Difference between revisions of "BioNLP 2023"

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==BIONLP 2014 1st Call for Papers==
+
[[SIGBIOMED]]
  
−
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.
+
==BIONLP 2015 Workshop Schedule==
 +
 
 +
<font face="verdana" color="#000080"> Keynote by Kevin Knight: The DARPA Big Mechanism Program </font>
 +
 
 +
DARPA's Big Mechanism Program aims to develop automatic machine-reading technology to distill grounded, causal mechanisms from technical literature, and to assemble those mechanisms into a large, operational model.  The first Big Mechanism domain is cancer biology.  This talk will describe the goals of the program and the techniques being developed.
 +
 
 +
==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.
 +
 
 +
<h5>Program committee:</h5>
 +
 
 +
* Emilia Apostolova, DePaul University, Chicago, USA
 +
* Eiji Aramaki, University of Tokyo
 +
* Alan Aronson, National Library of Medicine
 +
* Sabine Bergler, Concordia University, Canada
 +
* Olivier Bodenreider, National Library of Medicine
 +
* Aaron Cohen, Oregon Health and Science University
 +
* Nigel Collier, EBI, the National Institute of Informatics
 +
* Noémie Elhadad, Columbia University
 +
* Marcelo Fiszman, National Library of Medicine
 +
* Filip Ginter, University of Turku
 +
<!--* Graciela Gonzalez, Arizona State University -->
 +
* Cyril Grouin, LIMSI - CNRS, France
 +
* Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 +
* Halil Kilicoglu, National Library of Medicine
 +
* Jin-Dong Kim, Database Center for Life Science, Japan
 +
<!-- * Alexander Koller, University of Potsdam -->
 +
* Robert Leaman, National Library of Medicine
 +
* Zhiyong Lu, National Library of Medicine
 +
* Timothy Miller, Children's Hospital Boston
 +
* Makoto Miwa, Toyota Technological Institute, Japan
 +
* Aurelie Neveol, LIMSI - CNRS, France
 +
* Naoaki Okazaki, Tohoku University
 +
* Jong Park, KAIST
 +
* Sampo Pyysalo, University of Turku
 +
* Bastien Rance, Hopital Europeen Georges Pompidou
 +
* Thomas Rindflesch, National Library of Medicine
 +
* Kirk Roberts, National Library of Medicine
 +
* Andrey Rzhetsky, University of Chicago
 +
* Yoshimasa Tsuruoka, University of Tokyo, Japan
 +
* Karin Verspoor, The University of Melbourne, Australia
 +
* John Wilbur, National Library of Medicine
 +
* Pierre Zweigenbaum,  LIMSI - CNRS, France
 +
 
 +
<h5>Organizers</h5>
 +
  * 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, Microsoft Research Asia
 +
 
 +
<!--
 +
==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 208:
 
===KEYNOTE SPEAKER===
 
===KEYNOTE SPEAKER===
  
−
TBD
+
Jun-ichi Tsujii
  
 
===PANEL ON SHARED TASKS===
 
===PANEL ON SHARED TASKS===
Line 64: Line 229:
  
  
−
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 235:
 
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 263:
 
   * 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 12:39, 12 June 2015

SIGBIOMED

BIONLP 2015 Workshop Schedule

Keynote by Kevin Knight: The DARPA Big Mechanism Program

DARPA's Big Mechanism Program aims to develop automatic machine-reading technology to distill grounded, causal mechanisms from technical literature, and to assemble those mechanisms into a large, operational model. The first Big Mechanism domain is cancer biology. This talk will describe the goals of the program and the techniques being developed.

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:

  • Wide-scale entity identification and normalization
  • Extraction of complex relations and events
  • Discourse analysis
  • Coreference resolution
  • Text mining
  • Literature based discovery
  • Summarization
  • Question-answering
  • Lexical and terminological resources for BioNLP
  • Annotation (corpora), standards
  • Resources and strategies for system testing and evaluation
  • Processing and annotation platforms
  • Interoperable platforms for biomedical text mining
  • Domain adaptation
  • Translating NLP research to practice

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.

Program committee:
  • Emilia Apostolova, DePaul University, Chicago, USA
  • Eiji Aramaki, University of Tokyo
  • Alan Aronson, National Library of Medicine
  • Sabine Bergler, Concordia University, Canada
  • Olivier Bodenreider, National Library of Medicine
  • Aaron Cohen, Oregon Health and Science University
  • Nigel Collier, EBI, the National Institute of Informatics
  • Noémie Elhadad, Columbia University
  • Marcelo Fiszman, National Library of Medicine
  • Filip Ginter, University of Turku
  • Cyril Grouin, LIMSI - CNRS, France
  • Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
  • Halil Kilicoglu, National Library of Medicine
  • Jin-Dong Kim, Database Center for Life Science, Japan
  • Robert Leaman, National Library of Medicine
  • Zhiyong Lu, National Library of Medicine
  • Timothy Miller, Children's Hospital Boston
  • Makoto Miwa, Toyota Technological Institute, Japan
  • Aurelie Neveol, LIMSI - CNRS, France
  • Naoaki Okazaki, Tohoku University
  • Jong Park, KAIST
  • Sampo Pyysalo, University of Turku
  • Bastien Rance, Hopital Europeen Georges Pompidou
  • Thomas Rindflesch, National Library of Medicine
  • Kirk Roberts, National Library of Medicine
  • Andrey Rzhetsky, University of Chicago
  • Yoshimasa Tsuruoka, University of Tokyo, Japan
  • Karin Verspoor, The University of Melbourne, Australia
  • John Wilbur, National Library of Medicine
  • 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, Microsoft Research Asia


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