UZH in BioNLP 2013

We describe a biological event detection method implemented for the Genia Event Extraction task of BioNLP 2013. The method relies on syntactic dependency relations provided by a general NLP pipeline, supported by statistics derived from Maximum Entropy models for candidate trigger words, for potential arguments, and for argument frames.

[1]  Fabio Rinaldi,et al.  UZurich in the BioNLP 2009 Shared Task , 2009, BioNLP@HLT-NAACL.

[2]  Asif Ekbal,et al.  Evolutionary Approach for Classifier Ensemble: An Application to Bio-molecular Event Extraction , 2012, ISI.

[3]  F Rinaldi,et al.  OntoGene in BioCreative II.5 , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[4]  Marc Moens,et al.  LT TTT - A Flexible Tokenisation Tool , 2000, LREC.

[5]  Russ B. Altman,et al.  Using ODIN for a PharmGKB revalidation experiment , 2012, Database J. Biol. Databases Curation.

[6]  Fabio Rinaldi,et al.  Ranking relations between diseases, drugs and genes for a curation task , 2012, J. Biomed. Semant..

[7]  John A. Carroll,et al.  Applied morphological processing of English , 2001, Natural Language Engineering.

[8]  Fabio Rinaldi,et al.  An Incremental Model for the Coreference Resolution Task of BioNLP 2011 , 2011, BioNLP@ACL.

[9]  Fabio Rinaldi,et al.  Using the OntoGene pipeline for the triage task of BioCreative 2012 , 2013, Database J. Biol. Databases Curation.

[10]  Hal Daumé Notes on CG and LM-BFGS Optimization of Logistic Regression , 2008 .

[11]  Gerold Schneider,et al.  Hybrid Long-Distance Functional Dependency Parsing , 2009 .

[12]  Dietrich Rebholz-Schuhmann,et al.  OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization , 2011 .

[13]  Fabio Rinaldi,et al.  Relation mining experiments in the pharmacogenomics domain , 2012, J. Biomed. Informatics.

[14]  M. Romacker,et al.  OntoGene in BioCreative II , 2007, Genome Biology.

[15]  Yue Wang,et al.  The Genia Event Extraction Shared Task, 2013 Edition - Overview , 2013, BioNLP@ACL.

[16]  Fabio Rinaldi,et al.  UZurich in the BioNLP 2009 Shared Task , 2009, HLT-NAACL 2009.