BioNLP'09 Shared Task on Event Extraction
in conjunction with BioNLP, a NAACL-HLT 2009 workshop, June 4-5 2009, Boulder, Colorado

Program of BioNLP 2009 workshop

Thirsday, June 4, 2009

Main Sessions (Program)

Friday, June 5, 2009

Shared Task Sessions

  Session 1: Oral presentations
9:00–9:20Overview of BioNLP’09 Shared Task on Event Extraction [Slides]
Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano and Jun’ichi Tsujii
9:20–9:40Extracting Complex Biological Events with Rich Graph-Based Feature Sets [Slides]
Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala and Tapio Salakoski
9:40–10:00Event Extraction from Trimmed Dependency Graphs [Slides]
Ekaterina Buyko, Erik Faessler, Joachim Wermter and Udo Hahn
10:00–10:15UZurich in the BioNLP 2009 Shared Task
Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi
10:15–10:30Biomedical Event Extraction without Training Data [Slides]
Andreas Vlachos, Paula Buttery, Diarmuid O Seaghdha and Ted Briscoe
10:30–11:00Coffee break
 Session 2: Oral presentations
11:00–11:20A Markov Logic Approach to Bio-Molecular Event Extraction [Slides]
Sebastian Riedel, Hong-Woo Chun, Toshihisa Takagi and Jun’ichi Tsujii
11:20–11:40High-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
11:40–11:55A memory-based learning approach to event extraction in biomedical texts [Slides]
Roser Morante, Vincent Van Asch and Walter Daelemans
11:55–12:10Extraction of biomedical events using case-based reasoning [Slides]
Mariana Neves, José-María Carazo and Alberto Pascual-Montano
12:10–12:25Biomedical Event Annotation with CRFs and Precision Grammars [Slides]
Andrew MacKinlay, David Martinez and Timothy Baldwin
 Session 3: Poster presentations
14:00–14:15Introduction to poster presentations
14:15–15:30Poster 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
 Tunable Domain-Independent Event Extraction in the MIRA Framework
Georgi Georgiev, Kuzman Ganchev, Vassil Momchev, Deyan Peychev, Preslav Nakov and Angus Roberts
 BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing
Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel and Hasan Davulcu
 From Protein-Protein Interaction to Molecular Event Extraction
Rune Sætre, Makoto Miwa, Kazuhiro Yoshida and Jun’ichi Tsujii
 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
 Supervised Classification for Extracting Biomedical Events
Arzucan Ozgur and Dragomir Radev
 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
15:30–16:00Coffee break
 Session 4: Oral presentations and Discussion
16:00–16:20Syntactic Dependency Based Heuristics for Biological Event Extraction [Slides]
Halil Kilicoglu and Sabine Bergler
16:20–16:35Analyzing 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
16:35–16:50Exploring 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.]