Proceedings
- Proceedings at ACL Anthology
BioNLP-OST Workshop (Monday, November 4, 2019) @ SkyCity RM 2
9:00 | Opening | |||
09:10 - 10:30 | Session 1 (PharmaCoNER) | |||
9:10 | PharmaCoNER: Pharmacological Substances, Compounds and proteins Named Entity Recognition track | Aitor Gonzalez Agirre, Montserrat Marimon, Ander Intxaurrondo, Obdulia Rabal, Marta Villegas and Martin Krallinger | ||
9:30 | When Specialization Helps: Using Pooled Contextualized Embeddings to Detect Chemical and Biomedical Entities in Spanish | Manuel Stoeckel, Wahed Hemati and Alexander Mehler | ||
9:40 | VSP at PharmaCoNER 2019: Recognition of Pharmacological Substances, Compounds and Proteins with Recurrent Neural Networks in Spanish Clinical Cases | Víctor Suárez-Paniagua | ||
9:50 | IxaMed at PharmacoNER Challenge 2019 | Xabier Lahuerta, Iakes Goenaga, Koldo Gojenola, Aitziber Atutxa Salazar and Maite Oronoz | ||
10:00 | NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection | Lukas Lange, Heike Adel and Jannik Strötgen | ||
10:10 | A Deep Learning-Based System for PharmaCoNER | Ying Xiong, Yedan Shen, Yuanhang Huang, Shuai Chen, Buzhou Tang, Xiaolong Wang, Qingcai Chen, Jun Yan and Yi Zhou | ||
10:30 - 11:00 | Coffee Break | |||
11:00 - 12:30 | Session 2 (PharmaCoNER & AGAC) | |||
11:00 | Deep neural model with enhanced embeddings for pharmaceutical and chemical entities recognition in Spanish clinical text | Renzo Rivera and Paloma Martínez | ||
11:10 | A Neural Pipeline Approach for the PharmaCoNER Shared Task using Contextual Exhaustive Models [video] | Mohammad Golam Sohrab, Minh Thang Pham, Hiroya Takamura and Makoto Miwa | ||
11:20 | Biomedical Named Entity Recognition with Multilingual BERT | Kai Hakala and Sampo Pyysalo | ||
11:30 | An Overview of the Active Gene Annotation Corpus and the BioNLP OST 2019 AGAC Track Tasks | Yuxing Wang, Kaiyin Zhou, Mina Gachloo and Jingbo Xia | ||
11:50 | Trigger Word Detection and Thematic Role Identification via BERT and Multitask Learning | Dongfang Li, Ying Xiong, Baotian Hu, Buzhou Tang and Qingcai Chen | ||
12:00 | DeepGeneMD: A Joint Deep Learning Model for Extracting Gene Mutation-Disease Knowledge from PubMed Literature | Feifan Liu, Xiaoyu Zheng, Bo Wang and Catarina Kiefe | ||
12:10 | Biomedical relation extraction with pre-trained language representations and minimal task-specific architecture | Ashok Thillaisundaram and Theodosia Togia | ||
12:30 - 14:00 | Lunch Break & Poster Session | |||
| RACAI’s System at PharmaCoNER 2019 | Radu Ion, Vasile Florian Păiș and Maria Mitrofan | |||
| Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task | Cong Sun and Zhihao Yang | |||
| A Multi-Task Learning Framework for Extracting Bacteria Biotope Information | Qi Zhang, Chao Liu, Ying Chi, Xuansong Xie and Xiansheng Hua | |||
| YNU-junyi in BioNLP-OST 2019: Using CNN-LSTM Model with Embeddings for SeeDev Binary Event Extraction | Junyi Li, Xiaobing Zhou, Yuhang Wu and Bin Wang | |||
| Using Snomed to recognize and index chemical and drug mentions | Pilar López Úbeda, Manuel Carlos Díaz Galiano, L. Alfonso Urena Lopez and Maite Martin | |||
14:00 - 14:40 | Session 3 (BB & SeeDev) | |||
14:00 | Bacteria Biotope at BioNLP Open Shared Tasks 2019 | Robert Bossy, Louise Deléger, Estelle Chaix, Mouhamadou Ba and Claire Nédellec | ||
14:20 | Linguistically Informed Relation Extraction and Neural Architectures for Nested Named Entity Recognition in BioNLP-OST 2019 | Pankaj Gupta, Usama Yaseen and Hinrich Schütze | ||
14:40 | An ensemble CNN method for biomedical entity normalization | Pan Deng, Haipeng Chen, Mengyao Huang, Xiaowen Ruan and Liang Xu | ||
14:50 | BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes | İlknur Karadeniz, Ömer Faruk Tuna and Arzucan Özgür | ||
15:00 | Bacteria Biotope Relation Extraction via Lexical Chains and Dependency Graphs | Wuti Xiong, Fei Li, Ming Cheng, Hong Yu and Donghong Ji | ||
15:10 | Integration of Deep Learning and Traditional Machine Learning for Knowledge Extraction from Biomedical Literature | Jihang Mao and Wanli Liu | ||
15:30 - 16:00 | Coffee Break | |||
16:00 - 17:20 | Session 4 (CRAFT & RDoC) | |||
16:00 | CRAFT Shared Tasks 2019 Overview --- Integrated Structure, Semantics, and Coreference | William Baumgartner, Michael Bada, Sampo Pyysalo, Manuel R. Ciosici, Negacy Hailu, Harrison Pielke-Lombardo, Michael Regan and Lawrence Hunter | ||
16:20 | UZH@CRAFT-ST: a Sequence-labeling Approach to Concept Recognition | Lenz Furrer, Joseph Cornelius and Fabio Rinaldi | ||
16:30 | Coreference Resolution in Full Text Articles with BERT and Syntax-based Mention Filtering | Hai-Long Trieu, Anh-Khoa Duong Nguyen, Nhung Nguyen, Makoto Miwa, Hiroya Takamura and Sophia Ananiadou | ||
16:40 | Neural Dependency Parsing of Biomedical Text: TurkuNLP entry in the CRAFT Structural Annotation Task | Thang Minh Ngo, Jenna Kanerva, Filip Ginter and Sampo Pyysalo | ||
16:50 | RDoC Task at BioNLP-OST 2019 | Mohammad Anani, Nazmul Kazi, Matthew Kuntz and Indika Kahanda | ||
17:10 | BioNLP-OST 2019 RDoC Tasks: Multi-grain Neural Relevance Ranking Using Topics and Attention Based Query-Document-Sentence Interactions | Pankaj Gupta, Yatin Chaudhary and Hinrich Schütze | ||
17:20 - 18:00 | Closing (Discussions) |