Generalizing Biomedical Event Extraction

We present a system for extracting biomedical events (detailed descriptions of biomolecular interactions) from research articles. This system was developed for the BioNLP'11 Shared Task and extends our BioNLP'09 Shared Task winning Turku Event Extraction System. It uses support vector machines to first detect event-defining words, followed by detection of their relationships. The theme of the BioNLP'11 Shared Task is generalization, extending event extraction to varied biomedical domains. Our current system successfully predicts events for every domain case introduced in the BioNLP'11 Shared Task, being the only system to participate in all eight tasks and all of their subtasks, with best performance in four tasks.

[1]  Yvan Saeys,et al.  Analyzing text in search of bio-molecular events: a high-precision machine learning framework , 2009, BioNLP@HLT-NAACL.

[2]  Martin F. Porter,et al.  An algorithm for suffix stripping , 1997, Program.

[3]  Eugene Charniak,et al.  Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing , 2010 .

[4]  Christopher D. Manning,et al.  Generating Typed Dependency Parses from Phrase Structure Parses , 2006, LREC.

[5]  Halil Kilicoglu,et al.  Syntactic Dependency Based Heuristics for Biological Event Extraction , 2009, BioNLP@HLT-NAACL.

[6]  Udo Hahn,et al.  Event Extraction from Trimmed Dependency Graphs , 2009, BioNLP@HLT-NAACL.

[7]  Jun'ichi Tsujii,et al.  A Markov Logic Approach to Bio-Molecular Event Extraction , 2009, BioNLP@HLT-NAACL.

[8]  Thomas Hofmann,et al.  Large Margin Methods for Structured and Interdependent Output Variables , 2005, J. Mach. Learn. Res..

[9]  Jari Björne,et al.  EXTRACTING CONTEXTUALIZED COMPLEX BIOLOGICAL EVENTS WITH RICH GRAPH‐BASED FEATURE SETS , 2011, Comput. Intell..

[10]  Jari Björne,et al.  Reconstruction of Semantic Relationships from Their Projections in Biomolecular Domain , 2010, BioNLP@ACL.

[11]  Jari Björne,et al.  Scaling up Biomedical Event Extraction to the Entire PubMed , 2010, BioNLP@ACL.

[12]  Jari Björne,et al.  Extracting Complex Biological Events with Rich Graph-Based Feature Sets , 2009, BioNLP@HLT-NAACL.

[13]  J. Euzéby.  List of Bacterial Names with Standing in Nomenclature: a folder available on the Internet. , 1997, International journal of systematic bacteriology.

[14]  Eugene Charniak,et al.  Coarse-to-Fine n-Best Parsing and MaxEnt Discriminative Reranking , 2005, ACL.

[15]  Christiane Fellbaum,et al.  Book Reviews: WordNet: An Electronic Lexical Database , 1999, CL.

[16]  Sampo Pyysalo,et al.  A Comparative Study of Syntactic Parsers for Event Extraction , 2010, BioNLP@ACL.

[17]  Sampo Pyysalo,et al.  Overview of BioNLP’09 Shared Task on Event Extraction , 2009, BioNLP@HLT-NAACL.

[18]  Jun'ichi Tsujii,et al.  Event Extraction with Complex Event Classification Using Rich Features , 2010, J. Bioinform. Comput. Biol..

[19]  Christopher D. Manning,et al.  The Stanford Typed Dependencies Representation , 2008, CF+CDPE@COLING.