Difference between revisions of "BioNLP 2023"

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[[SIGBIOMED]]
 
[[SIGBIOMED]]
  
 +
<font size="4"><b>BIONLP 2017</b></font>
  
 +
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: Friday April 21, 2017 11:59 PM Eastern US
 +
*Notification of acceptance: Friday May 19, 2017
 +
*Camera-ready copy due from authors:  Friday May 26, 2017
 +
*Workshop: Friday August 4, 2017
 +
 +
 +
===SUBMISSION INSTRUCTIONS===
 +
 +
Two types of submissions are invited: full papers and short papers.
 +
Submissions are due by 11:59 PM EST on Friday April 21, 2017.
 +
 +
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/acl2017/bionlp/
 +
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 are available on the conference website, http://acl2017.org/. 
 +
 +
Submissions need to be anonymous.
 +
 +
Dual submission policy: papers may NOT be submitted to  the BioNLP 2017 workshop if they are or will be concurrently submitted to another meeting or publication.
 +
 +
 +
===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
 +
 +
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
 +
 +
===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.
 +
 +
<!--
 
==BIONLP 2016 ==
 
==BIONLP 2016 ==
  
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).
+
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
 +
* BioNLP workshop: Friday, August 12, 2016
 +
* BioNLP-ST and BioASQ workshop: Saturday August 13, 2016
 +
 
 +
 
 +
==BIONLP 2016 Workshop Schedule==
 +
 
 +
<table cellspacing="0" cellpadding="5" border="0"><tr><td colspan=2 style="padding-top: 14px;"><b>Friday August 12, 2016</b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>8:30&#8211;8:40</b></td><td valign=top style="padding-top: 14px;"><b>Opening remarks</b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>8:40&#8211;10:30</b></td><td valign=top style="padding-top: 14px;"><b>Session 1: Entity extraction and representation</b></td></tr>
 +
<tr><td valign=top width=100>8:40&#8211;9:00</td><td valign=top align=left><i>A Machine Learning Approach to Clinical Terms Normalization</i><br>
 +
Jose Castano, Mar&iacute;a Laura Gambarte, Hee Joon Park, Maria del Pilar Avila Williams, David Perez, Fernando Campos, Daniel Luna, Sonia Benitez, Hernan Berinsky and Sof&iacute;a Zanetti</td></tr>
 +
<tr><td valign=top width=100>9:00&#8211;9:20</td><td valign=top align=left><i>Improved Semantic Representation for Domain-Specific Entities</i><br>
 +
Mohammad Taher Pilehvar and Nigel Collier</td></tr>
 +
<tr><td valign=top width=100>9:20&#8211;9:40</td><td valign=top align=left><i>Identification, characterization, and grounding of gradable terms in clinical text</i><br>
 +
Chaitanya Shivade, Marie-Catherine de Marneffe, Eric Fosler-Lussier and Albert M. Lai</td></tr>
 +
<tr><td valign=top width=100>9:40&#8211;10:00</td><td valign=top align=left><i>Graph-based Semi-supervised Gene Mention Tagging</i><br>
 +
Golnar Sheikhshab, Elizabeth Starks, Aly Karsan, Anoop Sarkar and Inanc Birol</td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>10:00&#8211;10:30</b></td><td valign=top style="padding-top: 14px;"><b>Invited Talk: <i>The BioNLP-ST challenges on information extraction and knowledge acquisition in biology</i> <br> Speakers:  Robert Bossy and Jin-Dong Kim</b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>10:30&#8211;11:00</b></td><td valign=top style="padding-top: 14px;"><b><em>Coffee Break</em></b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>11:00&#8211;12:30</b></td><td valign=top style="padding-top: 14px;"><b>Session 2: Event and Relation Extraction</b></td></tr>
 +
<tr><td valign=top width=100>11:00&#8211;11:20</td><td valign=top align=left><i>Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses</i><br>
 +
Dayne Freitag and John Niekrasz</td></tr>
 +
<tr><td valign=top width=100>11:40&#8211;12:00</td><td valign=top align=left><i>Inferring Implicit Causal Relationships in Biomedical Literature</i><br>
 +
Halil Kilicoglu</td></tr>
 +
<tr><td valign=top width=100>12:00&#8211;12:20</td><td valign=top align=left><i>SnapToGrid: From Statistical to Interpretable Models for Biomedical Information Extraction</i><br>
 +
Marco A. Valenzuela-Esc&aacute;rcega, Gus Hahn-Powell, Dane Bell and Mihai Surdeanu</td></tr>
 +
<tr><td valign=top width=100>12:20&#8211;12:40</td><td valign=top align=left><i>Character based String Kernels for Bio-Entity Relation Detection</i><br>
 +
Ritambhara Singh and Yanjun Qi</td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>12:40&#8211;14:00</b></td><td valign=top style="padding-top: 14px;"><b><em>Lunch break</em></b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>14:00&#8211;15:40</b></td><td valign=top style="padding-top: 14px;"><b>Session 3: Disambiguation, Classification, and more</b></td></tr>
 +
<tr><td valign=top width=100>14:00&#8211;14:20</td><td valign=top align=left><i>Disambiguation of entities in MEDLINE abstracts by combining MeSH terms with knowledge</i><br>
 +
Amy Siu, Patrick Ernst and Gerhard Weikum</td></tr>
 +
<tr><td valign=top width=100>14:20&#8211;14:40</td><td valign=top align=left><i>Using Distributed Representations to Disambiguate Biomedical and Clinical Concepts</i><br>
 +
Stephan Tulkens, Simon Suster and Walter Daelemans</td></tr>
 +
<tr><td valign=top width=100>14:40&#8211;15:00</td><td valign=top align=left><i>Unsupervised Document Classification with Informed Topic Models</i><br>
 +
Timothy Miller, Dmitriy Dligach and Guergana Savova</td></tr>
 +
<tr><td valign=top width=100>15:00&#8211;15:20</td><td valign=top align=left><i>Vocabulary Development To Support Information Extraction of Substance Abuse from Psychiatry Notes</i><br>
 +
Sumithra Velupillai, Danielle L Mowery, Mike Conway, John Hurdle and Brent Kious</td></tr>
 +
<tr><td valign=top width=100>15:20&#8211;15:40</td><td valign=top align=left><i>Syntactic analyses and named entity recognition for PubMed and PubMed Central __ up-to-the-minute</i><br>
 +
Kai Hakala, Suwisa Kaewphan, Tapio Salakoski and Filip Ginter</td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>15:40&#8211;16:00</b></td><td valign=top style="padding-top: 14px;"><b><em>Coffee Break</em></b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>16:00&#8211;16:30</b></td><td valign=top style="padding-top: 14px;"><b>Invited Talk: <i> BioASQ: A challenge on large-scale biomedical semantic indexing and question answering</i> <br> Speaker: Anastasia Krithara</b></td></tr>
 +
<tr><td valign=top style="padding-top: 14px;"><b>16:30&#8211;17:30</b></td><td valign=top style="padding-top: 14px;"><b>Poster Session</b></td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Improving Temporal Relation Extraction with Training Instance Augmentation</i><br>
 +
Chen Lin, Timothy Miller, Dmitriy Dligach, Steven Bethard and Guergana Savova</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Using Centroids of Word Embeddings and Word Mover&rsquo;s Distance for Biomedical Document Retrieval in Question Answering</i><br>
 +
Georgios-Ioannis Brokos, Prodromos Malakasiotis and Ion Androutsopoulos</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Measuring the State of the Art of Automated Pathway Curation Using Graph Algorithms - A Case Study of the mTOR Pathway</i><br>
 +
Michael Spranger, Sucheendra Palaniappan and Samik Gosh</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Construction of a Personal Experience Tweet Corpus for Health Surveillance</i><br>
 +
Keyuan Jiang, Ricardo Calix and Matrika Gupta</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Modelling the Combination of Generic and Target Domain Embeddings in a Convolutional Neural Network for Sentence Classification</i><br>
 +
Nut Limsopatham and Nigel Collier</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>PubTermVariants: biomedical term variants and their use for PubMed search</i><br>
 +
Lana Yeganova, Won Kim, Sun Kim, Rezarta Islamaj Do&#287;an, Wanli Liu, Donald C Comeau, Zhiyong Lu and W John Wilbur</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>This before That: Causal Precedence in the Biomedical Domain</i><br>
 +
Gus Hahn-Powell, Dane Bell, Marco A. Valenzuela-Esc&aacute;rcega and Mihai Surdeanu</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Syntactic methods for negation detection in radiology reports in Spanish</i><br>
 +
Viviana Cotik, Vanesa Stricker, Jorge Vivaldi and Horacio Rodriguez</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>How to Train good Word Embeddings for Biomedical NLP</i><br>
 +
Billy Chiu, Gamal Crichton, Anna Korhonen and Sampo Pyysalo</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>An Information Foraging Approach to Determining the Number of Relevant Features</i><br>
 +
Brian Connolly, Benjamin Glass and John Pestian</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Assessing the Feasibility of an Automated Suggestion System for Communicating Critical Findings from Chest Radiology Reports to Referring Physicians</i><br>
 +
Brian E. Chapman, Danielle L Mowery, Evan Narasimhan, Neel Patel, Wendy Chapman and Marta Heilbrun</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Building a dictionary of lexical variants for phenotype descriptors</i><br>
 +
Simon Kocbek and Tudor Groza</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Applying deep learning on electronic health records in Swedish to predict healthcare-associated infections</i><br>
 +
Olof Jacobson and Hercules Dalianis</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Identifying First Episodes of Psychosis in Psychiatric Patient Records using Machine Learning</i><br>
 +
Genevieve Gorrell, Sherifat Oduola, Angus Roberts, Tom Craig, Craig Morgan and Rob Stewart</td></tr>
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Relation extraction from clinical texts using domain invariant convolutional neural network</i><br>
 +
Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu</td></tr>
 +
 
 +
<tr><td valign=top width=100>&nbsp;</td><td valign=top align=left><i>Results of the 4th edition of BioASQ Challenge</i><br>Anastasia Krithara, Anastasios Nentidis, Georgios Paliouras and Ioannis Kakadiaris</td></tr>
 +
 
 +
<tr><td valign=top width=100>&nbsp;</td> <td><b>All  August 13 talks are also presented as posters on August 12 and August 13</b></td></tr>
  
Berlin, Germany, August 12 -13, 2016
+
</table>
  
===TENTATIVE  DATES===
+
==BioASQ / BioNLP-ST Workshop Program, August 13==
  
* Submission deadline: April - May, 2016
+
<table>
* Notification of acceptance: June, 2016  
+
      <tr><td valign=top width=100>'''9:00-9:15'''</td> <td><b>Welcome</b></td></tr>
* Camera-ready copy due from authors: June, 2016
+
      <tr><td valign=top width=100>'''9:15-10:15'''</td> <td>'''Invited speaker: Sherri Matis-Mitchell''' <br>Solving Problems and Supporting Decisions in Pharma R&D using Text Analytics: A Recent History</td></tr>
* WorkshopAugust 12, 2016
+
      <tr><td valign=top width=100>10:15-10:30</td> <td>'''Overview of BioASQ'''</td></tr>
* Shared Tasks: August 13, 2016
+
      <tr><td valign=top width=100>10:30-11:00</td> <td><b>Coffee break</b></td></tr>
 +
      <tr><td valign=top width=100>11:00-12:30</td> <td><b>BioASQ participant session</b></td></tr>
 +
      <tr><td valign=top width=100>11:00-11:15</td> <td>Using Learning-To-Rank to Enhance NLM Medical Text Indexer Results<br>Ilya Zavorin, James Mork and Dina Demner-Fushman</td></tr>
 +
      <tr><td valign=top width=100>11:15-11:30</td> <td>LABDA at the 2016 BioASQ challenge task 4a: Semantic Indexing by using ElasticSearch <br>Isabel Segura-Bedmar, Adrián Carruana and Paloma Martínez</td></tr>
 +
      <tr><td valign=top width=100>11:30-11:45</td> <td>Learning to Answer Biomedical Questions: OAQA at BioASQ 4B<br>Zi Yang, Yue Zhou and Eric Nyberg</td></tr>
 +
        <tr><td valign=top width=100>11:45-12:00</td> <td>HPI Question Answering System in BioASQ 2016 <br>Frederik Schulze, Ricarda Schuler, Tim Draeger, Daniel Dummer, Alexander Ernst, Pedro Flemming, Cindy Perscheid, Mariana Neves</td></tr>
 +
      <tr><td valign=top width=100>12:00-12:15</td> <td>KSAnswer: Question-answering System of Kangwon National University and Sogang University in the 2016 BioASQ Challenge<br>Hyeon-gu Lee, Minkyoung Kim, Harksoo Kim, Juae Kim, Sunjae Kwon, Jungyun Seo, Yi-Reun Kim and Jung-Kyu Choi</td></tr>
 +
  <tr><td valign=top width=100>12:15-12:30</td> <td>Large-Scale Semantic Indexing and Question Answering in Biomedicine <br>Eirini Papagiannopoulou, Yiannis Papanikolaou, Dimitris Dimitriadis, Sakis Lagopoulos, Grigorios Tsoumakas, Manos Laliotis, Nikos Markantonatos and Ioannis Vlahavas</td></tr>
 +
   
 +
  <tr><td valign=top width=100>'''12:30-14:00'''</td> <td><b>Lunch break</b></td></tr>
 +
     
 +
      <tr><td valign=top width=100>'''14:00-14:15'''</td> <td><b>Overview of BioNLP-ST</b></td></tr>
 +
     
 +
      <tr><td valign=top width=100>'''14:15-15:30'''</td> <td>'''BioNLP-ST participant session 1'''</td></tr>
 +
     
 +
      <tr><td valign=top width=100>14:15-14:30</td> <td>LitWay, discriminative extraction for different bio-events<br>Chen Li, Zhiqiang Rao and Xiangrong Zhang</td></tr>
 +
      <tr><td valign=top width=100>14:30-14:45</td> <td>VERSE: Event and relation extraction in the BioNLP 2016 Shared Task<br>Jake Lever and Steven JM Jones</td></tr>
 +
      <tr><td valign=top width=100>14:45-15:00</td> <td>A dictionary- and rule-based system for identification of bacteria and habitats in text<br>Helen Cook, Evangelos Pafilis and Lars Juhl Jensen</td></tr>
 +
    <tr><td valign=top width=100>15:00-15:15</td> <td>Extraction of Regulatory Events Using Kernel-based Classifiers and Distant Supervision<br>Andre Lamurias, Miguel J. Rodrigues, Luka A. Clarke and Francisco M Couto</td></tr>
 +
      <tr><td valign=top width=100>15:15-15:30</td>  <td>Deep Learning With Minimal Training Data: TurkuNLP Entry in The BioNLP Shared Task 2016<br>Farrokh Mehryary, Jari Björne, Sampo Pyysalo, Tapio Salakoski and Filip Ginter</td></tr>
 +
    <tr><td valign=top width=100>'''15:30-16:00'''</td> <td>'''Coffee break'''</td></tr>
 +
      <tr><td valign=top width=100>16:00-17:00</td> <td>'''BioNLP-ST participant session 2'''</td></tr>
 +
      <tr><td valign=top width=100>16:00-16:15</td><td>Identification of mentions and relations between bacteria and biotope from PubMed abstracts<br>Cyril Grouin</td></tr>
 +
  <tr><td valign=top width=100>16:15-16:30</td> <td>SeeDev Binary Event Extraction Using SVMs and a Rich Feature set<br>Nagesh Panyam Chandrasekarasastry, Gitansh Khirbat, Karin Verspoor, Trevor Cohn and Kotagiri Ramamohanarao</td></tr>
 +
      <tr><td valign=top width=100>16:30-16:45</td> <td>Ontology Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques<br>Mert Tiftikci, Hakan Şahin, Berfu Büyüköz, Alper Yayıkçı and Arzucan Özgür</td></tr>
 +
      <tr><td valign=top width=100>16:45-17:00</td> <td>DUTIR in BioNLP-ST 2016: Utilizing convolutional network and distributed representation to extract complicate relations<br>Honglei Li, Jianhai Zhang, Jian Wang, Hongfei Lin and Zhihao Yang</td></tr>
 +
     
 +
      <tr><td valign=top width=100>'''17:00-17:30'''</td> <td><b>Closing session</b></td></tr>
  
===WORKSHOP OVERVIEW AND SCOPE===
+
</table>
 +
<!--
 +
==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.   
 
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.   
Line 38: Line 218:
 
* Translating NLP research to practice
 
* Translating NLP research to practice
 
* Theoretical underpinnings of biomedical language processing
 
* Theoretical underpinnings of biomedical language processing
 +
-->
 +
 +
 +
 +
<!-- <h5>SUBMISSION INSTRUCTIONS</h5>
 +
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.
 +
 +
<h6>Electronic Submission</h6>
 +
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>
 +
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>
+
<!--
 +
<b>Program Committee:</b>
 +
 
 +
  * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
 +
  * 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
 +
  * Kevin Bretonnel Cohen, University of Colorado School of Medicine, USA
 +
  * Aaron Cohen, Oregon Health and Science University
 +
  * Dina Demner-Fushman, US National Library of Medicine
 +
  * Filip Ginter, University of Turku, Finland
 +
  * Cyril Grouin, LIMSI - CNRS, France
 +
  * Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
 +
  * Halil Kilicoglu, US National Library of Medicine
 +
  * Robert Leaman, US National Library of Medicine
 +
  * Ulf Leser, Humboldt-Universit&auml;t zu Berlin, Germany
 +
  * Zhiyong Lu, US National Library of Medicine
 +
  * Timothy Miller, Children’s Hospital Boston, USA
 +
  * Makoto Miwa, Toyota Technological Institute, Japan
 +
  * Danielle L Mowery, VA Salt Lake City Health Care System, USA
 +
  * Yassine M'Rabet, US National Library of Medicine
 +
  * Aurelie Neveol, LIMSI - CNRS, France
 +
  * Nhung Nguyen, The University of Manchester, UK
 +
  * Naoaki Okazaki, Tohoku University, Japan
 +
  * Sampo Pyysalo, University of Cambridge, UK
 +
  * Bastien Rance, Hopital Europeen Georges Pompidou, France
 +
  * Fabio Rinaldi,  University of Zurich, Switzerland
 +
  * Thomas Rindflescht, US National Library of Medicine
 +
  * Kirk Roberts, The University of Texas Health Science Center at Houston, USA
 +
  * Angus Roberts, The University of Sheffield, UK
 +
  * Yoshimasa Tsuruoka, University of Tokyo, Japan
 +
  * Karin Verspoor, The University of Melbourne, Australia
 +
  * Byron C. Wallace,  University of Texas at Austin, USA
 +
  * W John Wilbur, US National Library of Medicine
 +
  * Pierre Zweigenbaum, LIMSI - CNRS, France
  
* Emilia Apostolova, DePaul University, Chicago, USA
 
* Eiji Aramaki, University of Tokyo, Japan
 
* 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
 
* Noémie Elhadad, Columbia University, USA
 
* 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
 
* Jin-Dong Kim, Database Center for Life Science, Japan
 
* Robert Leaman, National Library of Medicine, USA
 
* Zhiyong Lu, National Library of Medicine, USA
 
* Timothy Miller, Children's Hospital Boston, USA
 
* Makoto Miwa, Toyota Technological Institute, Japan
 
* Aurelie Neveol, LIMSI - CNRS, France
 
* Naoaki Okazaki, Tohoku University, Japan
 
* Jong Park, KAIST, Republic of Korea
 
* Sampo Pyysalo, University of Cambridge, UK
 
* 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>
+
<b>Organizers</b>
 
   * Kevin Bretonnel Cohen, University of Colorado School of Medicine
 
   * Kevin Bretonnel Cohen, University of Colorado School of Medicine
 
   * Dina Demner-Fushman, US National Library of Medicine
 
   * Dina Demner-Fushman, US National Library of Medicine
Line 78: Line 286:
  
  
<h5>Two tasks will be associated with the workshop this year:</h5>
+
<h5>The BioNLP Shared Task (BioNLP-ST) and the BioASQ Challenge associated with the workshop</h5>
 
   
 
   
 
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.
 
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.
 
   
 
   
<h5>Shared Task Organizers:</h5>
+
<b>Shared Task Organizers:</b>
  
 
* Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan
 
* Jin-Dong Kim, Database Center for Life Science (DBCLS), Japan
Line 93: Line 301:
 
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 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.
 
   
 
   
<h5>BioASQ Organizers:</h5>
+
<b>BioASQ Organizers:</b>
 
   
 
   
 
* Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA  
 
* Georgios Paliouras NCSR "Demokritos", Greece and University of Houston, USA  
Line 99: Line 307:
 
* Anastasia Krithara, NCSR "Demokritos", Greece
 
* Anastasia Krithara, NCSR "Demokritos", Greece
 
   
 
   
 +
-->
  
 
<!-- ==BIONLP 2015 Workshop Schedule==
 
<!-- ==BIONLP 2015 Workshop Schedule==

Revision as of 04:26, 16 February 2017

SIGBIOMED

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: Friday April 21, 2017 11:59 PM Eastern US
  • Notification of acceptance: Friday May 19, 2017
  • Camera-ready copy due from authors: Friday May 26, 2017
  • Workshop: Friday August 4, 2017


SUBMISSION INSTRUCTIONS

Two types of submissions are invited: full papers and short papers. Submissions are due by 11:59 PM EST on Friday April 21, 2017.

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/acl2017/bionlp/ 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 are available on the conference website, http://acl2017.org/

Submissions need to be anonymous.

Dual submission policy: papers may NOT be submitted to the BioNLP 2017 workshop if they are or will be concurrently submitted to another meeting or publication.


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

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

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.