Difference between revisions of "BioNLP 2023"

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[[SIGBIOMED]]
 
[[SIGBIOMED]]
 +
 +
 +
<font size="4"><b>BIONLP 2020</b></font>
 +
<br/>
 +
<font size="3">Seattle, Washington, July 9 '''or''' 10, 2020</font>
 +
 +
An ACL 2020 Workshop associated with the SIGBIOMED special interest group
 +
 +
===IMPORTANT DATES ===
 +
 +
*Submission deadline: Friday March 20, 2020 11:59 PM Eastern US
 +
*Notification of acceptance: Friday, April 24, 2020
 +
*Camera-ready copy due from authors: '''Sunday, May 3''', 2020
 +
*'''Workshop: July 9 or 10, 2020'''
 +
 +
===Program Committee===
 +
 +
  * Hadi Amiri, Harvard Medical School, USA
 +
  * 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
 +
  * Cosmin (Adi) Bejan, Vanderbilt University, Nashville, TN
 +
  * Siamak Barzegar, Barcelona Supercomputing Center, Spain
 +
<!--  * Sai Bhaskar, Carnegie Mellon University, Pittsburgh, PA -->
 +
  * Olivier Bodenreider, US National Library of Medicine
 +
  * Leonardo Campillos Llanos, Universidad Autónoma de Madrid, Spain
 +
  <!-- * Juan Miguel Cejuela, tagtog, Munich, Bavaria, Germany -->
 +
  * 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
 +
  * Dina Demner-Fushman, US National Library of Medicine
 +
<!--  * Graciela Gonzalez-Hernandez, University of Pennsylvania, 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
 +
<!--  * Ankita Gupta, Samsung Research, Bangalore, India -->
 +
  * Sadid Hasan, Philips Research, Cambridge, MA
 +
  * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 +
  * Meizhi Ju, National Centre for Text Mining and University of Manchester, UK
 +
  * Will Kearns, University of Washington, USA
 +
  * Halil Kilicoglu, US National Library of Medicine
 +
  * Ari Klein, University of Pennsylvania, USA
 +
  * Zfania Tom Korach, Harvard Medical School, 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-Universit&auml;t zu Berlin, Germany
 +
  * Gal Levy-Fix, Columbia University, NY
 +
  * Maolin Li, National Centre for Text Mining and University of Manchester, UK
 +
  * Ramon Maldonado, The University of Texas at Dallas, USA
 +
  * Timothy Miller, Children’s Hospital Boston, USA
 +
  <!-- * Roser Morante, VU University Amsterdam,  Netherlands -->
 +
  * Danielle L Mowery, VA Salt Lake City Health Care System, USA
 +
  * Yassine M'Rabet, US National Library of Medicine
 +
  * 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
 +
  * Yifan Peng, US National Library of Medicine
 +
  * Laura Plaza, UNED, Madrid, Spain
 +
  * Sampo Pyysalo, University of Cambridge, UK
 +
  * Alastair Rae, US National Library of Medicine
 +
  * Francisco J. Ribadas-Pena, University of Vigo, Spain
 +
  <!-- * Fabio Rinaldi,  University of Zurich, Switzerland -->
 +
  <!-- * 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
 +
  * Sumegh Roychowdhury, Indian Institute of Technology Kharagpur
 +
<!-- * Rashi Rungta, Carnegie Mellon University, Pittsburgh, PA -->
 +
  * Max Savery, US National Library of Medicine
 +
  <!-- * Prakhar Sharma, Indian Institute of Technology, Kharagpur -->
 +
  * Chaitanya Shivade, IBM Research, Almaden, USA
 +
  * Diana Sousa, University of Lisbon, Portugal
 +
  * Noha Seddik Tawfik, Arab Academy for Science and Technology, Egypt
 +
  * Thy Thy Tran, National Centre for Text Mining and University of Manchester, UK
 +
  * Sumithra Velupillai, King’s College London, UK
 +
  <!-- * Byron C. Wallace,  University of Texas at Austin, USA -->
 +
  * Davy Weissenbacher, University of Pennsylvania, USA
 +
  * W John Wilbur, US National Library of Medicine
 +
  * Shankai Yan, US National Library of Medicine
 +
  * Amir Yazdavar, Wright State University, USA
 +
  * Chrysoula Zerva, National Centre for Text Mining and University of Manchester, UK
 +
  * Ayah Zirikly, Clinical Center, National Institutes of Health, USA
 +
  * Seyedjamal Zolhavarieh, The University of Auckland, NZ
 +
  * 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.
 +
 +
 +
<!-- to open later
 +
====Electronic Submission====
 +
Submissions must be electronic and in PDF format, using the Softconf START conference management system at    https://www.softconf.com/acl2019/bionlp/
 +
We strongly recommend consulting the ACL Policies for Submission, Review, and Citation: https://www.aclweb.org/portal/content/new-policies-submission-review-and-citation and using ACL LaTeX style files tailored for this year's conference. Submissions must conform to the official style guidelines. Please see information about paper formatting requirements and style  at http://www.acl2019.org/EN/call-for-papers.xhtml. Scroll down to “Paper Submission and Templates.”
 +
 +
<b>Submissions need to be anonymous.</b>
 +
 +
-->
 +
 +
====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.
 +
 +
<!-- 2019
  
 
<font size="4"><b>BIONLP 2019</b></font>
 
<font size="4"><b>BIONLP 2019</b></font>
Line 158: Line 312:
 
   * Cosmin (Adi) Bejan, Vanderbilt University, Nashville, TN  
 
   * Cosmin (Adi) Bejan, Vanderbilt University, Nashville, TN  
 
   * Siamak Barzegar, Barcelona Supercomputing Center, Spain
 
   * Siamak Barzegar, Barcelona Supercomputing Center, Spain
−
<!--  * Sai Bhaskar, Carnegie Mellon University, Pittsburgh, PA -->
 
 
   * Olivier Bodenreider, US National Library of Medicine  
 
   * Olivier Bodenreider, US National Library of Medicine  
 
   * Leonardo Campillos Llanos, Universidad Autónoma de Madrid, Spain
 
   * Leonardo Campillos Llanos, Universidad Autónoma de Madrid, Spain
−
  <!-- * Juan Miguel Cejuela, tagtog, Munich, Bavaria, Germany -->
 
 
   * Qingyu Chen, US National Library of Medicine   
 
   * Qingyu Chen, US National Library of Medicine   
 
   * Fenia Christopoulou, National Centre for Text Mining and University of Manchester, UK  
 
   * Fenia Christopoulou, National Centre for Text Mining and University of Manchester, UK  
Line 169: Line 321:
 
   * Viviana Cotik, University of Buenos Aires, Argentina
 
   * Viviana Cotik, University of Buenos Aires, Argentina
 
   * Dina Demner-Fushman, US National Library of Medicine  
 
   * Dina Demner-Fushman, US National Library of Medicine  
−
<!--  * Graciela Gonzalez-Hernandez, University of Pennsylvania, USA -->
 
 
   * Travis Goodwin, The University of Texas at Dallas, USA
 
   * Travis Goodwin, The University of Texas at Dallas, USA
 
   * Natalia Grabar, CNRS, France  
 
   * Natalia Grabar, CNRS, France  
 
   * Cyril Grouin, LIMSI - CNRS, France  
 
   * Cyril Grouin, LIMSI - CNRS, France  
 
   * Tudor Groza, The Garvan Institute of Medical Research, Australia
 
   * Tudor Groza, The Garvan Institute of Medical Research, Australia
−
<!--  * Ankita Gupta, Samsung Research, Bangalore, India -->
 
 
   * Sadid Hasan, Philips Research, Cambridge, MA
 
   * Sadid Hasan, Philips Research, Cambridge, MA
 
   * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 
   * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
Line 191: Line 341:
 
   * Ramon Maldonado, The University of Texas at Dallas, USA
 
   * Ramon Maldonado, The University of Texas at Dallas, USA
 
   * Timothy Miller, Children’s Hospital Boston, USA  
 
   * Timothy Miller, Children’s Hospital Boston, USA  
−
  <!-- * Roser Morante, VU University Amsterdam,  Netherlands -->
 
 
   * Danielle L Mowery, VA Salt Lake City Health Care System, USA
 
   * Danielle L Mowery, VA Salt Lake City Health Care System, USA
 
   * Yassine M'Rabet, US National Library of Medicine
 
   * Yassine M'Rabet, US National Library of Medicine
Line 205: Line 354:
 
   * Alastair Rae, US National Library of Medicine  
 
   * Alastair Rae, US National Library of Medicine  
 
   * Francisco J. Ribadas-Pena, University of Vigo, Spain
 
   * Francisco J. Ribadas-Pena, University of Vigo, Spain
−
  <!-- * Fabio Rinaldi,  University of Zurich, Switzerland -->
 
−
  <!-- * Angus Roberts, The University of Sheffield, UK -->
 
 
   * Kirk Roberts, The University of Texas Health Science Center at Houston, USA  
 
   * Kirk Roberts, The University of Texas Health Science Center at Houston, USA  
 
   * Roland Roller, DFKI GmbH, Berlin, Germany
 
   * Roland Roller, DFKI GmbH, Berlin, Germany
 
   * Sumegh Roychowdhury, Indian Institute of Technology Kharagpur
 
   * Sumegh Roychowdhury, Indian Institute of Technology Kharagpur
−
<!-- * Rashi Rungta, Carnegie Mellon University, Pittsburgh, PA -->
 
 
   * Max Savery, US National Library of Medicine  
 
   * Max Savery, US National Library of Medicine  
−
  <!-- * Prakhar Sharma, Indian Institute of Technology, Kharagpur -->
 
 
   * Chaitanya Shivade, IBM Research, Almaden, USA
 
   * Chaitanya Shivade, IBM Research, Almaden, USA
 
   * Diana Sousa, University of Lisbon, Portugal
 
   * Diana Sousa, University of Lisbon, Portugal
Line 218: Line 363:
 
   * Thy Thy Tran, National Centre for Text Mining and University of Manchester, UK  
 
   * Thy Thy Tran, National Centre for Text Mining and University of Manchester, UK  
 
   * Sumithra Velupillai, King’s College London, UK
 
   * Sumithra Velupillai, King’s College London, UK
−
  <!-- * Byron C. Wallace,  University of Texas at Austin, USA -->
 
 
   * Davy Weissenbacher, University of Pennsylvania, USA
 
   * Davy Weissenbacher, University of Pennsylvania, USA
 
   * W John Wilbur, US National Library of Medicine  
 
   * W John Wilbur, US National Library of Medicine  
Line 290: Line 434:
 
See details at https://sites.google.com/view/mediqa2019
 
See details at https://sites.google.com/view/mediqa2019
  
−
 
+
-->
  
 
<!--  <font size="4"><b>BIONLP 2018</b></font>
 
<!--  <font size="4"><b>BIONLP 2018</b></font>

Revision as of 09:40, 25 October 2019

SIGBIOMED


BIONLP 2020
Seattle, Washington, July 9 or 10, 2020

An ACL 2020 Workshop associated with the SIGBIOMED special interest group

IMPORTANT DATES

  • Submission deadline: Friday March 20, 2020 11:59 PM Eastern US
  • Notification of acceptance: Friday, April 24, 2020
  • Camera-ready copy due from authors: Sunday, May 3, 2020
  • Workshop: July 9 or 10, 2020

Program Committee

 * Hadi Amiri, Harvard Medical School, USA
 * 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 
 * Cosmin (Adi) Bejan, Vanderbilt University, Nashville, TN 
 * 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
 * Dina Demner-Fushman, US National Library of Medicine 
 * 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
 * Sadid Hasan, Philips Research, Cambridge, MA
 * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 * Meizhi Ju, National Centre for Text Mining and University of Manchester, UK 
 * Will Kearns, University of Washington, USA
 * Halil Kilicoglu, US National Library of Medicine
 * Ari Klein, University of Pennsylvania, USA
 * Zfania Tom Korach, Harvard Medical School, 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 
 * Gal Levy-Fix, Columbia University, NY
 * Maolin Li, National Centre for Text Mining and University of Manchester, UK 
 * Ramon Maldonado, The University of Texas at Dallas, USA
 * Timothy Miller, Children’s Hospital Boston, USA 
 * Danielle L Mowery, VA Salt Lake City Health Care System, USA
 * Yassine M'Rabet, US National Library of Medicine
 * 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
 * Yifan Peng, US National Library of Medicine 
 * Laura Plaza, UNED, Madrid, Spain
 * Sampo Pyysalo, University of Cambridge, UK 
 * Alastair Rae, US National Library of Medicine 
 * Francisco J. Ribadas-Pena, University of Vigo, Spain
 * Kirk Roberts, The University of Texas Health Science Center at Houston, USA 
 * Roland Roller, DFKI GmbH, Berlin, Germany
 * Sumegh Roychowdhury, Indian Institute of Technology Kharagpur
 * Max Savery, US National Library of Medicine 
 * Chaitanya Shivade, IBM Research, Almaden, USA
 * Diana Sousa, University of Lisbon, Portugal
 * Noha Seddik Tawfik, Arab Academy for Science and Technology, Egypt
 * Thy Thy Tran, National Centre for Text Mining and University of Manchester, UK 
 * Sumithra Velupillai, King’s College London, UK
 * Davy Weissenbacher, University of Pennsylvania, USA
 * W John Wilbur, US National Library of Medicine 
 * Shankai Yan, US National Library of Medicine 
 * Amir Yazdavar, Wright State University, USA
 * Chrysoula Zerva, National Centre for Text Mining and University of Manchester, UK 
 * Ayah Zirikly, Clinical Center, National Institutes of Health, USA
 * Seyedjamal Zolhavarieh, The University of Auckland, NZ
 * 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.






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