BioNLP Shared Task 2011 Program

BioNLP Shared Task Sessions: June 24 (Friday)

Session 1: Oral presentations and discussion
09:00-09:25 Overview of BioNLP Shared Task 2011 - Overall Organization, and GE, EPI and ID Tasks

Shared Task Organizers
09:25-09:40 Biomedical Event Extraction from Abstracts and Full Papers using Search-based Structured Prediction

Andreas Vlachos and Mark Craven
09:40-09:55 Event Extraction as Dependency Parsing for BioNLP 2011

David McClosky, Mihai Surdeanu and Christopher Manning
09:55-10:10 Robust Biomedical Event Extraction with Dual Decomposition and Minimal Domain Adaptation

Sebastian Riedel and Andrew McCallum
10:10-10:25 Model Combination for Event Extraction in BioNLP 2011

Sebastian Riedel, David McClosky, Mihai Surdeanu, Andrew McCallum and Christopher D. Manning
10:25-10:30 Discussion
10:30-11:00 Morning break

Session 2: Oral presentations and discussion
11:00-11:20 Overview of BioNLP Shared Task 2011 - Bacteria Track (BB, BI) and Supporting Tasks (CO, REL and REN)

Shared Task Organizers
11:20-11:35 The Taming of Reconcile as a Biomedical Coreference Resolver

Youngjun Kim, Ellen Riloff and Nathan Gilbert
11:35-11:55 Extracting Bacteria Biotopes with Semi-supervised Named Entity Recognition and Coreference Resolution

Nhung T. H. Nguyen and Yoshimasa Tsuruoka
11:55-12:15 BioNLP 2011 Task Bacteria Biotope - The Alvis system

Zorana Ratkovic, Wiktoria Golik, Pierre Warnier, Philippe Veber and Claire Nédellec
12:15-12:30 Discussion
12:30-14:00 Lunch break

Session 3: Poster presentations
14:00-14:10 Spotlight presentations
14:10-15:30 Poster presentations

BioNLP Shared Task 2011: Supporting Resources

Pontus Stenetorp, Goran Topić, Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim and Jun'ichi Tsujii

Sentence Filtering for BioNLP: Searching for Renaming Acts

Pierre Warnier and Claire Nédellec

Complex Biological Event Extraction from Full Text using Signatures of Linguistic and Semantic Features

Liam R. McGrath, Kelly Domico, Courtney D. Corley and Bobbie-Jo Webb-Robertson

Using Kybots for Extracting Events in Biomedical Texts

Arantza Casillas, Arantza Díaz de Ilarraza, Koldo Gojenola, Maite Oronoz and German Rigau

Extracting Biological Events from Text Using Simple Syntactic Patterns

Quoc-Chinh Bui and Peter. M.A. Sloot

Detecting Entity Relations as a Supporting Task for Bio-Molecular Event Extraction

Sofie Van Landeghem, Thomas Abeel, Bernard De Baets and Yves Van de Peer

A Pattern Approach for Biomedical Event Annotation

Quang Le Minh, Son Nguyen Truong and Quoc Ho Bao

An Incremental Model for the Coreference Resolution Task of BioNLP 2011

Don Tuggener, Manfred Klenner, Gerold Schneider, Simon Clematide and Fabio Rinaldi

Double Layered Learning for Biological Event Extraction from Text

Ehsan Emadzadeh, Azadeh Nikfarjam and Graciela Gonzalez
15:30-16:00 Afternoon break

Session 4: Oral presentations and discussion
16:00-16:20 MSR-NLP Entry in BioNLP Shared Task 2011

Chris Quirk, Pallavi Choudhury, Michael Gamon and Lucy Vanderwende
16:20-16:40 From Graphs to Events: A Subgraph Matching Approach for Information Extraction from Biomedical Text

Haibin Liu, Ravikumar Komandur and Karin Verspoor
16:40-16:55 Adapting a General Semantic Interpretation Approach to Biological Event Extraction

Halil Kilicoglu and Sabine Bergler
16:55-17:15 Generalizing Biomedical Event Extraction

Jari Björne and Tapio Salakoski
17:15-17:30 Discussion