BioNLP 2023
BIONLP 2017
An ACL 2017 Workshop associated with the SIGBIOMED special interest group, featuring an associated task: BioASQ ( http://www.bioasq.org/)
Vancouver, Canada, Friday August 4, 2017
IMPORTANT DATES
- 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 | |
8:30–8:45 | Opening remarks |
8:45–10:30 | Session 1: Prediction and relation extraction |
8:45–9:00 | Target word prediction and paraphasia classification in spoken discourse
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9:00–9:15 | Extracting Drug-Drug Interactions with Attention CNNs
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9:15–9:30 | Insights into Analogy Completion from the Biomedical Domain
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9:30–9:45 | Deep learning for extracting protein-protein interactions from biomedical literature
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9:45–10:00 | Stacking With Auxiliary Features for Entity Linking in the Medical Domain
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10:00–10:30 | Invited Talk: Results of the 5th edition of BioASQ Challenge Speaker: Georgios Paliouras |
10:30–11:00 | Coffee Break |
11:00–12:30 | Session 2: BioASQ 2017 and more |
11:00–11:15 | Tackling Biomedical Text Summarization: OAQA at BioASQ 5B
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11:15–11:30 | Macquarie University at BioASQ 5b -- Query-based Summarisation Techniques for Selecting the Ideal Answers
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11:30–11:45 | Neural Question Answering at BioASQ 5B
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11:45–12:00 | End-to-End System for Bacteria Habitat Extraction
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12:00–12:15 | Creation and evaluation of a dictionary-based tagger for virus species and proteins |
12:15–12:30 | Representation of complex terms in a vector space structured by an ontology for a normalization task |
12:30–14:00 | Lunch break |
14:00–15:30 | Session 3: From bio to clinical NLP |
14:00–14:15 | Improving Correlation with Human Judgments by Integrating Semantic Similarity with Second--Order Vectors
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14:15–14:30 | Proactive Learning for Named Entity Recognition
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14:30–14:45 | Biomedical Event Extraction using Abstract Meaning Representation
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14:45–15:00 | Detecting Personal Medication Intake in Twitter: An Annotated Corpus and Baseline Classification System
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15:00–15:15 | Unsupervised Context-Sensitive Spelling Correction of Clinical Free-Text with Word and Character N-Gram Embeddings
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15:15–15:30 | Characterization of Divergence in Impaired Speech of ALS Patients
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15:30–16:00 | Coffee Break |
16:00–16:30 | Session 3: More clinical NLP |
16:00–16:15 | Deep Learning for Punctuation Restoration in Medical Reports
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16:15–16:30 | Unsupervised Domain Adaptation for Clinical Negation Detection
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16:30–18:00 | Poster Session |
BioCreative VI Precision Medicine Track: creating a training corpus for mining protein-protein interactions affected by mutations | |
Painless Relation Extraction with Kindred
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Noise Reduction Methods for Distantly Supervised Biomedical Relation Extraction | |
Role-Preserving Redaction of Medical Records to Enable Ontology-Driven Processing | |
Annotation of pain and anesthesia events for surgery-related processes and outcomes extraction | |
Identifying Comparative Structures in Biomedical Text
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Tagging Funding Agencies and Grants in Scientific Articles using Sequential Learning Models | |
Deep Learning for Biomedical Information Retrieval: Learning Textual Relevance from Click Logs | |
Detecting Dementia through Retrospective Analysis of Routine Blog Posts by Bloggers with Dementia | |
Protein Word Detection using Text Segmentation Techniques | |
External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway | |
Toward Automated Early Sepsis Alerting: Identifying Infection Patients from Nursing Notes | |
Enhancing Automatic ICD-9-CM Code Assignment for \\Medical Texts with PubMed
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Evaluating Feature Extraction Methods for Knowledge-based Biomedical Word Sense Disambiguation
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Investigating the Documentation of Electronic Cigarette Use in the Veteran Affairs Electronic Health Record: A Pilot Study
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Automated Preamble Detection in Dictated Medical Reports
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A Biomedical Question Answering System in BioASQ 2017
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Adapting Pre-trained Word Embeddings For Use In Medical Coding
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Initializing neural networks for hierarchical multi-label text classification
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Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models
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Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks
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Automatic Diagnosis Coding of Radiology Reports: A Comparison of Deep Learning and Conventional Classification Methods
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Automatic classification of doctor-patient questions for a virtual patient record query task.
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Assessing the performance of Olelo, a real-time biomedical question answering application
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Clinical Event Detection with Hybrid Neural Architecture
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Extracting Personal Medical Events for User Timeline Construction using Minimal Supervision
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Detecting mentions of pain and acute confusion in Finnish clinical text
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A Multi-strategy Query Processing Approach for Biomedical Question Answering: USTB\_PRIR at BioASQ 2017 Task 5B
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WORKSHOP OVERVIEW AND SCOPE
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, Language.ai, 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
Organizers:
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
ACL organizers provide letters needed for visas. Please scroll to the bottom of this page: http://acl2017.org/participants/ and click "Visa Letter Request Form."
ACL Anti-Harassment Policy
https://www.aclweb.org/adminwiki/index.php?title=Anti-Harassment_Policy
If you have any concerns or experience harassment or hostile behavior please contact Dina Demner-Fushman, Kevin Bretonnel Cohen or any current member of the ACL Executive Committee.