{"id":"https://openalex.org/W2769387903","doi":"https://doi.org/10.1093/bioinformatics/btx761","title":"An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition","display_name":"An attention-based BiLSTM-CRF approach to document-level chemical named entity recognition","publication_year":2017,"publication_date":"2017-11-23","ids":{"openalex":"https://openalex.org/W2769387903","doi":"https://doi.org/10.1093/bioinformatics/btx761","mag":"2769387903"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1381/25119984/btx761.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1381/25119984/btx761.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051597671","display_name":"Zhihao Yang","orcid":"https://orcid.org/0000-0001-6186-2024"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhihao Yang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102940794","display_name":"Pei Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pei Yang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100343737","display_name":"Yin Zhang","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yin Zhang","raw_affiliation_strings":["Beijing Institute of Health Administration and Medical Information, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beijing Institute of Health Administration and Medical Information, Beijing, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736263","display_name":"Lei Wang","orcid":"https://orcid.org/0000-0002-8420-6860"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Lei Wang","raw_affiliation_strings":["Beijing Institute of Health Administration and Medical Information, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Beijing Institute of Health Administration and Medical Information, Beijing, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023931221","display_name":"Hongfei Lin","orcid":"https://orcid.org/0000-0003-0872-7688"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Lin","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100370452","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0002-4656-7446"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5051597671","https://openalex.org/A5100736263"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":12.646,"has_fulltext":false,"cited_by_count":429,"citation_normalized_percentile":{"value":0.99191043,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"34","issue":"8","first_page":"1381","last_page":"1388"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9991000294685364,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.995199978351593,"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/conditional-random-field","display_name":"Conditional random field","score":0.935039758682251},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.8489452600479126},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8243310451507568},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6590102910995483},{"id":"https://openalex.org/keywords/crfs","display_name":"CRFS","score":0.633301317691803},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5938344597816467},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5364497303962708},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.535311222076416},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5330482721328735},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.5036455988883972},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.4714449644088745},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4589499235153198},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.41647377610206604},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38467487692832947},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.2908386290073395}],"concepts":[{"id":"https://openalex.org/C152565575","wikidata":"https://www.wikidata.org/wiki/Q1124538","display_name":"Conditional random field","level":2,"score":0.935039758682251},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.8489452600479126},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8243310451507568},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6590102910995483},{"id":"https://openalex.org/C2775953691","wikidata":"https://www.wikidata.org/wiki/Q5013874","display_name":"CRFS","level":3,"score":0.633301317691803},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5938344597816467},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5364497303962708},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.535311222076416},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5330482721328735},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.5036455988883972},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.4714449644088745},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4589499235153198},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.41647377610206604},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38467487692832947},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2908386290073395},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1093/bioinformatics/btx761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1381/25119984/btx761.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx761","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx761","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/8/1381/25119984/btx761.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.7099999785423279,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G6498840699","display_name":null,"funder_award_id":"61272373, 61572102 and 61572098","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G710307346","display_name":null,"funder_award_id":"NCET-13-0084","funder_id":"https://openalex.org/F4320321106","funder_display_name":"Ministry of Education of the People's Republic 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/F4320321106","display_name":"Ministry of Education of the People's Republic of China","ror":"https://ror.org/01mv9t934"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2769387903.pdf","grobid_xml":"https://content.openalex.org/works/W2769387903.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W947140380","https://openalex.org/W1991133427","https://openalex.org/W2016043834","https://openalex.org/W2033377040","https://openalex.org/W2064675550","https://openalex.org/W2097998348","https://openalex.org/W2101553882","https://openalex.org/W2121244856","https://openalex.org/W2136640051","https://openalex.org/W2145870108","https://openalex.org/W2147527908","https://openalex.org/W2148488766","https://openalex.org/W2153579005","https://openalex.org/W2158899491","https://openalex.org/W2160022416","https://openalex.org/W2166468803","https://openalex.org/W2169491861","https://openalex.org/W2171646645","https://openalex.org/W2174828870","https://openalex.org/W2265846598","https://openalex.org/W2346452181","https://openalex.org/W2414378847","https://openalex.org/W2560939934","https://openalex.org/W2565654849","https://openalex.org/W2951527505","https://openalex.org/W2952230511","https://openalex.org/W2962902328","https://openalex.org/W4294170691","https://openalex.org/W6674385629","https://openalex.org/W6682137061","https://openalex.org/W6682691769","https://openalex.org/W6683738474","https://openalex.org/W6693505360","https://openalex.org/W6704842505","https://openalex.org/W6729914986"],"related_works":["https://openalex.org/W1964783010","https://openalex.org/W4250494529","https://openalex.org/W2399696375","https://openalex.org/W2061834489","https://openalex.org/W3088215229","https://openalex.org/W182104056","https://openalex.org/W45206245","https://openalex.org/W50079190","https://openalex.org/W11196620","https://openalex.org/W2062502130"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"In":[2,64],"biomedical":[3,26],"research,":[4],"chemical":[5,13,32,88,130],"is":[6,18],"an":[7,19],"important":[8,20],"class":[9],"of":[10,25,107,149],"entities,":[11],"and":[12,41,132,138,151,155,158],"named":[14],"entity":[15],"recognition":[16,135],"(NER)":[17],"task":[21,145],"in":[22,111],"the":[23,48,59,108,127,139],"field":[24,83],"information":[27,95,165],"extraction.":[28],"However,":[29],"most":[30],"popular":[31],"NER":[33],"methods":[34,53,125],"are":[35,44,54,160,168],"based":[36],"on":[37,47,126],"traditional":[38],"machine":[39],"learning":[40],"their":[42],"performances":[43,117],"heavily":[45],"dependent":[46],"feature":[49,120],"engineering.":[50],"Moreover,":[51],"these":[52],"sentence-level":[55],"ones":[56],"which":[57],"have":[58],"tagging":[60,102],"inconsistency":[61],"problem.":[62],"Results":[63],"this":[65],"paper,":[66],"we":[67],"propose":[68],"a":[69,80,112],"neural":[70],"network":[71],"approach,":[72],"i.e.":[73],"attention-based":[74],"bidirectional":[75],"Long":[76],"Short-Term":[77],"Memory":[78],"with":[79,118],"conditional":[81],"random":[82],"layer":[84],"(Att-BiLSTM-CRF),":[85],"to":[86,100],"document-level":[87,93],"NER.":[89],"The":[90],"approach":[91],"leverages":[92],"global":[94],"obtained":[96],"by":[97],"attention":[98],"mechanism":[99],"enforce":[101],"consistency":[103],"across":[104],"multiple":[105],"instances":[106],"same":[109],"token":[110],"document.":[113],"It":[114],"achieves":[115],"better":[116],"little":[119],"engineering":[121],"than":[122],"other":[123],"state-of-the-art":[124],"BioCreative":[128,140],"IV":[129],"compound":[131],"drug":[133],"name":[134],"(CHEMDNER)":[136],"corpus":[137,146],"V":[141],"chemical-disease":[142],"relation":[143],"(CDR)":[144],"(the":[147],"F-scores":[148],"91.14":[150],"92.57%,":[152],"respectively).":[153],"Availability":[154],"implementation":[156],"Data":[157],"code":[159],"available":[161,169],"at":[162,170],"https://github.com/lingluodlut/Att-ChemdNER.":[163],"Supplementary":[164,166],"data":[167],"Bioinformatics":[171],"online.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":36},{"year":2024,"cited_by_count":55},{"year":2023,"cited_by_count":71},{"year":2022,"cited_by_count":78},{"year":2021,"cited_by_count":73},{"year":2020,"cited_by_count":60},{"year":2019,"cited_by_count":41},{"year":2018,"cited_by_count":12}],"updated_date":"2026-03-24T08:02:53.985720","created_date":"2017-12-04T00:00:00"}
