Ultraconservative online algorithms for multiclass problems
The Journal of Machine Learning Research
Coarse-to-fine n-best parsing and MaxEnt discriminative reranking
ACL '05 Proceedings of the 43rd Annual Meeting on Association for Computational Linguistics
Self-training for biomedical parsing
HLT-Short '08 Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics on Human Language Technologies: Short Papers
Extracting complex biological events with rich graph-based feature sets
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
A Markov logic approach to bio-molecular event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Joint inference for knowledge extraction from biomedical literature
HLT '10 Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics
On dual decomposition and linear programming relaxations for natural language processing
EMNLP '10 Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing
Dual decomposition for parsing with non-projective head automata
EMNLP '10 Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing
Event extraction as dependency parsing
HLT '11 Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies - Volume 1
Overview of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of Genia event task in BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the infectious diseases (ID) task of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Event extraction as dependency parsing for BioNLP 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Model combination for event extraction in BioNLP 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of Genia event task in BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Overview of the infectious diseases (ID) task of BioNLP Shared Task 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Model combination for event extraction in BioNLP 2011
BioNLP Shared Task '11 Proceedings of the BioNLP Shared Task 2011 Workshop
Fast and robust joint models for biomedical event extraction
EMNLP '11 Proceedings of the Conference on Empirical Methods in Natural Language Processing
ExProM '12 Proceedings of the Workshop on Extra-Propositional Aspects of Meaning in Computational Linguistics
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We present a joint model for biomedical event extraction and apply it to four tracks of the BioNLP 2011 Shared Task. Our model decomposes into three sub-models that concern (a) event triggers and outgoing arguments, (b) event triggers and incoming arguments and (c) protein-protein bindings. For efficient decoding we employ dual decomposition. Our results are very competitive: With minimal adaptation of our model we come in second for two of the tasks---right behind a version of the system presented here that includes predictions of the Stanford event extractor as features. We also show that for the Infectious Diseases task using data from the Genia track is a very effective way to improve accuracy.