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 | + | Berlin, Germany, August 12 -13, 2016 |
===IMPORTANT DATES=== | ===IMPORTANT DATES=== | ||
| − | + | * Submission deadline: Sunday, May 8, 2016, 11:59 PM Eastern US | |
* Notification of acceptance: Monday, June 13, 2016 | * Notification of acceptance: Monday, June 13, 2016 | ||
| − | * Camera-ready copy due from authors: Wednesday, June 22, 2016 | + | * Camera-ready copy due from authors: Wednesday, June 22, 2016 |
* BioNLP workshop: Friday, August 12, 2016 | * BioNLP workshop: Friday, August 12, 2016 | ||
* BioNLP-ST and BioASQ workshop: Saturday August 13, 2016 | * BioNLP-ST and BioASQ workshop: Saturday August 13, 2016 | ||
| Line 86: | Line 152: | ||
<tr><td valign=top width=100> </td><td valign=top align=left><i>Relation extraction from clinical texts using domain invariant convolutional neural network</i><br> | <tr><td valign=top width=100> </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> | Sunil Sahu, Ashish Anand, Krishnadev Oruganty and Mahanandeeshwar Gattu</td></tr> | ||
| + | |||
| + | <tr><td valign=top width=100> </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> </td> <td><b>All August 13 talks are also presented as posters on August 12 and August 13</b></td></tr> | ||
| + | |||
</table> | </table> | ||
| − | ==BioASQ / BioNLP-ST Workshop Program== | + | ==BioASQ / BioNLP-ST Workshop Program, August 13== |
<table> | <table> | ||
| Line 112: | Line 183: | ||
<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>14:30-14:45</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>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> | + | <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> | + | <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>'''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>16:00-17:00</td> <td>'''BioNLP-ST participant session 2'''</td></tr> | ||
| − | <tr><td valign=top width=100>16:00-16:15</td> <td> | + | <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>16:15-16:30</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> | + | <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>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> | <tr><td valign=top width=100>'''17:00-17:30'''</td> <td><b>Closing session</b></td></tr> | ||
| + | |||
</table> | </table> | ||
| − | + | <!-- | |
==WORKSHOP OVERVIEW AND SCOPE== | ==WORKSHOP OVERVIEW AND SCOPE== | ||
| Line 146: | 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> | <!-- <h5>SUBMISSION INSTRUCTIONS</h5> | ||
| Line 166: | Line 241: | ||
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. --> | 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. --> | ||
| + | <!-- | ||
<b>Program Committee:</b> | <b>Program Committee:</b> | ||
| Line 210: | Line 286: | ||
| − | <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. | ||
| Line 231: | 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
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.