{"id":"https://openalex.org/W2969181382","doi":"https://doi.org/10.1186/s12859-019-3000-5","title":"Multitask learning for biomedical named entity recognition with cross-sharing structure","display_name":"Multitask learning for biomedical named entity recognition with cross-sharing structure","publication_year":2019,"publication_date":"2019-08-16","ids":{"openalex":"https://openalex.org/W2969181382","doi":"https://doi.org/10.1186/s12859-019-3000-5","mag":"2969181382","pmid":"https://pubmed.ncbi.nlm.nih.gov/31419937"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3000-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3000-5","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1186/s12859-019-3000-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100442261","display_name":"Xi Wang","orcid":"https://orcid.org/0000-0002-5218-2761"},"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":"Xi Wang","raw_affiliation_strings":["State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014720744","display_name":"Jiagao Lyu","orcid":null},"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":"Jiagao Lyu","raw_affiliation_strings":["State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103661051","display_name":"Li Dong","orcid":null},"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":"Li Dong","raw_affiliation_strings":["State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China","institution_ids":["https://openalex.org/I82880672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107234003","display_name":"Ke Xu","orcid":"https://orcid.org/0000-0001-5447-8008"},"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":"Ke Xu","raw_affiliation_strings":["State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China. kexu@nlsde.buaa.edu.cn","State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China. kexu@nlsde.buaa.edu.cn","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Software Development Environment, Beihang University, Beijing, 100191, China","institution_ids":["https://openalex.org/I82880672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100442261"],"corresponding_institution_ids":["https://openalex.org/I82880672"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8804,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.86323356,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"20","issue":"1","first_page":"427","last_page":"427"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.682200014591217,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.682200014591217,"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/T10028","display_name":"Topic Modeling","score":0.2093999981880188,"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":0.051600001752376556,"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":0.8431183695793152},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6950108408927917},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6754565238952637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6274452805519104},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.4936579167842865},{"id":"https://openalex.org/keywords/multi-task-learning","display_name":"Multi-task learning","score":0.4785081446170807},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4653295874595642},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4356222450733185},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42723196744918823}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8431183695793152},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6950108408927917},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6754565238952637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6274452805519104},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.4936579167842865},{"id":"https://openalex.org/C28006648","wikidata":"https://www.wikidata.org/wiki/Q6934509","display_name":"Multi-task learning","level":3,"score":0.4785081446170807},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4653295874595642},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4356222450733185},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42723196744918823},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D033181","descriptor_name":"Information Dissemination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035843","descriptor_name":"Biomedical Research","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-019-3000-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3000-5","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31419937","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31419937","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:d805fe426fe34421a9f6eceae62433ac","is_oa":true,"landing_page_url":"https://doaj.org/article/d805fe426fe34421a9f6eceae62433ac","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-13 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5651584","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6697996","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3000-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3000-5","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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/G7692177269","display_name":null,"funder_award_id":"SKLSDE- 2017ZX-05","funder_id":"https://openalex.org/F4320326978","funder_display_name":"State Key Laboratory of Software Development Environment"},{"id":"https://openalex.org/G8055127673","display_name":null,"funder_award_id":"61421003","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/F4320326978","display_name":"State Key Laboratory of Software Development Environment","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W55204438","https://openalex.org/W1532940542","https://openalex.org/W1583837637","https://openalex.org/W1592053870","https://openalex.org/W1847618513","https://openalex.org/W1882958252","https://openalex.org/W2028689806","https://openalex.org/W2042595143","https://openalex.org/W2063073888","https://openalex.org/W2064675550","https://openalex.org/W2091155135","https://openalex.org/W2097851570","https://openalex.org/W2100627415","https://openalex.org/W2112657663","https://openalex.org/W2117130368","https://openalex.org/W2139259976","https://openalex.org/W2147880316","https://openalex.org/W2160022416","https://openalex.org/W2169491861","https://openalex.org/W2205981794","https://openalex.org/W2296283641","https://openalex.org/W2335791510","https://openalex.org/W2408811052","https://openalex.org/W2499659094","https://openalex.org/W2560674852","https://openalex.org/W2608568997","https://openalex.org/W2622687477","https://openalex.org/W2734608416","https://openalex.org/W2743028754","https://openalex.org/W2888872222","https://openalex.org/W2890830728","https://openalex.org/W2901677401","https://openalex.org/W2906566809","https://openalex.org/W2911489562","https://openalex.org/W2913668833","https://openalex.org/W2941868238","https://openalex.org/W2949159188","https://openalex.org/W2962902328","https://openalex.org/W2963024368","https://openalex.org/W2963339489","https://openalex.org/W2963625095","https://openalex.org/W3105491236","https://openalex.org/W4237040408"],"related_works":["https://openalex.org/W3199871245","https://openalex.org/W2915436880","https://openalex.org/W3123942215","https://openalex.org/W4285819037","https://openalex.org/W3198729192","https://openalex.org/W3121292129","https://openalex.org/W1964783010","https://openalex.org/W2983934248","https://openalex.org/W1605730749","https://openalex.org/W2951720331"],"abstract_inverted_index":{"BACKGROUND:":[0],"Biomedical":[1],"named":[2],"entity":[3,143,206],"recognition":[4],"(BioNER)":[5],"is":[6,221],"a":[7,162],"fundamental":[8],"and":[9,42,85,103,137,203],"essential":[10],"task":[11],"for":[12,166,216],"biomedical":[13,69],"literature":[14,70],"mining,":[15],"which":[16],"affects":[17],"the":[18,87,108,120,129,139,169,174,193],"performance":[19,88,121,175],"of":[20,68,80,89,112,122,132,141,176,187,201,211],"downstream":[21],"tasks.":[22],"Most":[23],"BioNER":[24,73,167],"models":[25,50,67,102],"rely":[26],"on":[27,110],"domain-specific":[28],"features":[29,35,81,188],"or":[30],"hand-crafted":[31],"rules,":[32],"but":[33],"extracting":[34],"from":[36,82,189],"massive":[37],"data":[38],"requires":[39],"much":[40],"time":[41],"human":[43],"efforts.":[44],"To":[45],"solve":[46],"this,":[47],"neural":[48,65],"network":[49,66],"are":[51],"used":[52],"to":[53,64,126,172],"automatically":[54],"learn":[55],"features.":[56],"Recently,":[57],"multi-task":[58,76,101,164,177,217],"learning":[59,77],"has":[60],"been":[61],"applied":[62],"successfully":[63],"mining.":[71],"For":[72],"models,":[74],"using":[75,146],"makes":[78,185],"use":[79,186],"multiple":[83],"datasets":[84,111,191,202],"improves":[86],"models.":[90,178],"RESULTS:":[91],"In":[92],"experiments,":[93],"we":[94,135],"compared":[95],"our":[96,105,153,183],"proposed":[97],"model":[98,106,154,165,184],"with":[99,168],"other":[100],"found":[104],"outperformed":[107],"others":[109],"gene,":[113],"protein,":[114],"disease":[115],"categories.":[116],"We":[117,160],"also":[118],"tested":[119],"different":[123,142],"dataset":[124,149,214],"pairs":[125,215],"find":[127],"out":[128],"best":[130,199],"partners":[131,200],"datasets.":[133],"Besides,":[134],"explored":[136],"analyzed":[138],"influence":[140,204],"types":[144],"by":[145],"sub-datasets.":[147],"When":[148],"size":[150],"was":[151],"reduced,":[152],"still":[155],"produced":[156],"positive":[157],"results.":[158],"CONCLUSION:":[159],"propose":[161],"novel":[163],"cross-sharing":[170,180],"structure":[171,181],"improve":[173],"The":[179],"in":[182,192],"both":[190],"training":[194],"procedure.":[195],"Detailed":[196],"analysis":[197],"about":[198],"between":[205],"categories":[207],"can":[208],"provide":[209],"guidance":[210],"choosing":[212],"proper":[213],"training.":[218],"Our":[219],"implementation":[220],"available":[222],"at":[223],"https://github.com/JogleLew/bioner-cross-sharing":[224],".":[225]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":9},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
