{"id":"https://openalex.org/W4407911766","doi":"https://doi.org/10.1186/s12859-025-06086-4","title":"Enhancing biomedical named entity recognition with parallel boundary detection and category classification","display_name":"Enhancing biomedical named entity recognition with parallel boundary detection and category classification","publication_year":2025,"publication_date":"2025-02-25","ids":{"openalex":"https://openalex.org/W4407911766","doi":"https://doi.org/10.1186/s12859-025-06086-4","pmid":"https://pubmed.ncbi.nlm.nih.gov/40000968"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06086-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06086-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06086-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06086-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071054399","display_name":"Yu Wang","orcid":"https://orcid.org/0000-0003-1606-6795"},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu Wang","raw_affiliation_strings":["School of Science, China Pharmaceutical University, Nanjing, China. wangyu@cpu.edu.cn","School of Science, China Pharmaceutical University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"School of Science, China Pharmaceutical University, Nanjing, China. wangyu@cpu.edu.cn","institution_ids":[]},{"raw_affiliation_string":"School of Science, China Pharmaceutical University, Nanjing, China","institution_ids":["https://openalex.org/I161716053"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068043486","display_name":"Hanghang Tong","orcid":"https://orcid.org/0000-0003-4405-3887"},"institutions":[{"id":"https://openalex.org/I157725225","display_name":"University of Illinois Urbana-Champaign","ror":"https://ror.org/047426m28","country_code":"US","type":"education","lineage":["https://openalex.org/I157725225"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hanghang Tong","raw_affiliation_strings":["Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA","institution_ids":["https://openalex.org/I157725225"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049800310","display_name":"Ziye Zhu","orcid":"https://orcid.org/0000-0001-6072-4738"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziye Zhu","raw_affiliation_strings":["Jiangsu Key Laboratory of Big Data Security and Intelligent Processing, Nanjing University of Posts and Telecommunications, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"Jiangsu Key Laboratory of Big Data Security and Intelligent Processing, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022687558","display_name":"Fengzhen Hou","orcid":null},"institutions":[{"id":"https://openalex.org/I161716053","display_name":"China Pharmaceutical University","ror":"https://ror.org/01sfm2718","country_code":"CN","type":"education","lineage":["https://openalex.org/I161716053"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fengzhen Hou","raw_affiliation_strings":["School of Science, China Pharmaceutical University, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"School of Science, China Pharmaceutical University, Nanjing, China","institution_ids":["https://openalex.org/I161716053"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076360288","display_name":"Yun Li","orcid":"https://orcid.org/0000-0002-2079-9484"},"institutions":[{"id":"https://openalex.org/I41198531","display_name":"Nanjing University of Posts and Telecommunications","ror":"https://ror.org/043bpky34","country_code":"CN","type":"education","lineage":["https://openalex.org/I41198531"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun Li","raw_affiliation_strings":["Jiangsu Key Laboratory of Big Data Security and Intelligent Processing, Nanjing University of Posts and Telecommunications, Nanjing, China"],"affiliations":[{"raw_affiliation_string":"Jiangsu Key Laboratory of Big Data Security and Intelligent Processing, Nanjing University of Posts and Telecommunications, Nanjing, China","institution_ids":["https://openalex.org/I41198531"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5071054399"],"corresponding_institution_ids":["https://openalex.org/I161716053"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":9.0838,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.9713694,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"26","issue":"1","first_page":"63","last_page":"63"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9973999857902527,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9940000176429749,"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/computer-science","display_name":"Computer science","score":0.6221587061882019},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5333195924758911},{"id":"https://openalex.org/keywords/boundary","display_name":"Boundary (topology)","score":0.4535067081451416},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.448365181684494},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.41654258966445923},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3953564465045929},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33853548765182495},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33254045248031616},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2069406509399414},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13437935709953308},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10447078943252563}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6221587061882019},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5333195924758911},{"id":"https://openalex.org/C62354387","wikidata":"https://www.wikidata.org/wiki/Q875399","display_name":"Boundary (topology)","level":2,"score":0.4535067081451416},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.448365181684494},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.41654258966445923},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3953564465045929},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33853548765182495},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33254045248031616},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2069406509399414},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13437935709953308},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10447078943252563},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06086-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06086-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06086-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40000968","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40000968","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:5fea6e5c9b634c68bb92ed9ef53a6215","is_oa":true,"landing_page_url":"https://doaj.org/article/5fea6e5c9b634c68bb92ed9ef53a6215","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-20 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11863403","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11863403","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06086-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06086-4","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06086-4","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1272427771","display_name":null,"funder_award_id":"BK20240647","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"},{"id":"https://openalex.org/G1415560127","display_name":null,"funder_award_id":"62306339","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3851893033","display_name":null,"funder_award_id":"62406148","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5310864386","display_name":null,"funder_award_id":"62476137","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4407911766.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1981276685","https://openalex.org/W2090630554","https://openalex.org/W2108218871","https://openalex.org/W2142920810","https://openalex.org/W2147880316","https://openalex.org/W2150766729","https://openalex.org/W2519969774","https://openalex.org/W2552110825","https://openalex.org/W2800535933","https://openalex.org/W2804221886","https://openalex.org/W2911489562","https://openalex.org/W2950697450","https://openalex.org/W2963351448","https://openalex.org/W2963571583","https://openalex.org/W2971019153","https://openalex.org/W2989149555","https://openalex.org/W2998456908","https://openalex.org/W3011594683","https://openalex.org/W3013678667","https://openalex.org/W3034744126","https://openalex.org/W3035058125","https://openalex.org/W3035375600","https://openalex.org/W3035625205","https://openalex.org/W3046375318","https://openalex.org/W3090015871","https://openalex.org/W3094130398","https://openalex.org/W3101188882","https://openalex.org/W3105240624","https://openalex.org/W3154065069","https://openalex.org/W3175301415","https://openalex.org/W3196105425","https://openalex.org/W3198080531","https://openalex.org/W3207397751","https://openalex.org/W3213175220","https://openalex.org/W4200058434","https://openalex.org/W4309323789","https://openalex.org/W4319594167","https://openalex.org/W4376274483","https://openalex.org/W4377695655","https://openalex.org/W4385571159","https://openalex.org/W4385571881","https://openalex.org/W4393094733"],"related_works":["https://openalex.org/W3199871245","https://openalex.org/W2915436880","https://openalex.org/W1964783010","https://openalex.org/W3017222382","https://openalex.org/W3128216712","https://openalex.org/W3136915866","https://openalex.org/W4390279576","https://openalex.org/W2886890203","https://openalex.org/W4313535650","https://openalex.org/W2287770975"],"abstract_inverted_index":{"The":[0],"proposed":[1],"BEAN":[2],"is":[3,25],"elaborately":[4],"designed":[5],"to":[6,30,46,65,75],"achieve":[7],"two":[8],"key":[9],"objectives":[10],"of":[11,58],"the":[12,26,56,63,72],"BioNER":[13,28,73],"task:":[14],"clearly":[15],"detecting":[16],"entity":[17,22,49,77],"boundaries":[18,50],"and":[19,34,43],"correctly":[20],"classifying":[21],"categories.":[23],"It":[24],"first":[27,64],"model":[29,70],"handle":[31],"nested":[32],"structures":[33],"category":[35,78],"correlations":[36],"in":[37],"parallel.":[38],"We":[39],"exploit":[40],"head,":[41],"tail,":[42],"contextualized":[44],"features":[45],"efficiently":[47],"detect":[48],"via":[51],"a":[52,67],"triaffine":[53],"model.":[54],"To":[55],"best":[57],"our":[59],"knowledge,":[60],"we":[61],"are":[62],"introduce":[66],"multi-label":[68],"classification":[69],"for":[71],"task":[74],"extract":[76],"information":[79],"without":[80],"boundary":[81],"guidance.":[82]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
