Difference between revisions of "BioNLP 2023"

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==BIONLP 2014 1st Call for Papers==
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[[SIGBIOMED]]
  
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An ACL 2014 2-day Workshop associated with the SIGBIOMED special interest group Featuring a special track on NLP approaches for assessment of clinical conditions and a panel on shared tasks.
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==BIONLP 2016 ==
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 +
An ACL 2016 Workshop associated with the [[SIGBIOMED]] special interest group Featuring two associated tasks: [http://www.bioasq.org/workshop/  BioASQ] (http://www.bioasq.org/workshop) and [http://2016.bionlp-st.org/  BioNLP-ST]  (http://2016.bionlp-st.org).
 +
 
 +
Berlin, Germany, August 12 -13, 2016
 +
 
 +
===IMPORTANT DATES===
 +
 
 +
* Submission deadline: Sunday, May 8, 2016, 11:59 PM Eastern US
 +
* Notification of acceptance: Monday, June 13, 2016
 +
* Camera-ready copy due from authors:  Wednesday, June 22, 2016
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* BioNLP workshop: Friday, August 12, 2016
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* BioNLP-ST and BioASQ workshop: Saturday August 13, 2016
 +
 
 +
 
 +
===WORKSHOP OVERVIEW AND SCOPE===
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 +
Over the course of the past fourteen 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:
 +
 
 +
* Entity identification and normalization for a broad range of semantic categories
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* Extraction of complex relations and events
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* Semantic parsing
 +
* Discourse analysis
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* Anaphora /Coreference resolution
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* Text mining
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** Literature based discovery
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* Summarization
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* Question Answering
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* Resources and novel strategies for system testing and evaluation
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** Infrastructures for biomedical text mining
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* Processing and annotation platforms
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* Translating NLP research to practice
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* Theoretical underpinnings of biomedical language processing
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 +
<h5>SUBMISSION INSTRUCTIONS</h5>
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We invite two types of submissions: full papers and short papers.
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Submissions are due by 11:59 PM EST on Sunday May 8, 2016.
 +
 
 +
Full papers should not exceed eight (8) pages of text, plus unlimited references. These are intended to be
 +
reports of original research. BioNLP aims to be the forum for interesting, innovative, and promising work
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involving biomedicine and language technology, whether or not yielding high performance at the moment.
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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. 
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Short papers may consist of up to four (4) pages of content, plus unlimited references.
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Appropriate short paper topics include preliminary results, application notes, descriptions of work in progress, etc.
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 +
<h6>Electronic Submission</h6>
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Submissions must be electronic and in PDF format, using the Softconf START conference management system at [https://www.softconf.com/acl2016/BioNLP16/ https://www.softconf.com/acl2016/BioNLP16/]
 +
We strongly recommend the use of ACL LaTeX style files tailored for this year's conference. Submissions must conform to the official style guidelines. Style files and other information about paper formatting requirements will be made available on the conference website,[http://acl2016.org http://acl2016.org].
 +
 
 +
<b>Submissions should be anonymous. </b>
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Dual submission policy: papers may <b>NOT</b> be submitted to  the BioNLP 2016 workshop if they are or will be concurrently submitted to another meeting or publication.
 +
 +
<h5>Tentative Program Committee:</h5>
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 +
* Emilia Apostolova, DePaul University, Chicago, USA
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* Eiji Aramaki, University of Tokyo, Japan
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* Asma Ben Abacha, National Library of Medicine, USA
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* Sabine Bergler, Concordia University, Canada
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* Olivier Bodenreider, National Library of Medicine, USA
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* Aaron Cohen, Oregon Health and Science University, USA
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* Nigel Collier, University of Cambridge, UK
 +
<!-- * Noémie Elhadad, Columbia University, USA -->
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* Marcelo Fiszman, National Library of Medicine, USA
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* Filip Ginter, University of Turku, Finland
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* Cyril Grouin, LIMSI - CNRS, France
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* Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
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* Halil Kilicoglu, National Library of Medicine, USA
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* Jin-Dong Kim, Database Center for Life Science, Japan
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* Robert Leaman, National Library of Medicine, USA
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* Ulf Leser, Humboldt-Universität zu Berlin, Germany
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* Zhiyong Lu, National Library of Medicine, USA
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* Timothy Miller, Children's Hospital Boston, USA
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* Makoto Miwa, Toyota Technological Institute, Japan
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* Danielle Mowery, University of Utah, USA
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* Yassine M'Rabet, National Library of Medicine, USA
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* Aurelie Neveol, LIMSI - CNRS, France
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* Nhung Nguyen, University of Manchester, UK
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* Naoaki Okazaki, Tohoku University, Japan
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* Jong Park, KAIST, Republic of Korea
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* Sampo Pyysalo, University of Cambridge, UK
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* Bastien Rance, Hopital Europeen Georges Pompidou, France
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* Fabio Rinaldi, University of Zurich, Switzerland
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* Thomas Rindflesch, National Library of Medicine
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* Angus Roberts, University of Sheffield, UK
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* Kirk Roberts, National Library of Medicine, USA
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* Yoshimasa Tsuruoka, University of Tokyo, Japan
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* Karin Verspoor, The University of Melbourne, Australia
 +
* Byron Wallace,  University of Texas at Austin, USA
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* John Wilbur, National Library of Medicine, USA
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* Pierre Zweigenbaum,  LIMSI - CNRS, France
 +
 
 +
<h5>Organizers</h5>
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  * Kevin Bretonnel Cohen, University of Colorado School of Medicine
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  * Dina Demner-Fushman, US National Library of Medicine
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  * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
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  * Jun-ichi Tsujii, National Institute of Advanced Industrial Science and Technology, Japan
 +
 
 +
 
 +
<h5>Two tasks will be associated with the workshop this year:</h5>
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The <b>BioNLP Shared Task (BioNLP-ST)</b> has been organized three times so far, leading to the development of information extraction systems for molecular biology and medicine in 2009, 2011 and 2013. One of the major contributions of BioNLP-ST is the availability of resources such as high quality manually curated corpora, tools, and evaluation services.
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<h5>Shared Task Organizers:</h5>
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* Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan
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* Claire Nedellec, INRA, France
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* Robert Bossy, INRA, France
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The second equally successful shared task, the <b>BioASQ challenge</b> on large-scale biomedical semantic indexing and question answering has been running on an annual basis since 2012. The results of the challenge were presented in a workshop, which has so far been taking place in conjunction with the CLEF conference and was extremely well-attended.
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BioASQ assesses the performance of information systems in supporting two tasks that are central in the biomedical question answering process: (a) the indexing of large volumes of unlabeled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material.  BioASQ has been making publicly available the following benchmark data and tools: more than 1300 questions and related answers, as well as online "oracle" for objective evaluation of any system throughout the year, not only during the challenge.
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<h5>BioASQ Organizers:</h5>
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* Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA
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* Ioannis Kakadiaris University of Houston, USA
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* Anastasia Krithara, NCSR "Demokritos", Greece
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 +
 
 +
<!-- ==BIONLP 2015 Workshop Schedule==
 +
 
 +
<table cellspacing="0" cellpadding="5" border="0">
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<tr><td colspan=2><b>Thursday, July 30</b></td></tr>
 +
<tr><td style="width:10%; vertical-align:top">8:00&#8211;8:20</td><td valign=top><b> Opening remarks</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 1: Reading biomedical literature</b></td></tr>
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<tr><td valign=top>8:20&#8211;8:40</td><td>Complex Event Extraction using DRUM<br><em>James Allen<sup>1</sup>,&nbsp;Will de Beaumont<sup>2</sup>,&nbsp;Lucian Galescu<sup>2</sup>,&nbsp;Choh Man Teng<sup>2</sup></em><br><sup>1</sup>Institute for Human and Machine Cognition and University of Rochester, <sup>2</sup>Institute for Human and Machine Cognition</td></tr>
 +
<tr><td valign=top>8:40&#8211;9:00</td><td>Making the most of limited training data using distant supervision<br><em>Roland Roller and Mark Stevenson</em><br>University of Sheffield</td></tr>
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<tr><td valign=top>9:00&#8211;9:20</td><td>An extended dependency graph for relation extraction in biomedical texts<br><em>Yifan Peng<sup>1</sup>,&nbsp;Samir Gupta<sup>2</sup>,&nbsp;Cathy Wu<sup>2</sup>,&nbsp;Vijay Shanker<sup>2</sup></em><br><sup>1</sup>Computer and Information Sciences,  University of Delaware,&nbsp;<sup>2</sup>University of Delaware</td></tr>
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<tr><td valign=top>9:20&#8211;9:40</td><td>Event Extraction in pieces:Tackling the partial event identification problem on unseen corpora<br><em>Chrysoula Zerva and Sophia Ananiadou</em><br>University of Manchester</td></tr>
 +
<tr><td valign=top>9:40&#8211;10:00</td><td>Extracting Biological Pathway Models From NLP Event Representations<br><em>Michael Spranger<sup>1</sup>,&nbsp;Sucheendra Palaniappan<sup>2</sup>,&nbsp;Samik Ghosh<sup>3</sup></em><br><sup>1</sup>Sony Computer Science Laboratories Inc., <sup>2</sup>INRIA, Campus de Beaulieu, Rennes, France, <sup>3</sup>The Systems Biology Institute, Minato-ku, Tokyo, Japan</td></tr>
 +
<tr><td valign=top>10:00&#8211;10:20</td><td>Shallow Training is cheap but is it good enough? Experiments with Medical Fact Coding<br><em>Ramesh Nallapati and Radu Florian</em><br>IBM T. J. Watson Research Center</td></tr>
 +
<tr><td valign=top>10:30&#8211;11:00</td><td valign=top><b>Coffee Break</b></td></tr>
 +
<tr><td valign=top>11:00&#8211;11:45</td><td valign=top><b><font face="verdana" color="#000080"> Keynote: "Machine Reading: Attempting to model and understand biological processes" - Christopher Manning</font></b></td></tr>
 +
<tr><td valign=top>11:45&#8211;12:30</td><td valign=top><b><font face="verdana" color="#000080"> Keynote: “The DARPA Big Mechanism Program” - Kevin Knight</font></b></td></tr>
 +
<tr><td valign=top>12:30&#8211;14:00</td><td valign=top><b>Lunch</b></td></tr>
 +
<tr><td valign=top>14:00&#8211;15:00</td><td valign=top><b>Poster session</b></td></tr>
 +
<tr><td valign=top>15:00&#8211;15:30</td><td valign=top><b><font face="verdana" color="#000080"> Invited Talk: “Overview of BioCreative V Challenge Tasks” - Zhiyong Lu</font></b></td></tr>
 +
<tr><td valign=top>15:30&#8211;16:00</td><td valign=top><b>Coffee Break</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 2: Clinical text processing</b></td></tr>
 +
<tr><td valign=top>16:00&#8211;16:20</td><td>Stacked Generalization for Medical Concept Extraction from Clinical Notes<br><em>Youngjun Kim and Ellen Riloff</em><br>University of Utah</td></tr>
 +
<tr><td valign=top>16:20&#8211;16:40</td><td>Extracting Disease-Symptom Relationships by Learning Syntactic Patterns from Dependency Graphs<br><em>Mohsen Hassan<sup>1</sup>,&nbsp;Olfa Makkaoui<sup>2</sup>,&nbsp;Adrien Coulet<sup>1</sup>,&nbsp;Yannick Toussain<sup>1</sup></em><br><sup>1</sup>LORIA (CNRS, Inria NGE, Universit&eacute;  de Lorraine), <sup>2</sup>LORIA (Inria NGE)</td></tr>
 +
<tr><td valign=top>16:40&#8211;17:00</td><td>Extracting Time Expressions from Clinical Text<br><em>Timothy Miller<sup>1</sup>,&nbsp;Steven Bethard<sup>2</sup>,&nbsp;Dmitriy Dligach<sup>1</sup>,&nbsp;Chen Lin<sup>3</sup>,&nbsp;Guergana Savova<sup>4</sup></em><br><sup>1</sup>Boston Children's Hospital and Harvard Medical School, <sup>2</sup>University of Alabama at Birmingham, <sup>3</sup>Boston Children's Hospital, <sup>4</sup>Harvard</td></tr>
 +
<tr><td valign=top>17:00&#8211;17:20</td><td>Exploiting Task-Oriented Resources to Learn Word Embeddings for Clinical Abbreviation Expansion<br><em>Yue Liu<sup>1</sup>,&nbsp;Tao Ge<sup>2</sup>,&nbsp;Kusum Mathews<sup>3</sup>,&nbsp;Heng Ji<sup>1</sup>,&nbsp;Deborah McGuinness<sup>1</sup></em><br><sup>1</sup>Rensselaer Polytechnic Institute, <sup>2</sup>Key Laboratory of Computational Linguistics, Peking University, <sup>3</sup>Departments of Medicine and Emergency Medicine, Icahn School of Medicine at Mount Sinai</td></tr>
 +
<tr><td valign=top>17:20&#8211;17:40</td><td>Semantic Type Classification of Common Words in Biomedical Noun Phrases<br><em>Amy Siu and Gerhard Weikum</em><br>Max Planck Institute for Informatics</td></tr>
 +
<tr><td valign=top>17:40&#8211;18:00</td><td>CoMAGD: Annotation of Gene-Depression Relations<br><em>Rize Jin<sup>1</sup>,&nbsp;Jinseon You<sup>1</sup>,&nbsp;Jin-Woo Chung<sup>2</sup>,&nbsp;Hee-Jin Lee<sup>1</sup>,&nbsp;Maria Wolters<sup>3</sup>,&nbsp;Jong Park<sup>2</sup></em><br><sup>1</sup>Korea Advanced Institute of Science and Technology, <sup>2</sup>KAIST, <sup>3</sup>The University of Edinburgh</td></tr>
 +
<tr><td valign=top>18:00</td><td valign=top><b>Closing remarks</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Posters</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Lexical Characteristics Analysis of Chinese Clinical Documents<br><em>Meizhi Ju<sup>1</sup>,&nbsp;Haomin Li<sup>2</sup>,&nbsp;Huilong Duan<sup>1</sup></em><br><sup>1</sup>College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China., <sup>2</sup>The Children’s Hospital of Zhejiang University, Hangzhou, China;The Institute of Translational Medicine, Zhejiang University, Hangzhou, China.</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Using word embedding for bio-event extraction<br><em>Chen Li<sup>1</sup>,&nbsp;Runqing Song<sup>2</sup>,&nbsp;Maria Liakata<sup>3</sup>,&nbsp;Andreas Vlachos<sup>4</sup>,&nbsp;Stephanie Seneff<sup>1</sup>,&nbsp;Xiangrong Zhang<sup>2</sup></em><br><sup>1</sup>Massachusetts Institute of Technology, <sup>2</sup>Xidian University, <sup>3</sup>University of Warwick, <sup>4</sup>University College London</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Measuring the readability of medical research journal abstracts<br><em>Samuel J. Severance<sup>1</sup> and K. Bretonnel Cohen<sup>2</sup></em><br><sup>1</sup>School of Education, Institute of Cognitive Science, University of Colorado, <sup>2</sup>U. Colorado School of Medicine</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Translating Electronic Health Record Notes from English to Spanish: A Preliminary Study<br><em>Weisong Liu<sup>1</sup> and Shu Cai<sup>2</sup></em><br><sup>1</sup>UMass Medical School, <sup>2</sup>Information Sciences Institute</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Automatic Detection of Answers to Research Questions from Medline Abstracts<br><em>Abdulaziz Alamri<sup>1</sup> and Mark Stevenson<sup>2</sup></em><br><sup>1</sup>PhD Student, The university of Sheffield, <sup>2</sup>University of Sheffield</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>A preliminary study on automatic identification of patient smoking status in unstructured electronic health records<br><em>Jitendra Jonnagaddala<sup>1</sup>,&nbsp;Hong-Jie Dai<sup>2</sup>,&nbsp;Pradeep Ray<sup>1</sup>,&nbsp;Siaw-Teng Liaw<sup>1</sup></em><br><sup>1</sup>UNSW Australia, <sup>2</sup>Taipei Medical University</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Restoring the intended structure of Hungarian ophthalmology documents<br><em>Borbala Siklosi<sup>1</sup> and Attila Novak<sup>2</sup></em><br><sup>1</sup>Pazmany Peter Catholic University, <sup>2</sup>MTA-PPKE Hungarian Language Technology Research Group, Faculty of Information Technology and Bionics, Pazmany Peter Catholic University, Budapest</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Evaluating distributed word representations for capturing semantics of biomedical concepts<br><em>MUNEEB TH<sup>1</sup>,&nbsp;Sunil Sahu<sup>2</sup>,&nbsp;Ashish Anand<sup>2</sup></em><br><sup>1</sup>IIT GUWAHATI, <sup>2</sup>Indian Institute of Technology Guwahati</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Investigating Public Health Surveillance using Twitter<br><em>Antonio Jimeno Yepes<sup>1</sup>,&nbsp;Andrew MacKinlay<sup>1</sup>,&nbsp;Bo Han<sup>2</sup></em><br><sup>1</sup>IBM, <sup>2</sup>IBM Research</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Clinical Abbreviation Disambiguation Using Neural Word Embeddings<br><em>Yonghui Wu<sup>1</sup>,&nbsp;Jun Xu<sup>2</sup>,&nbsp;Yaoyun Zhang<sup>3</sup>,&nbsp;Hua Xu<sup>1</sup></em><br><sup>1</sup>The University of Texas Health Science Center at Houston, <sup>2</sup>School of Biomedical Informatics, The University of Texas Health Science Center at Houston, <sup>3</sup>University of Texas School of Biomedical Informatics at Houston</td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top>Representing Clinical Diagnostic Criteria in Quality Data Model Using Natural Language Processing<br><em>Na Hong<sup>1</sup>,&nbsp;Dingcheng Li<sup>1</sup>,&nbsp;Yue Yu<sup>1</sup>,&nbsp;Hongfang Liu<sup>1</sup>,&nbsp;Christopher G. Chute<sup>2</sup>,&nbsp;Guoqian Jiang<sup>1</sup></em><br><sup>1</sup>Mayo Clinic, <sup>2</sup>Johns Hopkins University</td></tr>
 +
</table>
 +
 
 +
 
 +
==BIONLP 2015 Call for Papers==
 +
 
 +
Date of workshop: July 30, 2015
 +
 
 +
Venue: BioNLP 2015 will be held in conjunction with ACL 2015 in Beijing, People’s Republic of China.
 +
 
 +
===IMPORTANT DATES===
 +
* 14 May 2015: Submission due date
 +
* 4 June 2015: Notification of acceptance
 +
* 21 June 2015: Camera-ready papers due
 +
* 30 July 2015: Workshop, Beijing, PRC
 +
 
 +
 
 +
Over the course of the past thirteen 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 this fast-growing and important domain. The workshop will continue presenting work on a broad and interesting range of topics in NLP.  Submissions are particularly solicited in the areas of:
 +
<ul>
 +
<li> Wide-scale entity identification and normalization </li>
 +
<li> Extraction of complex relations and events </li>
 +
<li> Discourse analysis </li>
 +
<li> Coreference resolution </li>
 +
<li> Text mining </li>
 +
<li> Literature based discovery </li>
 +
<li> Summarization </li>
 +
<li> Question-answering </li>
 +
<li> Lexical and terminological resources for BioNLP </li>
 +
<li> Annotation (corpora), standards </li>
 +
<li> Resources and strategies for system testing and evaluation </li>
 +
<li> Processing and annotation platforms </li>
 +
<li> Interoperable platforms for biomedical text mining </li>
 +
<li> Domain adaptation </li>
 +
<li> Translating NLP research to practice </li>
 +
</ul>
 +
 
 +
Submission instructions:
 +
 
 +
Long papers may consist of up to eight (8) pages of content, plus two pages for references; final versions of long papers will be given one additional page (up to 9 pages with 2 pages for references) so that reviewers’comments can be taken into account.
 +
 
 +
Poster submissions may consist of up to four (4) pages of content, plus 2 pages for references. Upon acceptance, short papers will be given five (5) pages in the proceedings and 2 pages for references. Authors are encouraged to use this additional page to address reviewers comments in their final versions.
 +
 
 +
https://www.softconf.com/acl2015/BioNLP/
 +
Authors who cannot submit a PDF file electronically should contact the workshop organizers well in advance of the submission deadline.
 +
Dual submission policy: note that papers may NOT be submitted to the BioNLP 2014 workshop if they are or will be concurrently submitted to another meeting or publication.
 +
Submissions should be anonymous.
 +
 
 +
-->
 +
<!--
 +
==BIONLP 2014 Workshop Schedule==
 +
Registration is now open (scroll to 2-Day Workshops): [http://acl2014.org/Registration.htm ACL 2014 Registration ]
 +
<table cellspacing="0" cellpadding="5" border="0"><tr><td colspan=2><h4>Thursday, June 26, 2014</h4></td></tr>
 +
<tr><td valign=top>9:00&#8211;9:10</td><td valign=top><b> Opening remarks</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 1: Processing biomedical publications</b></td></tr>
 +
<tr><td valign=top width=100>9:10&#8211;9:30</td><td valign=top align=left><i>Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses</i><br>
 +
Tasnia Tahsin, Robert Rivera, Rachel Beard, Rob Lauder, Davy Weissenbacher, Matthew Scotch, Garrick Wallstrom and Graciela Gonzalez</td></tr>
 +
<tr><td valign=top width=100>9:30&#8211;9:50</td><td valign=top align=left><i>Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature</i><br>
 +
Negacy Hailu, Natalya Panteleyeva and Kevin Cohen</td></tr>
 +
<tr><td valign=top width=100>9:50&#8211;10:10</td><td valign=top align=left><i>Classifying Negative Findings in Biomedical Publications</i><br>
 +
Bei Yu and Daniele Fanelli</td></tr>
 +
<tr><td valign=top width=100>10:10&#8211;10:30</td><td valign=top align=left><i>Automated Disease Normalization with Low Rank Approximations</i><br>
 +
Robert Leaman and Zhiyong Lu</td></tr>
 +
<tr><td valign=top>10:30&#8211;11:00</td><td valign=top><b>Coffee Break</b></td></tr>
 +
<tr><td valign=top>11:00&#8211;11:50</td><td valign=top><b>
 +
<font face="verdana" color="#000080"> Keynote by Junichi Tsujii: BioNLP as the Pioneering field of linking text, knowledge and data </font>
 +
</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 2: Processing consumer language</b></td></tr>
 +
<tr><td valign=top width=100>11:50&#8211;12:10</td><td valign=top align=left><i>Decomposing Consumer Health Questions</i><br>
 +
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman and Dina Demner-Fushman</td></tr>
 +
<tr><td valign=top width=100>12:10&#8211;12:30</td><td valign=top align=left><i>Detecting Health Related Discussions in Everyday Telephone Conversations for Studying Medical Events in the Lives of Older Adults</i><br>
 +
Golnar Sheikhshab, Izhak Shafran and Jeffrey Kaye</td></tr>
 +
<tr><td valign=top>12:30&#8211;2:00</td><td valign=top><b>Lunch</b></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 3: Processing clinical text and gray literature</b></td></tr>
 +
<tr><td valign=top width=100>2:00&#8211;2:20</td><td valign=top align=left><i>Coreference Resolution for Structured Drug Product Labels</i><br>
 +
Halil Kilicoglu and Dina Demner-Fushman</td></tr>
 +
<tr><td valign=top width=100>2:20&#8211;2:40</td><td valign=top align=left><i>Generating Patient Problem Lists from the ShARe Corpus using SNOMED CT/SNOMED CT CORE Problem List</i><br>
 +
Danielle Mowery, Mindy Ross, Sumithra Velupillai, Stephane Meystre, Janyce Wiebe and Wendy Chapman</td></tr>
 +
<tr><td valign=top width=100>2:40&#8211;3:00</td><td valign=top align=left><i>A System for Predicting ICD-10-PCS Codes from Electronic Health Records</i><br>
 +
Michael Subotin and Anthony Davis</td></tr>
 +
<tr><td valign=top width=100>3:00&#8211;3:20</td><td valign=top align=left><i>Structuring Operative Notes using Active Learning</i><br>
 +
Kirk Roberts, Sanda Harabagiu and Michael Skinner</td></tr>
 +
<tr><td valign=top>3:30-4:00</td><td valign=top><b>Afternoon Break</b></td></tr>
 +
<tr><td valign=top width=100>4:00&#8211;4:20</td><td valign=top align=left><i>Chunking Clinical Text Containing Non-Canonical Language</i><br>
 +
Aleksandar Savkov, John Carroll and Jackie Cassell</td></tr>
 +
<tr><td valign=top width=100>4:20&#8211;4:40</td><td valign=top align=left><i>Decision Style in a Clinical Reasoning Corpus</i><br>
 +
Limor Hochberg, Cecilia Ovesdotter Alm, Esa M. Rantanen, Caroline M. DeLong and Anne Haake</td></tr>
 +
<tr><td valign=top>4:40-5:30</td><td valign=top><b>Poster session</b></td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Temporal Expressions in Swedish Medical Text &#8211; A Pilot Study</i><br>
 +
Sumithra Velupillai</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>A repository of semantic types in the MIMIC II database clinical notes</i><br>
 +
Richard Osborne, Alan Aronson and Kevin Cohen</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Extracting drug indications and adverse drug reactions from Spanish health social media</i><br>
 +
Isabel Segura-Bedmar, Santiago de la Pe&ntilde;a Gonz&aacute;lez and Paloma Mart&iacute;nez</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Symptom extraction issue</i><br>
 +
Laure Martin, Delphine Battistelli and Thierry Charnois</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Seeking Informativeness in Literature Based Discovery</i><br>
 +
Judita Preiss</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Towards Gene Recognition from Rare and Ambiguous Abbreviations using a Filtering Approach</i><br>
 +
Matthias Hartung, Roman Klinger, Matthias Zwick and Philipp Cimiano</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>FFTM: A Fuzzy Feature Transformation Method for Medical Documents</i><br>
 +
Amir Karami and Aryya Gangopadhyay</td></tr>
 +
<tr><td colspan=2><h4>Friday, June 27, 2014</h4></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b>Session 1: NLP approaches for assessment of clinical conditions</b></td></tr>
 +
<tr><td valign=top width=100>9:00&#8211;9:40</td><td valign=top align=left><i>Using statistical parsing to detect agrammatic aphasia</i><br>
 +
Kathleen C. Fraser, Graeme Hirst, Jed A. Meltzer, Jennifer E. Mack and Cynthia K. Thompson
 +
<br>
 +
<font face="verdana" color="#000080"> Discussants: Thamar Solorio and Yang Liu </font></td></tr>
 +
<tr><td valign=top>&nbsp;</td><td valign=top><b><font face="verdana" color="#000080">Panel: Life cycles of BioCreative, BioNLP-ST, i2b2, TREC Medical tracks, and ShARe /CLEF/ SemEval</font></b></td></tr>
 +
<tr><td valign=top>9:40-10:05</td><td valign=top>BioCreative by Lynette Hirschman and John Wilbur</td></tr>
 +
<tr><td valign=top>10:05-10:30</td><td valign=top>BioNLP-ST by Sophia Ananiadou and Junichi Tsujii</td></tr>
 +
<tr><td valign=top>10:30-11:00</td><td valign=top><b>Coffee Break</b></td></tr>
 +
<tr><td valign=top>11:00-11:20</td><td valign=top>TREC Medical tracks by Ellen Voorhees</td></tr>
 +
<tr><td valign=top>11:20-11:25</td><td valign=top>Introduction to the TAC 2014 Biomedical Summarization Track by Lucy Vanderwende</td></tr>
 +
<tr><td valign=top>11:25-11:50</td><td valign=top>i2b2 by Ozlem Uzuner</td></tr>
 +
<tr><td valign=top>11:50-12:10</td><td valign=top>ShARe/CLEF/SemEval by Danielle Mowery, Sumithra Velupillai and Sameer Pradhan</td></tr>
 +
<tr><td valign=top>12:10-12:30</td><td valign=top>Discussion</td></tr>
 +
<tr><td valign=top>12:30-2:00</td><td valign=top><b>Lunch</b></td></tr>
 +
<tr><td valign=top>2:00-3:30</td><td valign=top><b><font face="verdana" color="#000080">Tutorial by Olivier Bodenreider: UMLS in biomedical text processing</font></b></td></tr>
 +
<tr><td valign=top>3:30-4:00</td><td valign=top>Afternoon Break</td></tr>
 +
<tr><td valign=top>4:00-5:30</td><td valign=top><b><font face="verdana" color="#000080">Tutorial by Alan R. Aronson: Using MetaMap</font></b></td></tr>
 +
</table>
 +
 
 +
 
 +
==BIONLP 2014 Call for Papers==
 +
 
 +
An ACL 2014 2-day Workshop associated with the [[SIGBIOMED]] special interest group Featuring a special track on NLP approaches for assessment of clinical conditions and a panel on shared tasks.
 
Baltimore, MD, June 26-27, 2014
 
Baltimore, MD, June 26-27, 2014
−
Workshop web site: http://aclweb.org/aclwiki/index.php?title=BioNLP_Workshop
 
−
 
  
 
===IMPORTANT DATES===
 
===IMPORTANT DATES===
Line 43: Line 330:
 
===KEYNOTE SPEAKER===
 
===KEYNOTE SPEAKER===
  
−
TBD
+
Jun-ichi Tsujii
  
 
===PANEL ON SHARED TASKS===
 
===PANEL ON SHARED TASKS===
Line 64: Line 351:
  
  
−
Short papers should not exceed four (4) pages including references.  
+
Short papers should not exceed four (4) pages plus at most 2 pages for references.  
 
Accepted short papers will be published in a separate section of the  
 
Accepted short papers will be published in a separate section of the  
 
workshop proceedings.  
 
workshop proceedings.  
Line 70: Line 357:
 
notes, descriptions of work in progress, etc.
 
notes, descriptions of work in progress, etc.
  
−
Submissions must be electronic and in PDF format, and should follow
+
Electronic Submission:
−
the two-column format of ACL proceedings. Please see the conference
+
Submission must be electronic and in PDF format, using the Softconf submission software at
−
website for details.
 
−
Authors are strongly encouraged to use the style files and formatting
 
−
instructions available on the conference website:
 
  
 
[https://www.softconf.com/acl2014/BioNLP  https://www.softconf.com/acl2014/BioNLP]
 
[https://www.softconf.com/acl2014/BioNLP  https://www.softconf.com/acl2014/BioNLP]
 +
 +
Submissions should follow the two-column format of ACL 2014 proceedings.
 +
Please see  the style files and formatting
 +
instructions at http://www.cs.jhu.edu/ACL2014/CallforPapers.htm
  
 
Submissions need to be anonymous.  
 
Submissions need to be anonymous.  
Line 97: Line 385:
 
   * Thamar Solorio, The University of Alabama at Birmingham  
 
   * Thamar Solorio, The University of Alabama at Birmingham  
 
   * Yang Liu, The University of Texas at Dallas
 
   * Yang Liu, The University of Texas at Dallas
 +
-->

Revision as of 20:27, 16 May 2016

SIGBIOMED


BIONLP 2016

An ACL 2016 Workshop associated with the SIGBIOMED special interest group Featuring two associated tasks: BioASQ (http://www.bioasq.org/workshop) and BioNLP-ST (http://2016.bionlp-st.org).

Berlin, Germany, August 12 -13, 2016

IMPORTANT DATES

  • Submission deadline: Sunday, May 8, 2016, 11:59 PM Eastern US
  • Notification of acceptance: Monday, June 13, 2016
  • Camera-ready copy due from authors: Wednesday, June 22, 2016
  • BioNLP workshop: Friday, August 12, 2016
  • BioNLP-ST and BioASQ workshop: Saturday August 13, 2016


WORKSHOP OVERVIEW AND SCOPE

Over the course of the past fourteen 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:

  • 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
SUBMISSION INSTRUCTIONS

We invite two types of submissions: full papers and short papers. Submissions are due by 11:59 PM EST on Sunday May 8, 2016.

Full papers should not exceed eight (8) pages of text, plus unlimited references. These 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. Appropriate short paper topics include preliminary results, application notes, descriptions of work in progress, etc.

Electronic Submission

Submissions must be electronic and in PDF format, using the Softconf START conference management system at https://www.softconf.com/acl2016/BioNLP16/ We strongly recommend the use of ACL LaTeX style files tailored for this year's conference. Submissions must conform to the official style guidelines. Style files and other information about paper formatting requirements will be made available on the conference website,http://acl2016.org.

Submissions should be anonymous. Dual submission policy: papers may NOT be submitted to the BioNLP 2016 workshop if they are or will be concurrently submitted to another meeting or publication.

Tentative Program Committee:
  • Emilia Apostolova, DePaul University, Chicago, USA
  • Eiji Aramaki, University of Tokyo, Japan
  • Asma Ben Abacha, National Library of Medicine, USA
  • Sabine Bergler, Concordia University, Canada
  • Olivier Bodenreider, National Library of Medicine, USA
  • Aaron Cohen, Oregon Health and Science University, USA
  • Nigel Collier, University of Cambridge, UK
  • Marcelo Fiszman, National Library of Medicine, USA
  • Filip Ginter, University of Turku, Finland
  • Cyril Grouin, LIMSI - CNRS, France
  • Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
  • Halil Kilicoglu, National Library of Medicine, USA
  • Jin-Dong Kim, Database Center for Life Science, Japan
  • Robert Leaman, National Library of Medicine, USA
  • Ulf Leser, Humboldt-Universität zu Berlin, Germany
  • Zhiyong Lu, National Library of Medicine, USA
  • Timothy Miller, Children's Hospital Boston, USA
  • Makoto Miwa, Toyota Technological Institute, Japan
  • Danielle Mowery, University of Utah, USA
  • Yassine M'Rabet, National Library of Medicine, USA
  • Aurelie Neveol, LIMSI - CNRS, France
  • Nhung Nguyen, University of Manchester, UK
  • Naoaki Okazaki, Tohoku University, Japan
  • Jong Park, KAIST, Republic of Korea
  • Sampo Pyysalo, University of Cambridge, UK
  • Bastien Rance, Hopital Europeen Georges Pompidou, France
  • Fabio Rinaldi, University of Zurich, Switzerland
  • Thomas Rindflesch, National Library of Medicine
  • Angus Roberts, University of Sheffield, UK
  • Kirk Roberts, National Library of Medicine, USA
  • Yoshimasa Tsuruoka, University of Tokyo, Japan
  • Karin Verspoor, The University of Melbourne, Australia
  • Byron Wallace, University of Texas at Austin, USA
  • John Wilbur, National Library of Medicine, USA
  • Pierre Zweigenbaum, LIMSI - CNRS, France
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


Two tasks will be associated with the workshop this year:

The BioNLP Shared Task (BioNLP-ST) has been organized three times so far, leading to the development of information extraction systems for molecular biology and medicine in 2009, 2011 and 2013. One of the major contributions of BioNLP-ST is the availability of resources such as high quality manually curated corpora, tools, and evaluation services.

Shared Task Organizers:
  • Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan
  • Claire Nedellec, INRA, France
  • Robert Bossy, INRA, France


The second equally successful shared task, the BioASQ challenge on large-scale biomedical semantic indexing and question answering has been running on an annual basis since 2012. The results of the challenge were presented in a workshop, which has so far been taking place in conjunction with the CLEF conference and was extremely well-attended.

BioASQ assesses the performance of information systems in supporting two tasks that are central in the biomedical question answering process: (a) the indexing of large volumes of unlabeled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material. BioASQ has been making publicly available the following benchmark data and tools: more than 1300 questions and related answers, as well as online "oracle" for objective evaluation of any system throughout the year, not only during the challenge.

BioASQ Organizers:
  • Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA
  • Ioannis Kakadiaris University of Houston, USA
  • Anastasia Krithara, NCSR "Demokritos", Greece


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