{"id":"https://openalex.org/W2986178925","doi":"https://doi.org/10.18653/v1/d19-5706","title":"A Deep Learning-Based System for PharmaCoNER","display_name":"A Deep Learning-Based System for PharmaCoNER","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2986178925","doi":"https://doi.org/10.18653/v1/d19-5706","mag":"2986178925"},"language":"en","primary_location":{"id":"doi:10.18653/v1/d19-5706","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5706","pdf_url":"https://www.aclweb.org/anthology/D19-5706.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.aclweb.org/anthology/D19-5706.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031742177","display_name":"Ying Xiong","orcid":"https://orcid.org/0000-0001-7423-2937"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ying Xiong","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108761108","display_name":"Yedan Shen","orcid":"https://orcid.org/0009-0008-0514-9679"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yedan Shen","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030631742","display_name":"Yuanhang Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanhang Huang","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100396687","display_name":"Shuai Chen","orcid":"https://orcid.org/0000-0002-8511-911X"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuai Chen","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014238603","display_name":"Buzhou Tang","orcid":"https://orcid.org/0000-0003-0271-8246"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Buzhou Tang","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","Peng Cheng Laboratory"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Peng Cheng Laboratory","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100424254","display_name":"Xiaolong Wang","orcid":"https://orcid.org/0000-0001-9003-4252"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaolong Wang","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101895423","display_name":"Qingcai Chen","orcid":"https://orcid.org/0000-0001-8473-7293"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingcai Chen","raw_affiliation_strings":["Peng Cheng Laboratory"],"affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030330619","display_name":"Jun Yan","orcid":"https://orcid.org/0000-0003-2497-5518"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Yan","raw_affiliation_strings":["Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","Yidu Cloud (Beijing) Technology Co., Ltd, Beijing"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Harbin Institute of Technology, Shenzhen, China, 518055","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"Yidu Cloud (Beijing) Technology Co., Ltd, Beijing","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101854123","display_name":"Yi Zhou","orcid":"https://orcid.org/0009-0004-8877-5173"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yi Zhou","raw_affiliation_strings":["Sun YAT-SEN UNIVERSITY {xiongying0929, hyhang7, chenshuai726,"],"affiliations":[{"raw_affiliation_string":"Sun YAT-SEN UNIVERSITY {xiongying0929, hyhang7, chenshuai726,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5031742177"],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":null,"apc_paid":null,"fwci":1.0306,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.76573572,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"33","last_page":"37"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994999766349792,"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":0.9994999766349792,"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":0.9983999729156494,"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":0.9979000091552734,"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":0.8063216209411621},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.6356068849563599},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.624291718006134},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.6001418828964233},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.5982401967048645},{"id":"https://openalex.org/keywords/offset","display_name":"Offset (computer science)","score":0.5772985219955444},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.570961058139801},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5497518181800842},{"id":"https://openalex.org/keywords/track","display_name":"Track (disk drive)","score":0.5165123343467712},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5012357234954834},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4897499084472656},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.47007566690444946},{"id":"https://openalex.org/keywords/f1-score","display_name":"F1 score","score":0.41582566499710083},{"id":"https://openalex.org/keywords/speech-recognition","display_name":"Speech recognition","score":0.3623577356338501},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1154634952545166},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.08797973394393921},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.06882068514823914}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8063216209411621},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.6356068849563599},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.624291718006134},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6001418828964233},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.5982401967048645},{"id":"https://openalex.org/C175291020","wikidata":"https://www.wikidata.org/wiki/Q1156822","display_name":"Offset (computer science)","level":2,"score":0.5772985219955444},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.570961058139801},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5497518181800842},{"id":"https://openalex.org/C89992363","wikidata":"https://www.wikidata.org/wiki/Q5961558","display_name":"Track (disk drive)","level":2,"score":0.5165123343467712},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5012357234954834},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4897499084472656},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.47007566690444946},{"id":"https://openalex.org/C148524875","wikidata":"https://www.wikidata.org/wiki/Q6975395","display_name":"F1 score","level":2,"score":0.41582566499710083},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.3623577356338501},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1154634952545166},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.08797973394393921},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.06882068514823914},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/d19-5706","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5706","pdf_url":"https://www.aclweb.org/anthology/D19-5706.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/d19-5706","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/d19-5706","pdf_url":"https://www.aclweb.org/anthology/D19-5706.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of The 5th Workshop on BioNLP Open Shared Tasks","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5187284106","display_name":null,"funder_award_id":"HIT.NSRIF.2017052","funder_id":"https://openalex.org/F4320321940","funder_display_name":"Harbin Institute of Technology"}],"funders":[{"id":"https://openalex.org/F4320321940","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2986178925.pdf","grobid_xml":"https://content.openalex.org/works/W2986178925.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1940872118","https://openalex.org/W2105842272","https://openalex.org/W2143902665","https://openalex.org/W2147880316","https://openalex.org/W2168041406","https://openalex.org/W2183114698","https://openalex.org/W2184325618","https://openalex.org/W2593437763","https://openalex.org/W2726797548","https://openalex.org/W2763990719","https://openalex.org/W2896457183","https://openalex.org/W2915704452","https://openalex.org/W2963341956","https://openalex.org/W2963918774","https://openalex.org/W2985294119","https://openalex.org/W3086206064"],"related_works":["https://openalex.org/W3180764077","https://openalex.org/W4281560212","https://openalex.org/W3116252395","https://openalex.org/W2769084352","https://openalex.org/W4386322467","https://openalex.org/W4385574021","https://openalex.org/W2887593177","https://openalex.org/W2757016069","https://openalex.org/W4254089628","https://openalex.org/W2997394673"],"abstract_inverted_index":{"The":[0,38],"Biological":[1],"Text":[2],"Mining":[3],"Unit":[4],"at":[5],"BSC":[6],"and":[7,29,31,48,53,90,93,126],"CNIO":[8],"organized":[9],"the":[10,54,109],"first":[11],"shared":[12,39,74,110],"task":[13,40,111],"on":[14,68,80,97,108,123,132],"chemical":[15],"&":[16],"drug":[17],"mention":[18],"recognition":[19],"from":[20,85],"Spanish":[21],"medical":[22],"texts":[23],"called":[24],"PharmaCoNER":[25],"(Pharmacological":[26],"Substances,":[27],"Compounds":[28],"proteins":[30],"Named":[32],"Entity":[33],"Recognition":[34],"track)":[35],"in":[36],"2019.":[37],"includes":[41],"two":[42],"tracks:":[43],"one":[44,56],"for":[45,57,72,87,103],"NER":[46,88],"offset":[47,89],"entity":[49,91],"classification":[50,92],"(track":[51,60],"1)":[52],"other":[55],"concept":[58,104],"indexing":[59],"2).":[61],"We":[62],"developed":[63],"a":[64,77,94,118,127],"pipeline":[65],"system":[66,116],"based":[67,79,96],"deep":[69],"learning":[70],"methods":[71],"this":[73],"task,":[75],"specifically,":[76],"subsystem":[78,95],"BERT":[81],"(Bidirectional":[82],"Encoder":[83],"Representations":[84],"Transformers)":[86],"Bpool":[98],"(Bi-LSTM":[99],"with":[100],"max/mean":[101],"pooling)":[102],"indexing.":[105],"Evaluation":[106],"conducted":[107],"data":[112],"showed":[113],"that":[114],"our":[115],"achieves":[117],"micro-average":[119],"F1-score":[120,129],"of":[121,130],"0.9105":[122],"track":[124,133],"1":[125],"microaverage":[128],"0.8391":[131],"2.":[134]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":7}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}