Program of BioNLP 2009 workshop
Thirsday, June 4, 2009
Main Sessions (Program)
Friday, June 5, 2009
Shared Task Sessions
| Session 1: Oral presentations | |
| 9:00–9:20 | Overview of BioNLP’09 Shared Task on Event Extraction [Slides] Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano and Jun’ichi Tsujii |
| 9:20–9:40 | Extracting Complex Biological Events with Rich Graph-Based Feature Sets [Slides] Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala and Tapio Salakoski |
| 9:40–10:00 | Event Extraction from Trimmed Dependency Graphs [Slides] Ekaterina Buyko, Erik Faessler, Joachim Wermter and Udo Hahn |
| 10:00–10:15 | UZurich in the BioNLP 2009 Shared Task Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi |
| 10:15–10:30 | Biomedical Event Extraction without Training Data [Slides] Andreas Vlachos, Paula Buttery, Diarmuid O Seaghdha and Ted Briscoe |
| 10:30–11:00 | Coffee break |
| Session 2: Oral presentations | |
| 11:00–11:20 | A Markov Logic Approach to Bio-Molecular Event Extraction [Slides] Sebastian Riedel, Hong-Woo Chun, Toshihisa Takagi and Jun’ichi Tsujii |
| 11:20–11:40 | High-precision biological event extraction with a concept recognizer [Slides] K. Bretonnel Cohen, Karin Verspoor, Helen Johnson, Chris Roeder, Philip Ogren, William Baumgartner, Elizabeth White and Lawrence Hunter |
| 11:40–11:55 | A memory-based learning approach to event extraction in biomedical texts [Slides] Roser Morante, Vincent Van Asch and Walter Daelemans |
| 11:55–12:10 | Extraction of biomedical events using case-based reasoning [Slides] Mariana Neves, José-María Carazo and Alberto Pascual-Montano |
| 12:10–12:25 | Biomedical Event Annotation with CRFs and Precision Grammars [Slides] Andrew MacKinlay, David Martinez and Timothy Baldwin |
| 12:30–14:00 | Lunch |
| Session 3: Poster presentations | |
| 14:00–14:15 | Introduction to poster presentations |
| 14:15–15:30 | Poster presentations |
| Molecular event extraction from Link Grammar parse trees Jörg Hakenberg, Illes Solt, Domonkos Tikk, Luis Tari, Astrid Rheinländer, Nguyen Quang Long, Graciela Gonzalez and Ulf Leser |
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| Tunable Domain-Independent Event Extraction in the MIRA Framework Georgi Georgiev, Kuzman Ganchev, Vassil Momchev, Deyan Peychev, Preslav Nakov and Angus Roberts |
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| BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel and Hasan Davulcu |
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| From Protein-Protein Interaction to Molecular Event Extraction Rune Sætre, Makoto Miwa, Kazuhiro Yoshida and Jun’ichi Tsujii |
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| A Multi-Phase Approach to Biomedical Event Extraction Hyoung-Gyu Lee, Han-Cheol Cho, Min-Jeong Kim, Joo-Young Lee, Gumwon Hong and Hae-Chang Rim |
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| Supervised Classification for Extracting Biomedical Events Arzucan Ozgur and Dragomir Radev |
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| Biomedical Event Detection using Rules, Conditional Random Fields and Parse Tree Distances Farzaneh Sarafraz, James Eales, Reza Mohammadi, Jonathan Dickerson, David Robertson and Goran Nenadic |
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| 15:30–16:00 | Coffee break |
| Session 4: Oral presentations and Discussion | |
| 16:00–16:20 | Syntactic Dependency Based Heuristics for Biological Event Extraction [Slides] Halil Kilicoglu and Sabine Bergler |
| 16:20–16:35 | Analyzing text in search of bio-molecular events: a high-precision machine learning framework [Slides] Sofie Van Landeghem, Yvan Saeys, Bernard De Baets and Yves Van de Peer |
| 16:35–16:50 | Exploring ways beyond the simple supervised learning approach for biological event extraction György Móra, Richárd Farkas, György Szarvas and Zsolt Molnár [Note: The oral presentation was canceled, and this manuscript presented as a poster.] |
| 16:50–17:30 | Discussion |