Reconstruction of semantic relationships from their projections in biomolecular domain

Proceedings of the Annual Meeting of the Association for Computational Linguistics

Volumn , Issue , 2010, Pages 108-116

  Heimonen, Juho ^a   Björne, Jari ^a   Salakoski, Tapio ^a  

^a TURKU CENTRE FOR COMPUTER SCIENCE   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

DATA MINING; EXTRACTION; NATURAL LANGUAGE PROCESSING SYSTEMS; SEMANTICS;

BIO-MOLECULAR; BIOLOGICAL ENTITIES; BIOMEDICAL TEXT MININGS; EVENTS EXTRACTIONS; EXTRACTION METHOD; MINING COMMUNITIES; NAMED ENTITIES; NESTED RELATIONSHIPS; RELATIONSHIP GRAPHS; SEMANTIC RELATIONSHIPS;

EQUIVALENCE CLASSES;

EID: 85037353091     PISSN: 0736587X     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (28)

1. J. Allen, M. Swift, and W. de Beaumont. 2008. Deep semantic analysis of text. In Proceedings of the 2008 Conference on Semantics in Text Processing (STEP'08), pages 343-354.
2. J. Björne, 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), pages 125-128.
3. J. Björne, J. Heimonen, F. Ginter, A. Airola, T. Pahikkala, and T. Salakoski. 2010. Extracting contextualized complex biological events with rich graph-based feature sets. Computational Intelligence. To appear.
4. C. Brisson. 2003. Plurals, all, and the nonuniformity of collective predication. Linguistics and Philosophy, 26:129-184.
5. E. Charniak 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), pages 173-180.
6. M. Chein and M.-L. Mugnier. 2008. Graph-based Knowledge Representation: Computational Foundations of Conceptual Graphs. Springer Publishing Company Inc.
7. K. Crammer and Y. Singer. 2002. On the algorithmic implementation of multiclass kernel-based vector machines. Journal of Machine Learning Research, 2:265-292.
8. M.-C. de Marneffe and C. Manning. 2008. The stanford typed dependencies representation. In Proceedings of the Coling'08 Workshop on Cross-Framework and Cross-Domain Parser Evaluation, pages 1-8.
9. M.-C. de Marneffe, B. MacCartney, and C. Manning. 2006. Generating typed dependency parses from phrase structure parses. In Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC'06), pages 449-454.
10. K. Hacioglu. 2004. Semantic role labeling using dependency trees. In Proceedings of the 20th International Conference on Computational Linguistics (COLING'04), pages 1273-1276.
11. J. Heimonen, 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), pages 45-52.
12. J.-D. Kim, T. Ohta, and J. Tsujii. 2008. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9:10.
13. J.-D. Kim, 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'09 Workshop on BioNLP: Companion Volume for Shared Task (BioNLP'09), pages 1-9.
14. D. McClosky and E. Charniak. 2008. Self-training for biomedical parsing. In Proceedings of the 46th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies, Short Papers (ACL'08: HLT), pages 101-104.
15. D. McClosky. 2009. Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing. Ph.D. thesis, Department of Computer Science, Brown University, Providence, Rhode Island, USA.
16. M. Miwa, R. Saetre, J.-D. Kim, and J. Tsujii. 2010. Event extraction with complex event classification using rich features. Journal of Bioinformatics and Computational Biology, 8:131-146.
17. H. Poon and L. Vanderwende. 2010. Joint inference for knowledge extraction from biomedical literature. In Proceedings of Human Language Technologies: The 11th Annual Conference of the North American Chapter of the Association for Computational Linguistics (NAACL-HLT'10).
18. M. Porter. 1980. An algorithm for suffix stripping. Program, 14:130-137.
19. S. Pyysalo, 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, 8:50.
20. S. Pyysalo, T. Ohta, J.-D. Kim, and J. Tsujii. 2009. Static relations: a piece in the biomedical information extraction puzzle. In Proceedings of the NAACL-HLT'09 Workshop on BioNLP (BioNLP'09), pages 1-9.
21. J. Quinlan. 1993. C4.5: programs for machine learning. Morgan Kaufmann Publishers Inc.
22. S. Riedel, H.-W. Chun, T. Takagi, and J. Tsujii. 2009. A markov logic approach to bio-molecular event extraction. In Proceedings of the NAACL-HLT'09 Workshop on BioNLP: Companion Volume for Shared Task (BioNLP'09), pages 41-49.
23. R. Scha and D. Stallard. 1988. Multi-level plurals and distributivity. In Proceedings of the 26th Annual Meeting of the Association for Computational Linguistics (ACL'88), pages 17-24.
24. J. Sowa. 1976. Conceptual graphs for a data base interface. IBM Journal of Research and Development, 20:336-357.
25. M. Surdeanu, R. Johansson, A. Meyers, L. Màrquez, and J. Nivre. 2008. The CoNLL 2008 shared task on joint parsing of syntactic and semantic dependencies. In Proceedings of the Twelfth Conference on Computational Natural Language Learning (CoNLL'08), pages 159-177.
26. P. Thompson, S. Iqbal, J. McNaught, and S. Ananiadou. 2009. Construction of an annotated corpus to support biomedical information extraction. BMC Bioinformatics, 10:349.
27. I. Tsochantaridis, T. Hofmann, T. Joachims, and Y. Al-tun. 2004. Support vector machine learning for interdependent and structured output spaces. In Proceedings of the 21st International Machine Learning Conference (ICML'04), page 104.
28. F. Wilcoxon. 1945. Individual comparisons by ranking methods. Biometrics Bulletin, 1:80-83.