BioNLP Workshop

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An ACL 2017 Workshop associated with the SIGBIOMED special interest group, featuring an associated task: BioASQ (

Vancouver, Canada, Friday August 4, 2017


  • Submission deadline: Wednesday April 26, 2017 11:59 PM Eastern US
  • Notification of acceptance: Monday May 22, 2017
  • 'Camera-ready copy due from authors: Friday May 26, 2017
  • Workshop: Friday August 4, 2017

BIONLP 2017 Workshop Schedule

Friday August 4, 2017
8:30–8:45Opening remarks
8:45–10:30Session 1: Prediction and relation extraction
8:45–9:00Target word prediction and paraphasia classification in spoken discourse
  • Joel Adams, Steven Bedrick, Gerasimos Fergadiotis, Kyle Gorman and Jan van Santen
  • 9:00–9:15Extracting Drug-Drug Interactions with Attention CNNs
  • Masaki Asada, Makoto Miwa, Yutaka Sasaki
  • 9:15–9:30Insights into Analogy Completion from the Biomedical Domain
  • Denis Newman-Griffis, Albert Lai, Eric Fosler-Lussier
  • 9:30–9:45Deep learning for extracting protein-protein interactions from biomedical literature
  • Yifan Peng and Zhiyong Lu
  • 9:45–10:00Stacking With Auxiliary Features for Entity Linking in the Medical Domain
  • Nazneen Fatema Rajani, Mihaela Bornea, Ken Barker
  • 10:00–10:30Invited Talk: Results of the 5th edition of BioASQ Challenge
    Speaker: Georgios Paliouras
    10:30–11:00Coffee Break
    11:00–12:30Session 2: BioASQ 2017 and more
    11:00–11:15Tackling Biomedical Text Summarization: OAQA at BioASQ 5B
  • Khyathi Chandu, Aakanksha Naik, Aditya Chandrasekar, Zi Yang, Niloy Gupta, Eric Nyberg
  • 11:15–11:30Macquarie University at BioASQ 5b -- Query-based Summarisation Techniques for Selecting the Ideal Answers
  • Diego Molla
  • 11:30–11:45Neural Question Answering at BioASQ 5B
  • Georg Wiese, Dirk Weissenborn, Mariana Neves
  • 11:45–12:00End-to-End System for Bacteria Habitat Extraction
  • Farrokh Mehryary, Kai Hakala, Suwisa Kaewphan, Jari Björne, Tapio Salakoski, Filip Ginter
  • 12:00–12:15Creation and evaluation of a dictionary-based tagger for virus species and proteins
  • Helen Cook, Rudolfs Berzins, Cristina Leal Rodrıguez, Juan Miguel Cejuela, Lars Juhl Jensen
  • 12:15–12:30Representation of complex terms in a vector space structured by an ontology for a normalization task
  • Arnaud Ferré, Pierre Zweigenbaum, Claire Nédellec
  • 12:30–14:00Lunch break
    14:00–15:30Session 3: From bio to clinical NLP
    14:00–14:15Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second--Order Vectors
  • Bridget McInnes and Ted Pedersen
  • 14:15–14:30Proactive Learning for Named Entity Recognition
  • Maolin Li, Nhung Nguyen, Sophia Ananiadou
  • 14:30–14:45Biomedical Event Extraction using Abstract Meaning Representation
  • Sudha Rao, Daniel Marcu, Kevin Knight, Hal Daumé III
  • 14:45–15:00Detecting Personal Medication Intake in Twitter: An Annotated Corpus and Baseline Classification System
  • Ari Klein, Abeed Sarker, Masoud Rouhizadeh, Karen O'Connor, Graciela Gonzalez
  • 15:00–15:15Unsupervised Context-Sensitive Spelling Correction of Clinical Free-Text with Word and Character N-Gram Embeddings
  • Pieter Fivez, Simon Suster, Walter Daelemans
  • 15:15–15:30Characterization of Divergence in Impaired Speech of ALS Patients
  • Archna Bhatia, Bonnie Dorr, Kristy Hollingshead, Samuel L. Phillips, Barbara McKenzie
  • 15:30–16:00Coffee Break
    16:00–16:30Session 3: More clinical NLP
    16:00–16:15Deep Learning for Punctuation Restoration in Medical Reports
  • Wael Salloum, Greg Finley, Erik Edwards, Mark Miller, David Suendermann-Oeft
  • 16:15–16:30Unsupervised Domain Adaptation for Clinical Negation Detection
  • Timothy Miller, Steven Bethard, Hadi Amiri, Guergana Savova
  • 16:30–18:00Poster Session
     BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations
  • Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Sun Kim, Chih-Hsuan Wei, Yifan Peng, Donald Comeau, Zhiyong Lu
  •  Painless Relation Extraction with Kindred
  • Jake Lever and Steven Jones
  •  Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction
  • Gang Li, Cathy Wu, K. Vijay-Shanker
  •  Role-Preserving Redaction of Medical Records to Enable Ontology-Driven Processing
  • Seth Polsley, Atif Tahir, Muppala Raju, Akintayo Akinleye, Duane Steward
  •  Annotation of pain and anesthesia events for surgery-related processes and outcomes extraction
  • Wen-wai Yim, Dario Tedesco, Catherine Curtin, Tina Hernandez-Boussard
  •  Identifying Comparative Structures in Biomedical Text
  • Samir Gupta, A.S.M. Ashique Mahmood, Karen Ross, Cathy Wu, K. Vijay-Shanker
  •  Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models
  • Subhradeep Kayal, Zubair Afzal, George Tsatsaronis, Sophia Katrenko, Pascal Coupet, Marius Doornenbal, Michelle Gregory
  •  Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs
  • Sunil Mohan, Nicolas Fiorini, Sun Kim, Zhiyong Lu
  •  Detecting Dementia through Retrospective Analysis of Routine Blog Posts by Bloggers with Dementia
  • Vaden Masrani, Gabriel Murray, Thalia Field, Giuseppe Carenini
  •  Protein Word Detection using Text Segmentation Techniques
  • Devi Ganesan, Ashish V. Tendulkar, Sutanu Chakraborti
  •  External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway
  • Wojciech Kusa and Michael Spranger
  •  Toward Automated Early Sepsis Alerting: Identifying Infection Patients from Nursing Notes
  • Emilia Apostolova and Tom Velez
  •  Enhancing Automatic ICD-9-CM Code Assignment for \\Medical Texts with PubMed
  • Danchen Zhang, Daqing He, Sanqiang Zhao, Lei Li
  •  Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation
  • Sam Henry, Clint Cuffy, Bridget McInnes
  •  Investigating the Documentation of Electronic Cigarette Use in the Veteran Affairs Electronic Health Record: A Pilot Study
  • Danielle Mowery, Brett South, Olga Patterson, Shu-Hong Zhu, Mike Conway
  •   Automated Preamble Detection in Dictated Medical Reports
  • Wael Salloum, Greg Finley, Erik Edwards, Mark Miller, David Suendermann-Oeft
  •  A Biomedical Question Answering System in BioASQ 2017
  • Mourad Sarrouti and Said Ouatik El Alaoui
  •  Adapting Pre-trained Word Embeddings For Use In Medical Coding
  • Kevin Patel, Divya Patel, Mansi Golakiya, Pushpak Bhattacharyya, Nilesh Birari
  •  Initializing neural networks for hierarchical multi-label text classification
  • Simon Baker and Anna Korhonen
  •  Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models
  • Rahul V S S Patchigolla, Sunil Sahu, Ashish Anand
  •  Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks
  • Chen Lin, Timothy Miller, Dmitriy Dligach, Steven Bethard, Guergana Savova
  •  Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods
  • Sarvnaz Karimi, Xiang Dai, Hamedh Hassanzadeh, Anthony Nguyen
  •  Automatic classification of doctor-patient questions for a virtual patient record query task.
  • Leonardo Campillos Llanos, Sophie Rosset, Pierre Zweigenbaum
  •  Assessing the performance of Olelo, a real-time biomedical question answering application
  • Mariana Neves, Fabian Eckert, Hendrik Folkerts, Matthias Uflacker
  •  Clinical Event Detection with Hybrid Neural Architecture
  • Adyasha Maharana
  •  Extracting Personal Medical Events for User Timeline Construction using Minimal Supervision
  • Aakanksha Naik, Chris Bogart, Carolyn Rose
  •  Detecting mentions of pain and acute confusion in Finnish clinical text
  • Hans Moen, Kai Hakala, Farrokh Mehryary, Laura-Maria Peltonen, Tapio Salakoski, Filip Ginter, Sanna Salanterä
  •  A Multi-strategy Query Processing Approach for Biomedical Question Answering: USTB\_PRIR at BioASQ 2017 Task 5B
  • Zan-Xia Jin, Bo-Wen Zhang, Fan Fang, Le-Le Zhang, Xu-Cheng Yin

    Over the course of the past fifteen years, 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 for a broad range of semantic categories
    • Extraction of complex relations and events
    • Semantic parsing
    • 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
    • Theoretical underpinnings of biomedical language processing
    • Research Reproducibility

    Program Committee:

     * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK 
     * Ion Androutsopoulos, Athens University of Economics and Business, Greece
     * Emilia Apostolova,, USA
     * Eiji Aramaki, University of Tokyo, Japan 
     * Alan Aronson, US National Library of Medicine 
     * Asma Ben Abacha, US National Library of Medicine 
     * Olivier Bodenreider, US National Library of Medicine 
     * Leonardo Campillos Llanos, LIMSI - CNRS, France
     * Juan Miguel Cejuela, Technische Universität München, Germany
     * Kevin Bretonnel Cohen, University of Colorado School of Medicine, USA 
     * Nigel Collier, University of Cambridge, UK 
     * Dina Demner-Fushman, US National Library of Medicine 
     * Filip Ginter, University of Turku, Finland 
     * Graciela Gonzalez, University of Pennsylvania, USA
     * Cyril Grouin, LIMSI - CNRS, France 
     * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
     * Aris Kosmopoulos, NCSR Demokritos, Greece
     * Halil Kilicoglu, US National Library of Medicine
     * Robert Leaman, US National Library of Medicine 
     * Chris Lu, US National Library of Medicine 
     * Zhiyong Lu, US National Library of Medicine 
     * Prodromes Malakasiotis, Athens University of Economics and Business, Greece
     * Timothy Miller, Children’s Hospital Boston, USA 
     * Makoto Miwa, Toyota Technological Institute, Japan 
     * Diego Molla, Macquarie University, Australia
     * Jim Mork, National Library of Medicine, USA
     * Danielle L Mowery, VA Salt Lake City Health Care System, USA
     * Yassine M'Rabet, US National Library of Medicine
     * Henning Müller, University of Applied Sciences, Switzerland
     * Claire Nédellec, INRA, France
     * Anastasios Nentidis, NCSR Demokritos, Athens, Greece 
     * Aurelie Neveol, LIMSI - CNRS, France 
     * Mariana Neves, Hasso Plattner Institute and University of Potsdam, Germany
     * Nhung Nguyen, The University of Manchester, UK
     * Naoaki Okazaki, Tohoku University, Japan 
     * Georgios Paliouras, NCSR Demokritos, Athens, Greece 
     * Ioannis Partalas, Viseo group, France
     * John Prager, Thomas J. Watson Research Center, IBM, USA
     * Sampo Pyysalo, University of Cambridge, UK 
     * Francisco J. Ribadas-Pena, University of Vigo, Spain
     * Fabio Rinaldi,  University of Zurich, Switzerland 
     * Kirk Roberts, The University of Texas Health Science Center at Houston, USA 
     * Angus Roberts, The University of Sheffield, UK 
     * Hagit Shatkay, University of Delaware, USA 
     * Pontus Stenetorp, University College London, UK
     * Karin Verspoor, The University of Melbourne, Australia 
     * Ellen Voorhees, National Institute of Standards and Technology, USA
     * Byron C. Wallace,  University of Texas at Austin, USA 
     * W John Wilbur, US National Library of Medicine 
     * Hai Zhao, Shanghai Jiao Tong University, Shanghai
     * Pierre Zweigenbaum, LIMSI - CNRS, France

    Additional Reviewers:

     * Moumita Bhattacharya, University of Delaware, USA
     * Louise Deleger, INRA - MaIAGE, France
     * Lenz Furrer, Institute of Computational Linguistics, UZH, Zurich, Switzerland 
     * Genevieve Gorrell, Sheffield University, UK 
     * Ari Klein, University of Pennsylvania School of Medicine 
     * Yifan Peng, US National Library of Medicine 
     * Vassiliki Rentoumi, National Centre for Scientific Research Demokritos, Athens, Greece 
     * Masoud Rouhizadeh, University of Pennsylvania, USA 
     * Abeed Sarker, University of Pennsylvania, USA 
     * Xingyi Song, University of Sheffield, UK 
     * Tasnia Tahsin, Arizona State University, USA 
     * Hegler Tissot, Federal University of Parana, Brazil 
     * Ken Yano, Nara Institute of Science and Technology, Japan 


     Kevin Bretonnel Cohen, University of Colorado School of Medicine
     Dina Demner-Fushman, US National Library 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

    VISA information

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    ACL Anti-Harassment Policy

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