{"id":"https://openalex.org/W4416527905","doi":"https://doi.org/10.1007/s13755-025-00400-3","title":"Vaner2: towards more general biomedical named entity recognition using multi-task large language model encoders","display_name":"Vaner2: towards more general biomedical named entity recognition using multi-task large language model encoders","publication_year":2025,"publication_date":"2025-11-21","ids":{"openalex":"https://openalex.org/W4416527905","doi":"https://doi.org/10.1007/s13755-025-00400-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/41281609"},"language":"en","primary_location":{"id":"doi:10.1007/s13755-025-00400-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s13755-025-00400-3","pdf_url":null,"source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health Information Science and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100460411","display_name":"Yuxuan Liu","orcid":"https://orcid.org/0000-0002-9607-0518"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxuan Liu","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084369276","display_name":"Junyi Bian","orcid":"https://orcid.org/0009-0000-3329-8614"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junyi Bian","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047930363","display_name":"Weiqi Zhai","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiqi Zhai","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113102353","display_name":"Jiaxuan Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxuan Zheng","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I4210164150","https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004156261","display_name":"Y Zhang","orcid":"https://orcid.org/0009-0000-7181-1781"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuyi Zhang","raw_affiliation_strings":["School of Computer Science, Fudan University, Shanghai, 200433 China","Software School of Fudan University, Shanghai, 200433 China","School of Computer Science, Fudan University, Shanghai, 200433, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Software School of Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"School of Computer Science, Fudan University, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045866167","display_name":"Shanfeng Zhu","orcid":"https://orcid.org/0000-0002-6067-5312"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I2802974365","display_name":"Shanghai Innovative Research Center of Traditional Chinese Medicine","ror":"https://ror.org/01gnagj68","country_code":"CN","type":"facility","lineage":["https://openalex.org/I2802974365"]},{"id":"https://openalex.org/I4210164150","display_name":"Shanghai Center for Brain Science and Brain-Inspired Technology","ror":"https://ror.org/0551a0y31","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210164150"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shanfeng Zhu","raw_affiliation_strings":["Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, 200433 China","Shanghai Key Lab of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University, Shanghai, 200433 China","Zhangjiang Fudan International Innovation Center, Shanghai, 200433 China","Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, 200433, China","Zhangjiang Fudan International Innovation Center, Shanghai, 200433, China"],"raw_orcid":"https://orcid.org/0000-0002-6067-5312","affiliations":[{"raw_affiliation_string":"Institute of Science and Technology for Brain-Inspired Intelligence and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I4210164150"]},{"raw_affiliation_string":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, 200433 China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing and Shanghai Institute of Artificial Intelligence Algorithm, Fudan University, Shanghai, 200433 China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center, Shanghai, 200433 China","institution_ids":["https://openalex.org/I2802974365"]},{"raw_affiliation_string":"Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, 200433, China","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Zhangjiang Fudan International Innovation Center, Shanghai, 200433, China","institution_ids":["https://openalex.org/I2802974365"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5045866167"],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I2802974365","https://openalex.org/I4210164150"],"apc_list":{"value":2790,"currency":"EUR","value_usd":3590},"apc_paid":null,"fwci":1.396,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.87218916,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"14","issue":"1","first_page":"4","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.5963000059127808,"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":0.5963000059127808,"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":0.10559999942779541,"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/T13702","display_name":"Machine Learning in Healthcare","score":0.10019999742507935,"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/named-entity-recognition","display_name":"Named-entity recognition","score":0.801800012588501},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.6122000217437744},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.6103000044822693},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.5953999757766724},{"id":"https://openalex.org/keywords/relation","display_name":"Relation (database)","score":0.5694000124931335},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5321000218391418},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4975000023841858},{"id":"https://openalex.org/keywords/named-entity","display_name":"Named entity","score":0.47940000891685486},{"id":"https://openalex.org/keywords/presentation","display_name":"Presentation (obstetrics)","score":0.45649999380111694}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8468000292778015},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.801800012588501},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6638000011444092},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.651199996471405},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.6122000217437744},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.6103000044822693},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.5953999757766724},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.5694000124931335},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5321000218391418},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4975000023841858},{"id":"https://openalex.org/C2777889803","wikidata":"https://www.wikidata.org/wiki/Q25047676","display_name":"Named entity","level":2,"score":0.47940000891685486},{"id":"https://openalex.org/C2777601897","wikidata":"https://www.wikidata.org/wiki/Q3409113","display_name":"Presentation (obstetrics)","level":2,"score":0.45649999380111694},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4016999900341034},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.365200012922287},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.34380000829696655},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.319599986076355},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.31279999017715454},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.29420000314712524},{"id":"https://openalex.org/C171686336","wikidata":"https://www.wikidata.org/wiki/Q3532085","display_name":"Topic model","level":2,"score":0.2921000123023987},{"id":"https://openalex.org/C35639132","wikidata":"https://www.wikidata.org/wiki/Q7452468","display_name":"Sequence labeling","level":3,"score":0.2784999907016754},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.2599000036716461},{"id":"https://openalex.org/C159877910","wikidata":"https://www.wikidata.org/wiki/Q2202883","display_name":"Autoregressive model","level":2,"score":0.25949999690055847},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.25760000944137573},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2547999918460846},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.2515000104904175},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.25130000710487366},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.2508000135421753}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s13755-025-00400-3","is_oa":false,"landing_page_url":"https://doi.org/10.1007/s13755-025-00400-3","pdf_url":null,"source":{"id":"https://openalex.org/S4210178793","display_name":"Health Information Science and Systems","issn_l":"2047-2501","issn":["2047-2501"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health Information Science and Systems","raw_type":"journal-article"},{"id":"pmid:41281609","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41281609","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Health information science and systems","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W75790607","https://openalex.org/W1610821757","https://openalex.org/W1679133234","https://openalex.org/W1850865022","https://openalex.org/W2005058680","https://openalex.org/W2040298461","https://openalex.org/W2071879021","https://openalex.org/W2094591616","https://openalex.org/W2097678794","https://openalex.org/W2100627415","https://openalex.org/W2120754707","https://openalex.org/W2122496897","https://openalex.org/W2145386458","https://openalex.org/W2149369282","https://openalex.org/W2151025545","https://openalex.org/W2154142897","https://openalex.org/W2169099542","https://openalex.org/W2169974160","https://openalex.org/W2170189740","https://openalex.org/W2229453122","https://openalex.org/W2346452181","https://openalex.org/W2414451196","https://openalex.org/W2604990811","https://openalex.org/W2883897757","https://openalex.org/W2911489562","https://openalex.org/W2915623326","https://openalex.org/W2937192905","https://openalex.org/W2950021574","https://openalex.org/W2963341956","https://openalex.org/W2970998014","https://openalex.org/W3046375318","https://openalex.org/W3141797743","https://openalex.org/W3156936474","https://openalex.org/W4200455891","https://openalex.org/W4221142212","https://openalex.org/W4221153690","https://openalex.org/W4226265641","https://openalex.org/W4283318325","https://openalex.org/W4309659061","https://openalex.org/W4376274483","https://openalex.org/W4391292768","https://openalex.org/W4393832072","https://openalex.org/W4393936594","https://openalex.org/W4394547164","https://openalex.org/W4402697996","https://openalex.org/W4403488282","https://openalex.org/W4405427397","https://openalex.org/W4406261213","https://openalex.org/W4408501948","https://openalex.org/W4409190866","https://openalex.org/W6926259797"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-13T07:31:44.756512","created_date":"2025-11-23T00:00:00"}
