BioNLP 2023

SIGBIOMED

BIONLP 2022 @ ACL 2022

The 21st BioNLP workshop associated with the ACL SIGBIOMED special interest group is co-located with ACL 2022

IMPORTANT DATES

• March 7, 2022: Workshop Paper Due Date
• Submission site: https://www.softconf.com/acl2022/BioNLP2022
• March 28, 2022: Notification of Acceptance
• April 10, 2022: Camera-ready papers due
• BioNLP 2022 Workshop at ACL, May 26, 2022, Dublin, Ireland

BioNLP 2022 Program

All times are Ireland timezone (GMT+1)

09:00–09:10	Opening remarks
09:10–10:30	Session 1: Question Answering, Discourse Structure and Clinical Applications (Onsite oral presentations)
09:10–9:30	Explainable Assessment of Healthcare Articles with QA Alodie Boissonnet1, Marzieh Saeidi2, Vassilis Plachouras2, Andreas Vlachos1 1University of Cambridge, 2Facebook
09:30–9:50	A sequence-to-sequence approach for document-level relation extraction John Giorgi1, Gary Bader1, Bo Wang2 1University of Toronto, 2School of Artificial Intelligence, Jilin University
09:50–10:10	Position-based Prompting for Health Outcome Generation Micheal Abaho1, Danushka Bollegala2, Paula Williamson1, Susanna Dodd1 1University of Liverpool, 2University of Liverpool/Amazon
10:10-10:30	How You Say It Matters: Measuring the Impact of Verbal Disfluency Tags on Automated Dementia Detection Shahla Farzana, Ashwin Deshpande, Natalie Parde University of Illinois at Chicago
10:30–11:00	Coffee Break
11:00–12:30	Hybrid Poster Session 1
	Data Augmentation for Biomedical Factoid Question Answering Dimitris Pappas, Prodromos Malakasiotis, Ion Androutsopoulos Athens University of Economics and Business
	Slot Filling for Biomedical Information Extraction Yannis Papanikolaou, Marlene Staib, Justin Grace, Francine Bennett Healx Ltd
	Automatic Biomedical Term Clustering by Learning Fine-grained Term Representations Sihang Zeng, Zheng Yuan, Sheng Yu Tsinghua University
	BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model Hongyi Yuan1, Zheng Yuan1, Ruyi Gan2, Jiaxing Zhang2, Yutao Xie2, Sheng Yu1 1Tsinghua University, 2International Digital Economy Academy
	Incorporating Medical Knowledge to Transformer-based Language Models for Medical Dialogue Generation Usman Naseem1, Ajay Bandi2, Shaina Raza3, Junaid Rashid4, Bharathi Raja Chakravarthi5 1University of Sydney, 2Northwest Missouri State University, USA, 3University of Toronto, Canada, 4Kongju National University, South Korea, 5National University of Ireland Galway
	Memory-aligned Knowledge Graph for Clinically Accurate Radiology Image Report Generation Sixing Yan Hong Kong Baptist University
	Simple Semantic-based Data Augmentation for Named Entity Recognition in Biomedical Texts Uyen Phan1 and Nhung Nguyen2 1VNUHCM-University of Science, 2The University of Manchester
	Auxiliary Learning for Named Entity Recognition with Multiple Auxiliary Biomedical Training Data Taiki Watanabe1, Tomoya Ichikawa2, Akihiro Tamura2, Tomoya Iwakura3, Chunpeng Ma1, Tsuneo Kato2 1Fujitsu Ltd., 2Doshisha University, 3Fujitsu
	SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study Samuel Cahyawijaya, Tiezheng Yu, Zihan Liu, Xiaopu Zhou, Tze Wing Mak, Yuk Yu Ip, Pascale Fung The Hong Kong University of Science and Technology, Hong Kong, China
	Biomedical NER using Novel Schema and Distant Supervision Anshita Khandelwal, Alok Kar, Veera Chikka, Kamalakar Karlapalem International Institute of Information Technology
	Improving Supervised Drug-Protein Relation Extraction with Distantly Supervised Models Naoki Iinuma, Makoto Miwa, Yutaka Sasaki Toyota Technological Institute
	Named Entity Recognition for Cancer Immunology Research Using Distant Supervision Hai-Long Trieu1, Makoto Miwa2, Sophia Ananiadou3 1National Institute of Advanced Industrial Science and Technology, 2Toyota Technological Institute, 3University of Manchester
	Intra-Template Entity Compatibility based Slot-Filling for Clinical Trial Information Extraction Christian Witte and Philipp Cimiano Bielefeld University
	Pretrained Biomedical Language Models for Clinical NLP in Spanish Casimiro Pio Carrino, Joan Llop, Marc Pàmies, Asier Gutiérrez-Fandiño, Jordi Armengol-Estapé, Joaquín Silveira-Ocampo, Alfonso Valencia, Aitor Gonzalez-Agirre, Marta Villegas Barcelona Supercomputing Center
	Zero-Shot Aspect-Based Scientific Document Summarization using Self-Supervised Pre-training Amir Soleimani1, Vassilina Nikoulina2, Benoit Favre3, Salah Ait Mokhtar2 1University of Amsterdam, 2Naver Labs Europe, 3Aix Marseille Univ, Université de Toulon, CNRS, LIS, Marseille, France
	Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts Saadullah Amin1, Noon Pokaratsiri Goldstein2, Morgan Wixted3, Alejandro Garcia-Rudolph4, Catalina Martínez-Costa5, Guenter Neumann1 1DFKI ;amp; Saarland University, 2DFKI, 3Saarland University, 4Institut Guttmann, 5University of Murcia
	VPAI_Lab at MedVidQA 2022: A Two-Stage Cross-modal Fusion Method for Medical Instructional Video Classification Bin Li1, Yixuan Weng2, Fei Xia3, Bin Sun1, Shutao Li1 1Hunan University, 2Institute of Automation, Chinese Academy of Sciences, 31National Laboratory of Pattern Recognition,Institute of Automation 2University of Chinese Academy of Sciences, Beijing, China
12:30–14:00	Lunch Break
14:00–15:00	Summarization and text mining (Onsite oral presentations)
14:00-14:20	GenCompareSum: a hybrid unsupervised summarization method using salience Jennifer Bishop, Qianqian Xie, Sophia Ananiadou University of Manchester
14:20-14:40	BioCite: A Deep Learning-based Citation Linkage Framework for Biomedical Research Articles Sudipta Singha Roy and Robert E. Mercer The University of Western Ontario
14:40-15:00	Low Resource Causal Event Detection from Biomedical Literature Zhengzhong Liang, Enrique Noriega-Atala, Clayton Morrison, Mihai Surdeanu The University of Arizona
15:00–15:30	Coffee Break
15:30–17:00	Hybrid Poster Session 2
	Overview of the MedVidQA 2022 Shared Task on Medical Video Question-Answering Deepak Gupta and Dina Demner-Fushman National Library of Medicine, NIH
	Inter-annotator agreement is not the ceiling of machine learning performance: Evidence from a comprehensive set of simulations Russell Richie1, Sachin Grover1, Fuchiang Tsui2 1Children's Hospital of Philadelphia, 2Children's Hospital of Philadelphia; University of Pennsylvania
	Conversational Bots for Psychotherapy: A Study of Generative Transformer Models Using Domain-specific Dialogues Avisha Das1, Salih Selek2, Alia Warner2, Xu Zuo1, Yan Hu1, Vipina Kuttichi Keloth1, Jianfu Li1, W. Zheng1, Hua Xu1 1School of Biomedical Informatics, UTHealth, 2McGovern Medical School, UTHealth
	BanglaBioMed: A Biomedical Named-Entity Annotated Corpus for Bangla (Bengali) Salim Sazzed Old Dominion University
	BEEDS: Large-Scale Biomedical Event Extraction using Distant Supervision and Question Answering Xing David Wang, Ulf Leser, Leon Weber Humboldt-Universität zu Berlin
	Data Augmentation for Rare Symptoms in Vaccine Side-Effect Detection Bosung Kim and Ndapa Nakashole University of California, San Diego
	ICDBigBird: A Contextual Embedding Model for ICD Code Classification George Michalopoulos1, Michal Malyska2, Nicola Sahar3, Alexander Wong1, Helen Chen1 1University of Waterloo, 2University of Toronto, 3Semantic Health
	Doctor XAvIer: Explainable Diagnosis on Physician-Patient Dialogues and XAI Evaluation Hillary Ngai1 and Frank Rudzicz2 1Vector Institute for Artificial Intelligence, 2Vector Institute for Artificial Intelligence, University of Toronto
	DISTANT-CTO: A Zero Cost, Distantly Supervised Approach to Improve Low-Resource Entity Extraction Using Clinical Trials Literature Anjani Dhrangadhariya1 and Henning Müller2 1HES-SO Valais-Wallis, 2HES-SO
	Improving Romanian BioNER Using a Biologically Inspired System Maria Mitrofan1 and Vasile Pais2 1RACAI, 2Research Institute for Artificial Intelligence, Romanian Academy
	EchoGen: Generating Conclusions from Echocardiogram Notes Liyan Tang1, Shravan Kooragayalu2, Yanshan Wang2, Ying Ding1, Greg Durrett3, Justin Rousseau1, Yifan Peng4 1University of Texas at Austin, 2University of Pittsburgh, 3UT Austin, 4Cornell Medicine
	Quantifying Clinical Outcome Measures in Patients with Epilepsy Using the Electronic Health Record Kevin Xie1, Brian Litt2, Dan Roth1, Colin Ellis2 1University of Pennsylvania, 2Perelman School of Medicine, University of Pennsylvania
	Comparing Encoder-Only and Encoder-Decoder Transformers for Relation Extraction from Biomedical Texts: An Empirical Study on Ten Benchmark Datasets Mourad Sarrouti, Carson Tao, Yoann Mamy Randriamihaja Sumitovant Biopharma
	Utility Preservation of Clinical Text After De-Identification Thomas Vakili1 and Hercules Dalianis2 1Department of Computer and Systems Sciences, Stockholm University, 2DSV/Stockholm University
	Horses to Zebras: Ontology-Guided Data Augmentation and Synthesis for ICD-9 Coding Matúš Falis1, Hang Dong2, Alexandra Birch1, Beatrice Alex1 1The University of Edinburgh, 2Oxford University
	Towards Automatic Curation of Antibiotic Resistance Genes via Statement Extraction from Scientific Papers: A Benchmark Dataset and Models Sidhant Chandak1, Liqing Zhang2, Connor Brown2, Lifu Huang2 1Indian institute of Technology Kanpur, 2Virginia Tech
	Model Distillation for Faithful Explanations of Medical Code Predictions Zach Wood-Doughty, Isabel Cachola, Mark Dredze Johns Hopkins University
	Towards Generalizable Methods for Automating Risk Score Calculation Jennifer J Liang1, Eric Lehman2, Ananya Iyengar3, Diwakar Mahajan1, Preethi Raghavan1, Cindy Y. Chang4, Peter Szolovits2 1IBM Research, 2MIT, 3Northeastern University, 4Brigham and Women's Hospital
	DoSSIER at MedVidQA 2022: Text-based Approaches to Medical Video Answer Localization Problem Wojciech Kusa1, Georgios Peikos2, Óscar Espitia3, Allan Hanbury1, Gabriella Pasi4 1TU Wien, 2University of Milano-Bicocca, 3University of Milano Bicocca, 4Università degli Studi di Milano Bicocca

Submission Types & Requirements

Following the previous conferences, BioNLP 2022 will be open for two types of submissions: long and short papers. Please follow ACL guidelines https://acl-org.github.io/ACLPUB/formatting.html and templates: https://github.com/acl-org/acl-style-files

Overleaf templates: https://www.overleaf.com/project/5f64f1fb97c4c50001b60549

WORKSHOP OVERVIEW AND SCOPE

The BioNLP workshop associated with the ACL SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. Despite, or maybe due to reaching maturity, the field of Biomedical NLP continues getting stronger. BioNLP welcomes and encourages inclusion and diversity. BioNLP truly encompasses the breadth of the domain and brings together researchers in bio- and clinical NLP from all over the world. The workshop will continue presenting work on a broad and interesting range of topics in NLP.

BioNLP 2022 will be particularly interested in work on detection and mitigation of bias, BioNLP research in languages other than English, particularly, under-represented languages, and health disparities.

Other 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;
• Τext simplification;
• Question Answering;
• Resources and strategies for system testing and evaluation;
• Infrastructures and pre-trained language models for biomedical NLP / Processing and annotation platforms;
• Development of synthetic data;
• Translating NLP research into practice;
• Getting reproducible results.

Program Committee

 * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK 
 * Saadullah Amin, Saarland University, Germany
 * Emilia Apostolova, Anthem, Inc., USA
 * Eiji Aramaki, University of Tokyo, Japan 
 * Timothy Baldwin, University of Melbourne, Australia
 * Spandana Balumuri, National Institute of Technology Karnataka, India
 * Steven Bethard, University of Arizona, USA
 * Robert Bossy, Inrae, Université Paris Saclay, France
 * Berry de Bruijn, National Research Council Canada 
 * Leonardo Campillos-Llanos, Centro Superior de Investigaciones Científicas - CSIC, Spain
 * Kevin Bretonnel Cohen, University of Colorado School of Medicine, USA 
 * Fenia Christopoulou, Huawei Noah's Ark lab, UK
 * Brian Connolly, Ohio, USA
 * Mike Conway, University of Utah, USA
 * Manirupa Das, Amazon, USA
 * Surabhi Datta, The University of Texas Health Science Center at Houston, USA 
 * Dina Demner-Fushman, US National Library of Medicine 
 * Dmitriy Dligach,  Loyola University Chicago, USA
 * Kathleen C. Fraser,  National Research Council Canada
 * Travis Goodwin, US National Library of Medicine 
 * Natalia Grabar, CNRS, U Lille, France
 * Cyril Grouin, LIMSI - CNRS, France 
 * Tudor Groza, EMBL-EBI
 * Deepak Gupta, US National Library of Medicine 
 * Sam Henry, Christopher Newport University, USA
 * William Hogan, UCSD, USA
 * Kexin Huang, Stanford University, USA
 * Brian Hur, University of Melbourne, Australia
 * Richard Jackson, AstraZeneca
 * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 * Sarvnaz Karimi, CSIRO, Australia
 * Nazmul Kazi,  Montana State University, USA
 * Won Gyu KIM, US National Library of Medicine 
 * Ari Klein, University of Pennsylvania, USA
 * Roman Klinger, University of Stuttgart, Germany
 * Andre Lamurias, Aalborg University, DK
 * Majid Latifi, National College of Ireland 
 * Alberto Lavelli, FBK-ICT, Italy
 * Robert Leaman, US National Library of Medicine 
 * Lung-Hao Lee, National Central University, Taiwan
 * Ulf Leser, Humboldt-Universität zu Berlin, Germany 
 * Diwakar Mahajan,  IBM Thomas J. Watson Research Center, USA
 * Mark-Christoph Müller, Heidelberg Institute for Theoretical Studies, Germany
 * Claire Nédellec, INRA, Université Paris-Saclay, FR
 * Guenter Neumann, DFKI, Saarland, Germany
 * Aurelie Neveol, LIMSI - CNRS, France 
 * Mariana Neves, Hasso-Plattner-Institute at the University of Potsdam, Germany
 * Yifan Peng,  Weill Cornell Medical College, USA
 * Francisco J. Ribadas-Pena, Universidade de Vigo, Spain
 * Anthony Rios, The University of Texas at San Antonio, USA
 * Angus Roberts, King's College London, UK 
 * Kirk Roberts, The University of Texas Health Science Center at Houston, USA 
 * Roland Roller, DFKI, Germany
 * Mourad Sarrouti, Sumitovant Biopharma, Inc., USA
 * Mario Sänger, Humboldt-Universität zu Berlin, Germany 
 * Diana Sousa, Universidade de Lisboa, Portugal
 * Michael Spranger, Sony, Tokyo, Japan
 * Peng Su, University of Delaware, USA
 * Madhumita Sushil, University of California, San Francisco, USA
 * Karin Verspoor, RMIT University, Melbourne, Australia 
 * Roger Wattenhofer, ETH Zurich, Switzerland
 * Leon Weber, Humboldt Universität Berlin, Germany
 * Nathan M. White, James Cook University, Australia
 * Davy Weissenbacher, University of Pennsylvania, USA
 * W John Wilbur, US National Library of Medicine 
 * Amelie Wührl,  University of Stuttgart, Germany
 * Dongfang Xu, Harvard University, USA
 * Shweta Yadav, University of Illinois Chicago, USA
 * Jingqing Zhang,  Imperial College London, UK
 * Ayah Zirikly, Johns Hopkins University, USA
 * Pierre Zweigenbaum, LIMSI - CNRS, France

SHARED TASK: MedVidQA 2022

The first challenge on Medical Video Question Answering is collocated with the BioNLP 2022 Workshop. MedVidQA focuses on providing relevant segments of videos as answers to health-related questions. Medical videos may provide the best possible answers to many first aid, medical emergency, and medical education questions. Please check the challenge website for details on the tasks, datasets, and submission guidelines: https://medvidqa.github.io

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 

Dual submission policy

Papers may NOT be submitted to the BioNLP 2022 workshop if they are or will be concurrently submitted to another meeting or publication.