Extracting contextualized complex biological events with rich graph-based feature sets

Computational Intelligence

Volumn 27, Issue 4, 2011, Pages 541-557

  Björne, Jari ^a   Heimonen, Juho ^a   Ginter, Filip ^a   Airola, Antti ^a   Pahikkala, Tapio ^a   Salakoski, Tapio ^a  

^a UNIVERSITY OF TURKU   (Finland)

Author keywords

biomedical domain; BioNLP'09 Shared Task; event extraction; machine learning; natural language processing

Indexed keywords

BIOMEDICAL DOMAIN; BIONLP'09 SHARED TASK; EVENT EXTRACTION; MACHINE-LEARNING; NATURAL LANGUAGE PROCESSING;

COMPUTATIONAL LINGUISTICS; DATA MINING; GENES; LEARNING ALGORITHMS; LEARNING SYSTEMS;

NATURAL LANGUAGE PROCESSING SYSTEMS;

EID: 82455189738     PISSN: 08247935     EISSN: 14678640     Source Type: Journal    
DOI: 10.1111/j.1467-8640.2011.00399.x     Document Type: Article

References (24)

1. Airola, A., S. Pyysalo, J. Björne, T. Pahikkala, F. Ginter, and, T. Salakoski,. 2008. All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics, 9 (Suppl 11): S2.
2. Altun, Y., I. Tsochantaridis, and, T. Hofmann,. 2003. Hidden Markov support vector machines. In Proceedings of the Twentieth International Conference on Machine Learning (ICML'03), Washington, DC, pp. 3-10.
3. Björne, J., S. Pyysalo, F. Ginter, and, T. Salakoski,. 2008. How complex are complex protein-protein interactions? In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS, Turku, Finland, pp. 125-128.
4. Björne, J., F. Ginter, J. Heimonen, S. Pyysalo, and, T. Salakoski,. 2009. Learning to extract biological event and relation graphs. In Proceedings of the 17th Nordic Conference on Computational Linguistics (NODALIDA'09), Odense, Denmark, pp. 18-25.
5. Buyko, E., E. Beisswanger, and, U. Hahn,. 2008. Testing different ACE-style feature sets for the extraction of gene regulation relations from MEDLINE abstracts. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS, Turku, Finland, pp. 21-28.
6. Buyko, E., E. Faessler, J. Wermter, and, U. Hahn,. 2009. Event extraction from trimmed dependency graphs. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, ACL, Boulder, CO, pp. 19-27.
7. Charniak, E., and, M. 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), ACL, Ann Arbor, MI, pp. 173-180.
8. Crammer, K., and, Y. Singer,. 2002. On the algorithmic implementation of multiclass kernel-based vector machines. Journal of Machine Learning Research, 2: 265-292.
9. De Marneffe, M.-C., and, C. Manning,. 2008. Stanford typed hierarchies representation. In Proceedings of the COLING'08 Workshop on Cross-Framework and Cross-Domain Parser Evaluation, Manchester, UK, pp. 1-8.
10. Heimonen, J., S. Pyysalo, F. Ginter, and, T. Salakoski,. 2008. Complex-to-pairwise mapping of biological relationships using a semantic network representation. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS, Turku, Finland, pp. 45-52.
11. Katrenko, S., and, P. Adriaans,. 2008. A local alignment kernel in the context of NLP. In Proceedings of the 22nd International Conference on Computational Linguistics (Coling'08), Manchester, UK, pp. 417-424.
12. Kilicoglu, H., and, S. Bergler,. 2009. Syntactic dependency based heuristics for biological event extraction. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, ACL, Boulder, CO, pp. 119-127.
13. Kim, J.-D., T. Ohta, and, T. Jun'ichi,. 2008a. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9 (1): 10.
14. Kim, J.-D., T. Ohta, S. Pyysalo, Y. Kano, and, J. Tsujii,. 2009. Overview of BioNLP'09 shared task on event extraction. In Proceedings of the NAACL-HLT 2009 Workshop on Natural Language Processing in Biomedicine (BioNLP'09), ACL, Boulder, CO, pp. 1-9.
15. Kim, S., J. Yoon, and, J. Yang,. 2008b. Kernel approaches for genic interaction extraction. Bioinformatics, 24 (1): 118-126.
16. Lafferty, J., A. McCallum, and, F. Pereira,. 2001. Conditional random fields: Probabilistic models for segmenting and labeling sequence data. In Proceedings of the 18th International Conference on Machine Learning (ICML'01), Williamstown, MA, pp. 282-289.
17. McClosky, D., 2009. Any domain parsing: Automatic domain adaptation for natural language parsing. Ph.D. Thesis, Department of Computer Science, Brown University.
18. Miwa, M., R. SÃtre, Y. Miyao, T. Ohta, and, J. Tsujii,. 2008. Combining multiple layers of syntactic information for protein-protein interaction extraction. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS, Turku, Finland, pp. 101-108.
19. Porter, M. F., 1980. An algorithm for suffix stripping. Program, 14 (3): 130-137.
20. Pyysalo, S., F. Ginter, J. Heimonen, J. Björne, J. Boberg, J. Järvinen, and, T. Salakoski,. 2007. BioInfer: A corpus for information extraction in the biomedical domain. BMC Bioinformatics, 8 (1): 50.
21. Riedel, S., H.-W. Chun, T. Takagi, and, J. Tsujii,. 2009. A Markov Logic Approach to bio-molecular event extraction. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, ACL, Boulder, CO, pp. 41-49.
22. Tsochantaridis, I., T. Hofmann, T. Joachims, and, Y. Altun,. 2004. Support vector machine learning for interdependent and structured output spaces. In Proceedings of the Twenty-first International Conference on Machine Learning (ICML'04), ACM, Banff, Canada, pp. 104-111.
23. Van Landeghem, S., Y. Saeys, B. De Baets, and, Y. Van de Peer,. 2008. Extracting protein-protein interactions from text using rich feature vectors and feature selection. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM'08), TUCS, Turku, Finland, pp. 77-84.
24. Van Landeghem, S., Y. Saeys, B. De Baets, and, Y. Van de Peer,. 2009. Analyzing text in search of bio-molecular events: A high-precision machine learning framework. In Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, ACL, Boulder, CO, pp. 128-136.