Difference between revisions of "BioNLP 2023"
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[[SIGBIOMED]] | [[SIGBIOMED]] | ||
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==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 | ||
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<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> | ||
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| + | <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> | ||
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| + | <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> | ||
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</table> | </table> | ||
| − | ==BioASQ / BioNLP-ST Workshop Program== | + | ==BioASQ / BioNLP-ST Workshop Program, August 13== |
<table> | <table> | ||
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<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> | ||
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</table> | </table> | ||
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==WORKSHOP OVERVIEW AND SCOPE== | ==WORKSHOP OVERVIEW AND SCOPE== | ||
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* Translating NLP research to practice | * Translating NLP research to practice | ||
* Theoretical underpinnings of biomedical language processing | * Theoretical underpinnings of biomedical language processing | ||
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<!-- <h5>SUBMISSION INSTRUCTIONS</h5> | <!-- <h5>SUBMISSION INSTRUCTIONS</h5> | ||
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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. --> | 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. --> | ||
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<b>Program Committee:</b> | <b>Program Committee:</b> | ||
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| − | <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. | ||
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* Anastasia Krithara, NCSR "Demokritos", Greece | * Anastasia Krithara, NCSR "Demokritos", Greece | ||
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<!-- ==BIONLP 2015 Workshop Schedule== | <!-- ==BIONLP 2015 Workshop Schedule== | ||