{"id":"https://openalex.org/W4283585122","doi":"https://doi.org/10.1093/bioinformatics/btac422","title":"Improving biomedical named entity recognition by dynamic caching inter-sentence information","display_name":"Improving biomedical named entity recognition by dynamic caching inter-sentence information","publication_year":2022,"publication_date":"2022-06-27","ids":{"openalex":"https://openalex.org/W4283585122","doi":"https://doi.org/10.1093/bioinformatics/btac422","pmid":"https://pubmed.ncbi.nlm.nih.gov/35758612"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/3976/49889952/btac422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/3976/49889952/btac422.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006839003","display_name":"Yiqi Tong","orcid":"https://orcid.org/0000-0002-6671-9208"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiqi Tong","raw_affiliation_strings":["Institute of Artificial Intelligence, Beihang University , Beijing 100191, China"],"raw_orcid":"https://orcid.org/0000-0002-6671-9208","affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041921496","display_name":"Fuzhen Zhuang","orcid":"https://orcid.org/0000-0001-9170-7009"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Fuzhen Zhuang","raw_affiliation_strings":["Institute of Artificial Intelligence, Beihang University , Beijing 100191, China","SKLSDE, School of Computer Science, Beihang University , Beijing 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]},{"raw_affiliation_string":"SKLSDE, School of Computer Science, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101507883","display_name":"Huajie Zhang","orcid":"https://orcid.org/0009-0004-3730-710X"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huajie Zhang","raw_affiliation_strings":["Institute of Artificial Intelligence, Beihang University , Beijing 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103003095","display_name":"Chuyu Fang","orcid":"https://orcid.org/0009-0007-8353-7979"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chuyu Fang","raw_affiliation_strings":["Institute of Artificial Intelligence, Beihang University , Beijing 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Artificial Intelligence, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100660064","display_name":"Yu Zhao","orcid":"https://orcid.org/0000-0002-8454-0025"},"institutions":[{"id":"https://openalex.org/I204831749","display_name":"Southwestern University of Finance and Economics","ror":"https://ror.org/04ewct822","country_code":"CN","type":"education","lineage":["https://openalex.org/I204831749"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Zhao","raw_affiliation_strings":["School of Computing and Artificial Intelligence, Southwestern University of Finance and Economics , Chengdu 611130, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Artificial Intelligence, Southwestern University of Finance and Economics , Chengdu 611130, China","institution_ids":["https://openalex.org/I204831749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100612161","display_name":"Deqing Wang","orcid":"https://orcid.org/0000-0001-6441-4390"},"institutions":[{"id":"https://openalex.org/I82880672","display_name":"Beihang University","ror":"https://ror.org/00wk2mp56","country_code":"CN","type":"education","lineage":["https://openalex.org/I82880672"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Deqing Wang","raw_affiliation_strings":["SKLSDE, School of Computer Science, Beihang University , Beijing 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SKLSDE, School of Computer Science, Beihang University , Beijing 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049015446","display_name":"Hengshu Zhu","orcid":"https://orcid.org/0000-0003-4570-643X"},"institutions":[{"id":"https://openalex.org/I98301712","display_name":"Baidu (China)","ror":"https://ror.org/03vs3wt56","country_code":"CN","type":"company","lineage":["https://openalex.org/I98301712"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hengshu Zhu","raw_affiliation_strings":["Baidu Inc , Beijing 100085, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Baidu Inc , Beijing 100085, China","institution_ids":["https://openalex.org/I98301712"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107299529","display_name":"Bin Ni","orcid":"https://orcid.org/0009-0004-8937-4566"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bin Ni","raw_affiliation_strings":["Xiamen Data Intelligence Academy of ICT, CAS , Xiamen 361021, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiamen Data Intelligence Academy of ICT, CAS , Xiamen 361021, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041921496"],"corresponding_institution_ids":["https://openalex.org/I82880672"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2754,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.82205996,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"38","issue":"16","first_page":"3976","last_page":"3983"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.6103000044822693,"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":0.6103000044822693,"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":0.31040000915527344,"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":0.008200000040233135,"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":0.8201881647109985},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.6817336082458496},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5230192542076111},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4995427131652832},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4913693964481354},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.34404343366622925}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8201881647109985},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.6817336082458496},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5230192542076111},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4995427131652832},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4913693964481354},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.34404343366622925},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","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":true},{"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/3976/49889952/btac422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35758612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35758612","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac422","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac422","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/16/3976/49889952/btac422.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G245388120","display_name":null,"funder_award_id":"62176014","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G461350835","display_name":null,"funder_award_id":"U1836206","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"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283585122.pdf","grobid_xml":"https://content.openalex.org/works/W4283585122.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1666916593","https://openalex.org/W2095705004","https://openalex.org/W2127836646","https://openalex.org/W2154142897","https://openalex.org/W2169099542","https://openalex.org/W2174828870","https://openalex.org/W2250539671","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2734608416","https://openalex.org/W2740887992","https://openalex.org/W2753709519","https://openalex.org/W2769387903","https://openalex.org/W2799051177","https://openalex.org/W2890830728","https://openalex.org/W2911489562","https://openalex.org/W2925613093","https://openalex.org/W2948909602","https://openalex.org/W2962712961","https://openalex.org/W2963339489","https://openalex.org/W2963854351","https://openalex.org/W2964289193","https://openalex.org/W2971258845","https://openalex.org/W3107083523","https://openalex.org/W3114784081","https://openalex.org/W3115095335","https://openalex.org/W3137481621","https://openalex.org/W3157876196","https://openalex.org/W3172340245","https://openalex.org/W3175873000","https://openalex.org/W4238846128","https://openalex.org/W4239019441","https://openalex.org/W6674330103"],"related_works":["https://openalex.org/W3199871245","https://openalex.org/W3005759282","https://openalex.org/W3017222382","https://openalex.org/W3128216712","https://openalex.org/W3204019825","https://openalex.org/W3136915866","https://openalex.org/W4390279576","https://openalex.org/W2886890203","https://openalex.org/W4313535650","https://openalex.org/W2287770975"],"abstract_inverted_index":{"MOTIVATION:":[0],"Biomedical":[1],"Named":[2],"Entity":[3],"Recognition":[4],"(BioNER)":[5],"aims":[6],"to":[7,53,103,118,143,162,183,197],"identify":[8],"biomedical":[9,195],"domain-specific":[10],"entities":[11],"(e.g.":[12],"gene,":[13],"chemical":[14],"and":[15,46,178,219],"disease)":[16],"from":[17,148],"unstructured":[18],"texts.":[19],"Despite":[20],"deep":[21],"learning-based":[22],"methods":[23,39],"for":[24,34,122],"BioNER":[25,61,87],"achieving":[26],"satisfactory":[27],"results,":[28],"there":[29,82],"is":[30,69,160],"still":[31,84],"much":[32],"room":[33],"improvement.":[35],"Firstly,":[36],"most":[37],"existing":[38],"use":[40],"independent":[41],"sentences":[42],"as":[43,77,151],"training":[44],"units":[45],"ignore":[47],"inter-sentence":[48,67,92,99,120,220],"context,":[49],"which":[50],"usually":[51],"leads":[52],"the":[54,66,105,125,137,149,152,171,199,208],"labeling":[55],"inconsistency":[56],"problem.":[57],"Secondly,":[58],"previous":[59],"document-level":[60],"works":[62],"have":[63,90],"approved":[64],"that":[65,89],"information":[68,73,121],"essential,":[70],"but":[71,113],"what":[72],"should":[74],"be":[75,226],"regarded":[76],"context":[78],"remains":[79],"ambiguous.":[80],"Moreover,":[81],"are":[83,234],"few":[85],"pre-training-based":[86],"models":[88],"introduced":[91],"information.":[93],"Hence,":[94],"we":[95,173],"propose":[96,110],"a":[97,111,140,175,180,190],"cache-based":[98],"model":[100,138,200],"called":[101],"BioNER-Cache":[102,213],"alleviate":[104],"aforementioned":[106],"problems.":[107],"RESULTS:":[108],"We":[109,188],"simple":[112],"effective":[114],"dynamic":[115],"caching":[116,134],"module":[117],"capture":[119],"BioNER.":[123],"Specifically,":[124],"cache":[126,150],"stores":[127],"recent":[128],"hidden":[129],"representations":[130],"constrained":[131],"by":[132],"predefined":[133],"rules.":[135],"And":[136],"uses":[139],"query-and-read":[141],"mechanism":[142],"retrieve":[144],"similar":[145],"historical":[146],"records":[147],"local":[153],"context.":[154],"Then,":[155],"an":[156],"attention-based":[157],"gated":[158],"network":[159],"adopted":[161],"generate":[163],"context-related":[164],"features":[165],"with":[166,215],"BioBERT.":[167],"To":[168],"dynamically":[169],"update":[170],"cache,":[172],"design":[174],"scoring":[176],"function":[177],"implement":[179],"multi-task":[181],"approach":[182],"jointly":[184],"train":[185],"our":[186,211],"model.":[187],"build":[189],"comprehensive":[191],"benchmark":[192],"on":[193],"four":[194],"datasets":[196],"evaluate":[198],"performance":[201],"fairly.":[202],"Finally,":[203],"extensive":[204],"experiments":[205],"clearly":[206],"validate":[207],"superiority":[209],"of":[210],"proposed":[212],"compared":[214],"various":[216],"state-of-the-art":[217],"intra-sentence":[218],"baselines.":[221],"AVAILABILITYAND":[222],"IMPLEMENTATION:":[223],"Code":[224],"will":[225],"available":[227,235],"at":[228,236],"https://github.com/zgzjdx/BioNER-Cache.":[229],"SUPPLEMENTARY":[230],"INFORMATION:":[231],"Supplementary":[232],"data":[233],"Bioinformatics":[237],"online.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4}],"updated_date":"2026-07-17T09:13:05.818461","created_date":"2025-10-10T00:00:00"}
