Protein-protein interaction extraction by leveraging multiple kernels and parsers

International Journal of Medical Informatics

Volumn 78, Issue 12, 2009, Pages

  Miwa, Makoto ^a   Sætre, Rune ^a   Miyao, Yusuke ^a   Tsujii, Jun'ichi ^a,b,c  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF MANCHESTER   (United Kingdom)

^c National Center for Text Mining   (United Kingdom)

Author keywords

Machine learning; Protein protein interaction extraction; Relation extraction; Support vector machine

Indexed keywords

MACHINE LEARNING METHODS; MACHINE-LEARNING; MULTIPLE KERNELS; NATURAL LANGUAGE PROCESSING; PROTEIN-PROTEIN INTERACTIONS; RELATION EXTRACTION; SENTENCE STRUCTURES; SYNTACTIC PARSERS;

COMPUTATIONAL LINGUISTICS; IMAGE RETRIEVAL; NATURAL LANGUAGE PROCESSING SYSTEMS; ROBOT LEARNING; SUPPORT VECTOR MACHINES;

PROTEINS;

ARTICLE; DATA EXTRACTION; INFORMATION RETRIEVAL; MACHINE LEARNING; MEDICAL INFORMATICS; NATURAL LANGUAGE PROCESSING; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SUPPORT VECTOR MACHINE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES AS TOPIC; NATURAL LANGUAGE PROCESSING; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS, PROTEIN;

EID: 71549135535     PISSN: 13865056     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ijmedinf.2009.04.010     Document Type: Article

References (22)

1. Mathivanan S., Periaswamy B., Gandhi T., Kandasamy K., Suresh S., Mohmood R., Ramachandra Y., and Pandey A. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics 7 Suppl. 5 (2006) 19
2. S. Pyysalo, A. Airola, J. Heimonen, J. Björne, F. Ginter, T. Salakoski, Comparative analysis of five protein-protein interaction corpora. BMC Bioinformatics 9 (Suppl. 3) (2008), p. S6.
3. Blaschke C., Andrade M.A., Ouzounis C., and Valencia A. Automatic extraction of biological information from scientific text: protein-protein interactions. Proceedings of the AAAI Conference on Intelligent Systems in Molecular Biology (1999) 60-67
4. Bunescu R.C., Ge R., Kate R.J., Marcotte E.M., Mooney R.J., Ramani A.K., and Wong Y.W. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 33 2 (2005) 139-155
5. Sagae K., and Tsujii J. Dependency parsing and domain adaptation with LR models and parser ensembles. Proceedings of the EMNLP-CoNLL 2007 (2007)
6. Cristianini N., and Shawe-Taylor J. An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods (2000), Cambridge University Press, Cambridge, U.K.
7. Bunescu R.C., and Mooney R.J. Subsequence kernels for relation extraction. NIPS 2005 (2005)
8. Moschitti A. Making tree kernels practical for natural language processing. Proceedings of the EACL 2006 (2006)
9. R. Sætre, K. Sagae, J. Tsujii, Syntactic features for protein-protein interaction extraction, in: LBM 2007 short papers, 2007.
10. Bunescu R.C., and Mooney R.J. A shortest path dependency kernel for relation extraction. HLT'05: Proceedings of the conference on Human Language Technology and Empirical Methods in Natural Language Processing (2005), Association for Computational Linguistics, Morristown, NJ, USA 724-731
11. A. Airola, S. Pyysalo, J. Björne, T. Pahikkala, F. Ginter, T. Salakoski. A graph kernel for protein-protein interaction extraction, in: Proceedings of the BioNLP 2008 Workshop, 2008.
12. Miyao Y., Sætre R., Sagae K., Matsuzaki T., and Tsujii J. Task-oriented evaluation of syntactic parsers and their representations. Proceedings of the 45th Meeting of the Association for Computational Linguistics (ACL'08:HLT) (2008)
13. Dijkstra E.W. A note on two problems in connexion with graphs. Numerische Mathematik 1 (1959) 269-271. http://jmvidal.cse.sc.edu/library/dijkstra59a.pdf http://jmvidal.cse.sc.edu/library/dijkstra59a.pdf
14. Miyao Y., and Tsujii J. Feature forest models for probabilistic HPSG parsing. Computational Linguistics 34 1 (2008) 35-80
15. Gärtner T., Flach P.A., and Wrobel S. On graph kernels: hardness results and efficient alternatives. Proceedings of the 16th Annual Conference on Computational Learning Theory and the 7th Kernel Workshop (2003)
16. Kim J.-D., Ohta T., Tateisi Y., and Tsujii J. GENIA corpus-a semantically annotated corpus for bio-textmining. Bioinformatics 19 (2003) i180-i182
17. Giuliano C., Lavelli A., and Romano L. Exploiting shallow linguistic information for relation extraction from biomedical literature. Proceedings of the EACL 2006 (2006)
18. M. Miwa, R. Sætre, Y. Miyao, T. Ohta, J. Tsujii, 2008. Combining multiple layers of syntactic information for protein-protein interaction extraction. In: Salakoski, T., Rebholz-Schuhmann, D., Pyysalo, S., (Eds.). Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku Centre for Computer Science (TUCS), Turku, Finland, pp. 101-108.
19. Mitsumori T., Murata M., Fukuda Y., Doi K., and Doi H. Extracting protein-protein interaction information from biomedical text with SVM. IEICE-Transactions on Information and Systems E89-D 8 (2006) 2464-2466
20. Yakushiji A., Miyao Y., Tateisi Y., and Tsujii J. Biomedical information extraction with predicate-argument structure patterns. Proceedings of the First International Symposium on Semantic Mining in Biomedicine (2005)
21. Erkan G., Ozgur A., and Radev D.R. Semi-supervised classification for extracting protein interaction sentences using dependency parsing. EMNLP 2007 (2007)
22. Katrenko S., and Adriaans P. Learning relations from biomedical corpora using dependency trees. Proceedings of the KDECB (2006) 61-80