{"id":"https://openalex.org/W2972051378","doi":"https://doi.org/10.1186/s12859-019-3030-z","title":"Multiple-level biomedical event trigger recognition with transfer learning","display_name":"Multiple-level biomedical event trigger recognition with transfer learning","publication_year":2019,"publication_date":"2019-09-06","ids":{"openalex":"https://openalex.org/W2972051378","doi":"https://doi.org/10.1186/s12859-019-3030-z","mag":"2972051378","pmid":"https://pubmed.ncbi.nlm.nih.gov/31492112"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-3030-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3030-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3030-z","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://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3030-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101401584","display_name":"Yifei Chen","orcid":"https://orcid.org/0000-0001-8251-6630"},"institutions":[{"id":"https://openalex.org/I206777745","display_name":"Nanjing Audit University","ror":"https://ror.org/04zj2bd87","country_code":"CN","type":"education","lineage":["https://openalex.org/I206777745"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yifei Chen","raw_affiliation_strings":["School of Information Engineering, Nanjing Audit University, 86 West Yushan Road, Nanjing, China. yifeichen91@nau.edu.cn","School of Information Engineering, Nanjing Audit University, 86 West Yushan Road, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0001-8251-6630","affiliations":[{"raw_affiliation_string":"School of Information Engineering, Nanjing Audit University, 86 West Yushan Road, Nanjing, China. yifeichen91@nau.edu.cn","institution_ids":["https://openalex.org/I206777745"]},{"raw_affiliation_string":"School of Information Engineering, Nanjing Audit University, 86 West Yushan Road, Nanjing, China","institution_ids":["https://openalex.org/I206777745"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5101401584"],"corresponding_institution_ids":["https://openalex.org/I206777745"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3036,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.5497454,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"20","issue":"1","first_page":"459","last_page":"459"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9674999713897705,"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":0.9674999713897705,"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":0.006899999920278788,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.00559999980032444,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.8548007607460022},{"id":"https://openalex.org/keywords/transfer-of-learning","display_name":"Transfer of learning","score":0.7352397441864014},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6884962320327759},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.6675276756286621},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6189374327659607},{"id":"https://openalex.org/keywords/biomedical-text-mining","display_name":"Biomedical text mining","score":0.5621762871742249},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.5594423413276672},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5492609739303589},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5387194752693176},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4826365113258362},{"id":"https://openalex.org/keywords/multi-task-learning","display_name":"Multi-task learning","score":0.4622615873813629},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43655872344970703},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3432387411594391},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34139037132263184},{"id":"https://openalex.org/keywords/text-mining","display_name":"Text mining","score":0.19905486702919006}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8548007607460022},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.7352397441864014},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6884962320327759},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.6675276756286621},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6189374327659607},{"id":"https://openalex.org/C165141518","wikidata":"https://www.wikidata.org/wiki/Q4915126","display_name":"Biomedical text mining","level":3,"score":0.5621762871742249},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.5594423413276672},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5492609739303589},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5387194752693176},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4826365113258362},{"id":"https://openalex.org/C28006648","wikidata":"https://www.wikidata.org/wiki/Q6934509","display_name":"Multi-task learning","level":3,"score":0.4622615873813629},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43655872344970703},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3432387411594391},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34139037132263184},{"id":"https://openalex.org/C71472368","wikidata":"https://www.wikidata.org/wiki/Q676880","display_name":"Text mining","level":2,"score":0.19905486702919006},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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/s12859-019-3030-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3030-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3030-z","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:31492112","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31492112","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:af733ec273924b5e9ea1c829d6b9da57","is_oa":false,"landing_page_url":"https://doaj.org/article/af733ec273924b5e9ea1c829d6b9da57","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-15 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6731566","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6731566","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-3030-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-3030-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-3030-z","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/G6315894205","display_name":null,"funder_award_id":"BK20171495","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"},{"id":"https://openalex.org/G7557194285","display_name":null,"funder_award_id":"No.BK20171495","funder_id":"https://openalex.org/F4320322769","funder_display_name":"Natural Science Foundation of Jiangsu Province"}],"funders":[{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"},{"id":"https://openalex.org/F4320322769","display_name":"Natural Science Foundation of Jiangsu Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2972051378.pdf","grobid_xml":"https://content.openalex.org/works/W2972051378.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W76749362","https://openalex.org/W1514621373","https://openalex.org/W1553529581","https://openalex.org/W1810943226","https://openalex.org/W1847618513","https://openalex.org/W1940872118","https://openalex.org/W1978486653","https://openalex.org/W1988622308","https://openalex.org/W2032566933","https://openalex.org/W2064675550","https://openalex.org/W2075655036","https://openalex.org/W2088634345","https://openalex.org/W2098722636","https://openalex.org/W2098830640","https://openalex.org/W2099369363","https://openalex.org/W2101918096","https://openalex.org/W2108706252","https://openalex.org/W2108791029","https://openalex.org/W2133013156","https://openalex.org/W2143419558","https://openalex.org/W2146864948","https://openalex.org/W2147788440","https://openalex.org/W2147880316","https://openalex.org/W2149803936","https://openalex.org/W2165698076","https://openalex.org/W2171283231","https://openalex.org/W2250389961","https://openalex.org/W2251771443","https://openalex.org/W2271840356","https://openalex.org/W2296283641","https://openalex.org/W2317130090","https://openalex.org/W2469171125","https://openalex.org/W2493342586","https://openalex.org/W2527896214","https://openalex.org/W2604986524","https://openalex.org/W2615487675","https://openalex.org/W2617927774","https://openalex.org/W2763438644","https://openalex.org/W2781528640","https://openalex.org/W2806486415","https://openalex.org/W2914431807","https://openalex.org/W2923652028","https://openalex.org/W2949176808","https://openalex.org/W2950938254","https://openalex.org/W2963522845","https://openalex.org/W2963826794","https://openalex.org/W2964352358"],"related_works":["https://openalex.org/W3149011051","https://openalex.org/W2134429551","https://openalex.org/W3004288456","https://openalex.org/W2548624545","https://openalex.org/W2821676139","https://openalex.org/W2017675085","https://openalex.org/W3043695725","https://openalex.org/W4288094423","https://openalex.org/W4382138864","https://openalex.org/W2980250610"],"abstract_inverted_index":{"BACKGROUND:":[0],"Automatic":[1],"extraction":[2],"of":[3,21,39,66,225,244,247,262,290,336],"biomedical":[4],"events":[5,31],"from":[6,60,230],"literature":[7,62],"is":[8,32,55,146,200,301],"an":[9],"important":[10],"task":[11,51],"in":[12,36,52,134],"the":[13,22,37,47,61,75,101,113,118,143,184,196,206,211,222,231,245,267,280,284,288,291,307,316,332,337,340],"understanding":[14],"biological":[15,67],"systems,":[16],"allowing":[17],"for":[18,130],"faster":[19],"update":[20],"latest":[23],"discoveries":[24],"automatically.":[25],"Detecting":[26],"trigger":[27,132,160],"words":[28],"which":[29,135,175,319],"indicate":[30],"a":[33,88,136,152,165,215],"critical":[34],"step":[35],"process":[38],"event":[40,58],"extraction,":[41],"because":[42],"following":[43],"steps":[44],"depend":[45],"on":[46,87,100,112,142,151,266,339],"recognized":[48],"triggers.":[49],"The":[50,272,297,312],"this":[53,122],"study":[54],"to":[56,71,98,126,148,202,209],"identify":[57],"triggers":[59,213],"across":[63],"multiple":[64,102],"levels":[65],"organization.":[68],"In":[69,121,195],"order":[70],"achieve":[72],"high":[73],"performances,":[74],"machine":[76],"learning":[77,129,171,275],"based":[78],"approaches,":[79],"such":[80],"as":[81,178,181,214,239],"neural":[82,168],"networks,":[83],"must":[84],"be":[85,96],"trained":[86],"dataset":[89,138],"with":[90,139,155,228,283],"plentiful":[91],"annotations.":[92],"However,":[93],"annotations":[94,141,157],"might":[95],"difficult":[97],"obtain":[99],"levels,":[103],"and":[104,115,158,173,186,204,233,293,334],"annotated":[105],"resources":[106],"have":[107],"so":[108],"far":[109],"mainly":[110],"focused":[111],"relations":[114],"processes":[116],"at":[117],"molecular":[119,144],"level.":[120],"work,":[123],"we":[124],"aim":[125],"apply":[127],"transfer":[128,170,274],"multiple-level":[131,212],"recognition,":[133],"source":[137,185,240,292],"sufficient":[140],"level":[145],"utilized":[147],"improve":[149,279,331],"performance":[150,257,281,333],"target":[153,187,216,294,341],"domain":[154,342],"insufficient":[156],"more":[159,321,326],"types.":[161],"RESULTS:":[162],"We":[163],"propose":[164],"generalized":[166],"cross-domain":[167],"network":[169],"architecture":[172],"approach,":[174],"can":[176,277],"share":[177],"much":[179],"knowledge":[180],"possible":[182],"between":[183,329],"domains,":[188],"especially":[189],"when":[190,287],"their":[191],"label":[192],"sets":[193],"overlap.":[194,296],"experiments,":[197],"MLEE":[198,229,269],"corpus":[199],"used":[201,238],"train":[203],"test":[205],"proposed":[207,250,273],"model":[208,338],"recognize":[210],"dataset.":[217],"Two":[218],"different":[219],"corpora":[220],"having":[221],"varying":[223],"degrees":[224],"overlapping":[226],"labels":[227,289],"BioNLP'09":[232],"BioNLP'11":[234],"Shared":[235],"Tasks":[236],"are":[237,310],"datasets,":[241],"respectively.":[242],"Regardless":[243],"degree":[246],"overlap,":[248],"our":[249,303],"approach":[251,304],"achieves":[252],"recognition":[253],"improvement.":[254],"Moreover,":[255],"its":[256],"exceeds":[258],"previously":[259],"reported":[260],"results":[261],"other":[263],"leading":[264],"systems":[265],"same":[268],"corpus.":[270],"CONCLUSIONS:":[271],"method":[276],"further":[278],"compared":[282],"traditional":[285],"method,":[286],"datasets":[295],"most":[298],"essential":[299],"reason":[300],"that":[302],"has":[305],"changed":[306],"way":[308],"parameters":[309,328],"shared.":[311],"vertical":[313],"sharing":[314],"replaces":[315],"horizontal":[317],"sharing,":[318],"brings":[320],"sharable":[322],"parameters.":[323],"Hence,":[324],"these":[325],"shared":[327],"networks":[330],"generalization":[335],"effectively.":[343]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
