050","wikidata":"https://www.wikidata.org/wiki/Q7884934","display_name":"Unified Model","level":2,"score":0.3084999918937683},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.30070000886917114},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.28769999742507935},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.28380000591278076},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.25270000100135803}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11357050","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11357050","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.8528527021408081,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2163107094","https://openalex.org/W2169099542","https://openalex.org/W2346452181","https://openalex.org/W2911489562","https://openalex.org/W3169341408","https://openalex.org/W4226470037","https://openalex.org/W4283318325","https://openalex.org/W4376274483","https://openalex.org/W4385571881","https://openalex.org/W4387251711","https://openalex.org/W4392282268","https://openalex.org/W4393094733","https://openalex.org/W4399790320","https://openalex.org/W4402671644"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"recognition":[1],"of":[2],"biomedical":[3],"named":[4],"entities":[5,70],"is":[6],"critical":[7],"for":[8],"medical":[9],"information":[10],"extraction":[11],"and":[12,26,57,68,78,89,110,119,130],"knowledge":[13],"discovery.":[14],"However,":[15],"existing":[16],"methods":[17],"often":[18],"struggle":[19],"with":[20,71],"nested":[21,69],"entities,":[22],"entity":[23,98],"boundary":[24,73],"ambiguity,":[25],"cross-lingual":[27],"generalization.":[28],"In":[29],"this":[30],"paper,":[31],"we":[32,81,93],"propose":[33],"a":[34,53,59,95],"unified":[35],"Biomedical":[36],"Named":[37],"Entity":[38],"Recognition":[39],"(BioNER)":[40],"framework":[41],"based":[42],"on":[43,115],"Large":[44],"Language":[45],"Models":[46],"(LLMs).":[47],"We":[48],"first":[49],"reformulate":[50],"BioNER":[51],"as":[52],"text":[54],"generation":[55],"task":[56],"design":[58],"symbolic":[60],"tagging":[61],"strategy":[62],"to":[63],"jointly":[64],"handle":[65],"both":[66],"flat":[67],"explicit":[72],"annotation.":[74],"To":[75],"enhance":[76],"multilingual":[77],"multi-task":[79],"generalization,":[80],"perform":[82],"bilingual":[83],"joint":[84],"fine-tuning":[85],"across":[86,134],"multiple":[87],"Chinese":[88],"English":[90],"datasets.":[91],"Additionally,":[92],"introduce":[94],"contrastive":[96],"learning-based":[97],"selector":[99],"that":[100,124],"filters":[101],"incorrect":[102],"or":[103],"spurious":[104],"predictions":[105],"by":[106],"leveraging":[107],"boundary-sensitive":[108],"positive":[109],"negative":[111],"samples.":[112],"Experimental":[113],"results":[114],"four":[116],"benchmark":[117],"datasets":[118],"two":[120],"unseen":[121],"corpora":[122],"show":[123],"our":[125],"method":[126],"achieves":[127],"state-of-the-art":[128],"performance":[129],"robust":[131],"zero-shot":[132],"generalization":[133],"languages.":[135],"The":[136],"source":[137],"codes":[138],"are":[139],"freely":[140],"available":[141],"at":[142],"https://github.com/dreamer-tx/LLMNER.":[143]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2026-01-30T00:00:00"}
