Proceedings of the 5th Workshop on BioNLP Open Shared Tasks

Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor 2019-11 Association for Computational Linguistics Hong Kong, China text conference publication emnlp-2019-bionlp https://aclanthology.org/D19-5700/ PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track Aitor Gonzalez-Agirre author Montserrat Marimon author Ander Intxaurrondo author Obdulia Rabal author Marta Villegas author Martin Krallinger author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication gonzalez-agirre-etal-2019-pharmaconer 10.18653/v1/D19-5701 https://aclanthology.org/D19-5701/ 2019-11 1 10 When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in Spanish Manuel Stoeckel author Wahed Hemati author Alexander Mehler author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication stoeckel-etal-2019-specialization 10.18653/v1/D19-5702 https://aclanthology.org/D19-5702/ 2019-11 11 15 VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases Víctor Suárez-Paniagua author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication suarez-paniagua-2019-vsp 10.18653/v1/D19-5703 https://aclanthology.org/D19-5703/ 2019-11 16 20 IxaMed at PharmacoNER Challenge 2019 Xabier Lahuerta author Iakes Goenaga author Koldo Gojenola author Aitziber Atutxa Salazar author Maite Oronoz author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication lahuerta-etal-2019-ixamed 10.18653/v1/D19-5704 https://aclanthology.org/D19-5704/ 2019-11 21 25 NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection Lukas Lange author Heike Adel author Jannik Strötgen author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication lange-etal-2019-nlnde 10.18653/v1/D19-5705 https://aclanthology.org/D19-5705/ 2019-11 26 32 A Deep Learning-Based System for PharmaCoNER Ying Xiong author Yedan Shen author Yuanhang Huang author Shuai Chen author Buzhou Tang author Xiaolong Wang author Qingcai Chen author Jun Yan author Yi Zhou author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication xiong-etal-2019-deep 10.18653/v1/D19-5706 https://aclanthology.org/D19-5706/ 2019-11 33 37 Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text Renzo Rivera author Paloma Martínez author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication rivera-martinez-2019-deep 10.18653/v1/D19-5707 https://aclanthology.org/D19-5707/ 2019-11 38 46 A Neural Pipeline Approach for the PharmaCoNER Shared Task using Contextual Exhaustive Models Mohammad Golam Sohrab author Minh Thang Pham author Makoto Miwa author Hiroya Takamura author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication sohrab-etal-2019-neural 10.18653/v1/D19-5708 https://aclanthology.org/D19-5708/ 2019-11 47 55 Biomedical Named Entity Recognition with Multilingual BERT Kai Hakala author Sampo Pyysalo author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication hakala-pyysalo-2019-biomedical 10.18653/v1/D19-5709 https://aclanthology.org/D19-5709/ 2019-11 56 61 An Overview of the Active Gene Annotation Corpus and the BioNLP OST 2019 AGAC Track Tasks Yuxing Wang author Kaiyin Zhou author Mina Gachloo author Jingbo Xia author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication wang-etal-2019-overview 10.18653/v1/D19-5710 https://aclanthology.org/D19-5710/ 2019-11 62 71 Trigger Word Detection and Thematic Role Identification via BERT and Multitask Learning Dongfang Li author Ying Xiong author Baotian Hu author Hanyang Du author Buzhou Tang author Qingcai Chen author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication li-etal-2019-trigger 10.18653/v1/D19-5711 https://aclanthology.org/D19-5711/ 2019-11 72 76 DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature Feifan Liu author Xiaoyu Zheng author Bo Wang author Catarina Kiefe author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication liu-etal-2019-deepgenemd 10.18653/v1/D19-5712 https://aclanthology.org/D19-5712/ 2019-11 77 83 Biomedical relation extraction with pre-trained language representations and minimal task-specific architecture Ashok Thillaisundaram author Theodosia Togia author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication thillaisundaram-togia-2019-biomedical 10.18653/v1/D19-5713 https://aclanthology.org/D19-5713/ 2019-11 84 89 RACAI’s System at PharmaCoNER 2019 Radu Ion author Vasile Florian Păiș author Maria Mitrofan author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication ion-etal-2019-racais 10.18653/v1/D19-5714 https://aclanthology.org/D19-5714/ 2019-11 90 99 Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task Cong Sun author Zhihao Yang author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication sun-yang-2019-transfer 10.18653/v1/D19-5715 https://aclanthology.org/D19-5715/ 2019-11 100 104 A Multi-Task Learning Framework for Extracting Bacteria Biotope Information Qi Zhang author Chao Liu author Ying Chi author Xuansong Xie author Xiansheng Hua author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication zhang-etal-2019-multi-task 10.18653/v1/D19-5716 https://aclanthology.org/D19-5716/ 2019-11 105 109 YNU-junyi in BioNLP-OST 2019: Using CNN-LSTM Model with Embeddings for SeeDev Binary Event Extraction Junyi Li author Xiaobing Zhou author Yuhang Wu author Bin Wang author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication li-etal-2019-ynu 10.18653/v1/D19-5717 https://aclanthology.org/D19-5717/ 2019-11 110 114 Using Snomed to recognize and index chemical and drug mentions. Pilar López Úbeda author Manuel Carlos Díaz Galiano author L Alfonso Urena Lopez author Maite Martin author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication lopez-ubeda-etal-2019-using 10.18653/v1/D19-5718 https://aclanthology.org/D19-5718/ 2019-11 115 120 Bacteria Biotope at BioNLP Open Shared Tasks 2019 Robert Bossy author Louise Deléger author Estelle Chaix author Mouhamadou Ba author Claire Nédellec author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication bossy-etal-2019-bacteria 10.18653/v1/D19-5719 https://aclanthology.org/D19-5719/ 2019-11 121 131 Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019 Pankaj Gupta author Usama Yaseen author Hinrich Schütze author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication gupta-etal-2019-linguistically 10.18653/v1/D19-5720 https://aclanthology.org/D19-5720/ 2019-11 132 142 An ensemble CNN method for biomedical entity normalization Pan Deng author Haipeng Chen author Mengyao Huang author Xiaowen Ruan author Liang Xu author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication deng-etal-2019-ensemble 10.18653/v1/D19-5721 https://aclanthology.org/D19-5721/ 2019-11 143 149 BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes İlknur Karadeniz author Ömer Faruk Tuna author Arzucan Özgür author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication karadeniz-etal-2019-boun 10.18653/v1/D19-5722 https://aclanthology.org/D19-5722/ 2019-11 150 157 Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs Wuti Xiong author Fei Li author Ming Cheng author Hong Yu author Donghong Ji author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication xiong-etal-2019-bacteria 10.18653/v1/D19-5723 https://aclanthology.org/D19-5723/ 2019-11 158 167 Integration of Deep Learning and Traditional Machine Learning for Knowledge Extraction from Biomedical Literature Jihang Mao author Wanli Liu author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication mao-liu-2019-integration 10.18653/v1/D19-5724 https://aclanthology.org/D19-5724/ 2019-11 168 173 CRAFT Shared Tasks 2019 Overview — Integrated Structure, Semantics, and Coreference William Baumgartner author Michael Bada author Sampo Pyysalo author Manuel R Ciosici author Negacy Hailu author Harrison Pielke-Lombardo author Michael Regan author Lawrence Hunter author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication baumgartner-etal-2019-craft 10.18653/v1/D19-5725 https://aclanthology.org/D19-5725/ 2019-11 174 184 UZH@CRAFT-ST: a Sequence-labeling Approach to Concept Recognition Lenz Furrer author Joseph Cornelius author Fabio Rinaldi author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication furrer-etal-2019-uzh 10.18653/v1/D19-5726 https://aclanthology.org/D19-5726/ 2019-11 185 195 Coreference Resolution in Full Text Articles with BERT and Syntax-based Mention Filtering Hai-Long Trieu author Anh-Khoa Duong Nguyen author Nhung Nguyen author Makoto Miwa author Hiroya Takamura author Sophia Ananiadou author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication trieu-etal-2019-coreference 10.18653/v1/D19-5727 https://aclanthology.org/D19-5727/ 2019-11 196 205 Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task Thang Minh Ngo author Jenna Kanerva author Filip Ginter author Sampo Pyysalo author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication ngo-etal-2019-neural 10.18653/v1/D19-5728 https://aclanthology.org/D19-5728/ 2019-11 206 215 RDoC Task at BioNLP-OST 2019 Mohammad Anani author Nazmul Kazi author Matthew Kuntz author Indika Kahanda author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication anani-etal-2019-rdoc 10.18653/v1/D19-5729 https://aclanthology.org/D19-5729/ 2019-11 216 226 BioNLP-OST 2019 RDoC Tasks: Multi-grain Neural Relevance Ranking Using Topics and Attention Based Query-Document-Sentence Interactions Pankaj Gupta author Yatin Chaudhary author Hinrich Schütze author 2019-11 text Proceedings of the 5th Workshop on BioNLP Open Shared Tasks Kim Jin-Dong editor Nédellec Claire editor Bossy Robert editor Deléger Louise editor Association for Computational Linguistics Hong Kong, China conference publication gupta-etal-2019-bionlp 10.18653/v1/D19-5730 https://aclanthology.org/D19-5730/ 2019-11 227 236