Robust biomedical event extraction with dual decomposition and minimal domain adaptation

Proceedings of BioNLP Shared Task 2011 Workshop at the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, ACL HLT 2011

Volumn , Issue , 2011, Pages 46-50

  Riedel, Sebastian ^a   McCallum, Andrew ^a  

^a Biologically Inspired Neural and Dynamical Systems Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; COMPUTATIONAL LINGUISTICS; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS;

DOMAIN ADAPTATION; DUAL DECOMPOSITION; EVENT TRIGGER; EVENTS EXTRACTIONS; INFECTIOUS DISEASE; JOINT MODELS; PROTEIN-PROTEIN BINDING; STANFORD; SUBMODELS;

EXTRACTION;

EID: 84888276650     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, and Tapio Salakoski. 2009. Extracting complex biological events with rich graph-based feature sets. In Proceedings of the Natural Language Processing in Biomedicine NAACL 2009 Workshop (BioNLP’09), pages 10–18, Morristown, NJ, USA. Association for Computational Linguistics.
2. Eugene Charniak and Mark Johnson. 2005. Coarse-to-fine n-best parsing and maxent discriminative reranking. In Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL’05), pages 173–180.
3. Koby Crammer and Yoram Singer. 2003. Ultraconservative online algorithms for multiclass problems. Journal of Machine Learning Research, 3:951–991.
4. Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Robert Bossy, and Jun’ichi Tsujii. 2011a. Overview of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
5. Jin-Dong Kim, Yue Wang, Toshihisa Takagi, and Akinori Yonezawa. 2011b. Overview of the Genia Event task in BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
6. Nikos Komodakis, Nikos Paragios, and Georgios Tziritas. 2007. Mrf optimization via dual decomposition: Message-passing revisited. In In ICCV.
7. Terry Koo, Alexander M. Rush, Michael Collins, Tommi Jaakkola, and David Sontag. 2010. Dual decomposition for parsing with non-projective head automata. In Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing (EMNLP).
8. David McClosky and Eugene Charniak. 2008. Self-training for biomedical parsing. In Proceedings of the 46rd Annual Meeting of the Association for Computational Linguistics (ACL’08).
9. David McClosky, Mihai Surdeanu, and Chris Manning. 2011a. Event extraction as dependency parsing. In Proceedings of the Association for Computational Linguistics: Human Language Technologies 2011 Conference (ACL-HLT’11), Main Conference (to appear), Portland, Oregon, June.
10. David McClosky, Mihai Surdeanu, and Christopher D. Manning. 2011b. Event extraction as dependency parsing in BioNLP 2011. In BioNLP 2011 Shared Task.
11. Makoto Miwa, Rune Saetre, Jin-Dong D. Kim, and Jun’ichi Tsujii. 2010. Event extraction with complex event classification using rich features. Journal of bioinformatics and computational biology, 8(1):131–146, February.
12. Tomoko Ohta, Sampo Pyysalo, and Jun’ichi Tsujii. 2011. Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
13. Hoifung Poon and Lucy Vanderwende. 2010. Joint Inference for Knowledge Extraction from Biomedical Literature. In Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, pages 813–821, Los Angeles, California, June. Association for Computational Linguistics.
14. Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno Sobral, Jun’ichi Tsujii, and Sophia Ananiadou. 2011. Overview of the Infectious Diseases (ID) task of BioNLP Shared Task 2011. In Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, Portland, Oregon, June. Association for Computational Linguistics.
15. Sebastian Riedel, Hong-Woo Chun, Toshihisa Takagi, and Jun’ichi Tsujii. 2009. A markov logic approach to bio-molecular event extraction. In Proceedings of the Natural Language Processing in Biomedicine NAACL 2009 Workshop (BioNLP’09), pages 41–49.
16. Sebastian Riedel, David McClosky, Mihai Surdeanu, Christopher D. Manning, and Andrew McCallum. 2011. Model combination for event extraction in BioNLP 2011. In BioNLP 2011 Shared Task.
17. Alexander M. Rush, David Sontag, Michael Collins, and Tommi Jaakkola. 2010. On dual decomposition and linear programming relaxations for natural language processing. In In Proc. EMNLP.