BioNLP 2023

SIGBIOMED

BIONLP 2020
July 9, 2020 -- Online

An ACL 2020 Workshop associated with the SIGBIOMED special interest group

IMPORTANT DATES

• Submission deadline: Friday, March 20, 2020 New: Friday, April, 3, 2020, 11:59 PM Eastern US

https://www.softconf.com/acl2020/BioNLP2020/

• Notification of acceptance: Friday, April 24, 2020 New: Tuesday, April 28, 2020
• Camera-ready copy due from authors: 'Sunday, May 3, 2020 New: Wednesday, May 6, 2020
• Workshop: July 9, 2020

The 19th Workshop on Biomedical Language Processing

	ALL TIMES IN SEATTLE PT TIME ZONE
08:30–08:40	Opening remarks
08:40–10:30	Session 1: High accuracy information retrieval, spin and bias
08:40–09:10	Invited Talk Kirk Roberts
09:10–09:20	Quantifying 60 Years of Gender Bias in Biomedical Research with Word Embeddings Anthony Rios, Reenam Joshi and Hejin Shin
09:20–09:30	Sequence-to-Set Semantic Tagging for Complex Query Reformulation and Automated Text Categorization in Biomedical IR using Self-Attention Manirupa Das, Juanxi Li, Eric Fosler-Lussier, Simon Lin, Steve Rust, Yungui Huang and Rajiv Ramnath
09:30–09:40	Interactive Extractive Search over Biomedical Corpora Hillel Taub Tabib, Micah Shlain, Shoval Sadde, Dan Lahav, Matan Eyal, Yaara Cohen and Yoav Goldberg
09:40–09:50	Improving Biomedical Analogical Retrieval with Embedding of Structural Dependencies Amandalynne Paullada, Bethany Percha and Trevor Cohen
09:50–10:00	DeSpin: a prototype system for detecting spin in biomedical publications Anna Koroleva, Sanjay Kamath, Patrick Bossuyt and Patrick Paroubek
10:00–10:30	Discussion
10:30–10:45	Coffee Break
10:45–13:00	Session 2: Clinical Language Processing
10:45–11:15	Invited Talk Tim Miller
11:15–11:25	Towards Visual Dialog for Radiology Olga Kovaleva, Chaitanya Shivade, Satyananda Kashyap, Karina Kanjaria, Joy Wu, Deddeh Ballah, Adam Coy, Alexandros Karargyris, Yufan Guo, David Beymer, Anna Rumshisky and Vandana Mukherjee Mukherjee
11:25–11:35	A BERT-based One-Pass Multi-Task Model for Clinical Temporal Relation Extraction Chen Lin, Timothy Miller, Dmitriy Dligach, Farig Sadeque, Steven Bethard and Guergana Savova
11:35–11:45	Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset Thomas Searle, Zina Ibrahim and Richard Dobson
11:45–11:55	Comparative Analysis of Text Classification Approaches in Electronic Health Records Aurelie Mascio, Zeljko Kraljevic, Daniel Bean, Richard Dobson, Robert Stewart, Rebecca Bendayan and Angus Roberts
11:55–12:05	Noise Pollution in Hospital Readmission Prediction: Long Document Classification with Reinforcement Learning Liyan Xu, Julien Hogan, Rachel E. Patzer and Jinho D. Choi
12:05–12:15	Evaluating the Utility of Model Configurations and Data Augmentation on Clinical Semantic Textual Similarity Yuxia Wang, Fei Liu, Karin Verspoor and Timothy Baldwin
12:15–12:45	Discussion
12:45–13:30	Lunch
13:30–15:30	Session 3: Language Understanding
13:30–14:00	Invited Talk Anna Rumshisky
14:00–14:10	Entity-Enriched Neural Models for Clinical Question Answering Bhanu Pratap Singh Rawat, Wei-Hung Weng, So Yeon Min, Preethi Raghavan and Peter Szolovits
14:10–14:20	Evidence Inference 2.0: More Data, Better Models Jay DeYoung, Eric Lehman, Benjamin Nye, Iain Marshall and Byron C. Wallace
14:20–14:30	Personalized Early Stage Alzheimer’s Disease Detection: A Case Study of President Reagan’s Speeches Ning Wang, Fan Luo, Vishal Peddagangireddy, Koduvayur Subbalakshmi and Rajarathnam Chandramouli
14:30–14:40	BioMRC: A Dataset for Biomedical Machine Reading Comprehension Dimitris Pappas, Petros Stavropoulos, Ion Androutsopoulos and Ryan McDonald
14:40–14:50	Neural Transduction of Letter Position Dyslexia using an Anagram Matrix Representation Avi Bleiweiss
14:50–15:00	Domain Adaptation and Instance Selection for Disease Syndrome Classification over Veterinary Clinical Notes Brian Hur, Timothy Baldwin, Karin Verspoor, Laura Hardefeldt and James Gilkerson
15:00–15:30	Discussion
15:30–15:45	Coffee Break
15:45–17:45	Session 4: Named Entity Recognition and Knowledge Representation
15:45–16:25	Invited Talk Machine Reading for Precision Medicine Hoifung Poon
16:25–16:35	Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings David Chang, Ivana Balažević, Carl Allen, Daniel Chawla, Cynthia Brandt and Andrew Taylor
16:35–16:45	Extensive Error Analysis and a Learning-Based Evaluation of Medical Entity Recognition Systems to Approximate User Experience Isar Nejadgholi, Kathleen C. Fraser and Berry de Bruijn
16:45–16:55	A Data-driven Approach for Noise Reduction in Distantly Supervised Biomedical Relation Extraction Saadullah Amin, Katherine Ann Dunfield, Anna Vechkaeva and Guenter Neumann
16:55–17:05	Global Locality in Biomedical Relation and Event Extraction Elaheh ShafieiBavani, Antonio Jimeno Yepes, Xu Zhong and David Martinez Iraola
17:05–17:15	An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining Yifan Peng, Qingyu Chen and Zhiyong Lu
17:15–17:45	Discussion
17:45–18:00	Closing remarks

Program Committee

 * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK 
 * Emilia Apostolova, Language.ai, USA
 * Eiji Aramaki, University of Tokyo, Japan 
 * Asma Ben Abacha, US National Library of Medicine  
 * Siamak Barzegar, Barcelona Supercomputing Center, Spain  
 * Olivier Bodenreider, US National Library of Medicine 
 * Leonardo Campillos Llanos, Universidad Autónoma de Madrid, Spain
 * Qingyu Chen, US National Library of Medicine  
 * Fenia Christopoulou, National Centre for Text Mining and University of Manchester, UK 
 * Aaron Cohen, Oregon Health & Science University, USA 
 * Kevin Bretonnel Cohen, University of Colorado School of Medicine, USA 
 * Brian Connolly, Kroger Digital, USA 
 * Viviana Cotik, University of Buenos Aires, Argentina 
 * Manirupa Das, Amazon Search, Seattle, WA, USA
 * Dina Demner-Fushman, US National Library of Medicine 
 * Bart Desmet, Clinical Center, National Institutes of Health, USA
 * Travis Goodwin, The University of Texas at Dallas, USA
 * Natalia Grabar, CNRS, France 
 * Cyril Grouin, LIMSI - CNRS, France 
 * Tudor Groza, The Garvan Institute of Medical Research, Australia
 * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 * Halil Kilicoglu, University of Illinois at Urbana-Champaign, USA
 * Ari Klein, University of Pennsylvania, USA
 * André Lamúrias, University of Lisbon, Portugal
 * Majid Latifi,  Trinity College Dublin, Ireland
 * Alberto Lavelli, FBK-ICT, Italy
 * Robert Leaman, US National Library of Medicine
 * Ulf Leser, Humboldt-Universität zu Berlin, Germany 
 * Maolin Li, National Centre for Text Mining and University of Manchester, UK 
 * Zhiyong Lu, US National Library of Medicine
 * Timothy Miller, Children’s Hospital Boston, USA 
 * Aurelie Neveol, LIMSI - CNRS, France 
 * Claire Nédellec, INRA, France
 * Mariana Neves, German Federal Institute for Risk Assessment, Germany 
 * Denis Newman-Griffis, Clinical Center, National Institutes of Health, USA
 * Nhung Nguyen, The University of Manchester, UK
 * Karen O'Connor, University of Pennsylvania, USA
 * Naoaki Okazaki, Tokyo Institute of Technology, Japan
 * Yifan Peng, US National Library of Medicine 
 * Laura Plaza, UNED, Madrid, Spain
 * Francisco J. Ribadas-Pena, University of Vigo, Spain
 * Angus Roberts, The University of Sheffield, UK
 * Kirk Roberts, The University of Texas Health Science Center at Houston, USA 
 * Roland Roller, DFKI GmbH, Berlin, Germany
 * Diana Sousa, University of Lisbon, Portugal
 * Karin Verspoor, The University of Melbourne, Australia
 * Davy Weissenbacher, University of Pennsylvania, USA
 * W John Wilbur, US National Library of Medicine 
 * Shankai Yan, US National Library of Medicine 
 * Chrysoula Zerva, National Centre for Text Mining and University of Manchester, UK 
 * Ayah Zirikly, Clinical Center, National Institutes of Health, USA
 * Pierre Zweigenbaum, LIMSI - CNRS, France

Organizers

  Dina Demner-Fushman, US National Library of Medicine
  Kevin Bretonnel Cohen, University of Colorado School of Medicine
  Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
  Jun-ichi Tsujii, National Institute of Advanced Industrial Science and Technology, Japan and University of Manchester, UK

WORKSHOP OVERVIEW AND SCOPE

The ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about the fast growing and important domain. The workshop will continue presenting work on a broad and interesting range of topics in NLP.

The active areas of research include, but are not limited to:

• Entity identification and normalization (linking) for a broad range of semantic categories
• Extraction of complex relations and events
• Discourse analysis
• Anaphora/coreference resolution
• Text mining / Literature based discovery
• Summarization
• Question Answering
• Resources and novel strategies for system testing and evaluation
• Infrastructures for biomedical text mining / Processing and annotation platforms
• Translating NLP research to practice
• Explainable models for biomedical NLP
• Multi-modal models for biomedical NLP
• Getting reproducible results
• BioNLP research in languages other than English

SUBMISSION INSTRUCTIONS

Two types of submissions are invited: full papers and short papers.

Full papers should not exceed eight (8) pages of text, plus unlimited references. Final versions of full papers will be given one additional page of content (up to 9 pages) so that reviewers' comments can be taken into account. Full papers are intended to be reports of original research. BioNLP aims to be the forum for interesting, innovative, and promising work involving biomedicine and language technology, whether or not yielding high performance at the moment. This by no means precludes our interest in and preference for mature results, strong performance, and thorough evaluation. Both types of research and combinations thereof are encouraged.

Short papers may consist of up to four (4) pages of content, plus unlimited references. Upon acceptance, short papers will still be given up to five (5) content pages in the proceedings. Appropriate short paper topics include preliminary results, application notes, descriptions of work in progress, etc.

Please see https://acl2020.org/calls/papers/ for templates.

Dual submission policy

Papers may NOT be submitted to the BioNLP 2020 workshop if they are or will be concurrently submitted to another meeting or publication.