A rich feature vector for protein-protein interaction extraction from multiple corpora

EMNLP 2009 - Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: A Meeting of SIGDAT, a Special Interest Group of ACL, Held in Conjunction with ACL-IJCNLP 2009

Volumn , Issue , 2009, Pages 121-130

  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

[No Author keywords available]

Indexed keywords

EXTRACTION; LEARNING ALGORITHMS; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS; SUPPORT VECTOR MACHINES; VECTORS;

EXTRACTION SYSTEMS; FEATURE VECTORS; MULTIPLE CORPORA; PROTEIN-PROTEIN INTERACTION EXTRACTIONS; PROTEIN-PROTEIN INTERACTIONS; RICH FEATURES; STATE OF THE ART;

LINGUISTICS;

EID: 71749116134     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.3115/1699510.1699527     Document Type: Conference Paper

References (29)

1. Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter, and Tapio Salakoski. 2008. All-paths graph kernel for protein-protein interaction extraction with evaluation of cross corpus learning. BMC Bioinformatics.
2. Rie Kubota Ando, Tong Zhang, and Peter Bartlett. 2005. A framework for learning predictive structures from multiple tasks and unlabeled data. Journal of Machine Learning Research, 6:1817-1853.
3. Rie Kubota Ando. 2006. Applying alternating structure optimization to word sense disambiguation. In Proceedings of the Tenth Conference on Computational Natural Language Learning (CoNLL-X), pages 77-84, June.
4. C. M. Bishop. 1995. Neural Networks for Pattern Recognition. Oxford University Press.
5. Razvan C. Bunescu and Raymond J. Mooney. 2005. Subsequence kernels for relation extraction. In NIPS 2005.
6. Razvan C. Bunescu, Ruifang Ge, Rohit J. Kate, Edward M. Marcotte, Raymond J. Mooney, Arun K. Ramani, and Yuk Wah Wong. 2005. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine, 33(2):139-155.
7. Michael Collins. 2002. Discriminative training methods for hidden markov models: theory and experiments with perceptron algorithms. In EMNLP 2002, pages 1-8.
8. Wenyuan Dai, Qiang Yang, Gui-Rong Xue, and Yong Yu. 2007. Boosting for transfer learning. In ICML 2007, pages 193-200.
9. J. Ding, D. Berleant, D. Nettleton, and E. Wurtele. 2002. Mining medline: abstracts, sentences, or phrases? Pacific Symposium on Biocomputing, pages 326-337.
10. Mark Dredze, Koby Crammer, and Fernando Pereira. 2008. Confidence-weighted linear classification. In ICML 2008, pages 264-271.
11. Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. 2007. Semi-supervised classification for extracting protein interaction sentences using dependency parsing. In EMNLP 2007.
12. Rong-En Fan, Kai-Wei Chang, Cho-Jui Hsieh, Xiang-Rui Wang, and Chih-Jen Lin. 2008. LIBLINEAR: A library for large linear classification. Journal of Machine Learning Research, 9:1871-1874.
13. Katrin Fundel, Robert Küffner, and Ralf Zimmer. 2006. Relex-relation extraction using dependency parse trees. Bioinformatics, 23(3):365-371.
14. Cho-Jui Hsieh, Kai-Wei Chang, Chih-Jen Lin, S. Sathiya Keerthi, and S. Sundararajan. 2008. A dual coordinate descent method for large-scale linear SVM. In ICML 2008, pages 408-415.
15. Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, and Jun'ichi Tsujii. 2003. GENIA corpus-a semantically annotated corpus for bio-textmining. Bioinformatics, 19:i180-i182.
16. Jin-Dong Kim, Tomoko Ohta, and Jun'ichi Tsujii. 2008a. Corpus annotation for mining biomedical events from literature. BMC Bioinformatics, 9:10.
17. Seonho Kim, Juntae Yoon, and Jihoon Yang. 2008b. Kernel approaches for genic interaction extraction. Bioinformatics, 24(1):118-126.
18. Suresh Mathivanan, Balamurugan Periaswamy, TKB Gandhi, Kumaran Kandasamy, Shubha Suresh, Riaz Mohmood, YL Ramachandra, and Akhilesh Pandey. 2006. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinformatics, 7 Suppl 5:S19.
19. Quinn McNemar. 1947. Note on the sampling error of the difference between correlated proportions or percentages. Psychometrika, 12(2):153-157, June.
20. Makoto Miwa, Rune Sætre, Yusuke Miyao, Tomoko Ohta, and Jun'ichi Tsujii. 2008. Combining multiple layers of syntactic information for proteinprotein interaction extraction. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), pages 101-108.
21. Yusuke Miyao, Rune Sætre, Kenji Sagae, Takuya Matsuzaki, and Jun'ichi Tsujii. 2008. Taskoriented evaluation of syntactic parsers and their representations. In Proceedings of the 45th Meeting of the Association for Computational Linguistics (ACL'08:HLT).
22. Claire Nédellec. 2005. Learning language in logic-genic interaction extraction challenge. In Proceedings of the LLL'05 Workshop.
23. Sinno Jialin Pan and Qiang Yang. 2008. A survey on transfer learning. Technical Report HKUST-CS08-08, Department of Computer Science and Engineering, Hong Kong University of Science and Technology, Hong Kong, China, November.
24. Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, and Tapio Salakoski. 2007. BioInfer: A corpus for information extraction in the biomedical domain. BMC Bioinformatics, 8:50.
25. Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, and Tapio Salakoski. 2008. Comparative analysis of five protein-protein interaction corpora. In BMC Bioinformatics, volume 9(Suppl 3), page S6.
26. Gunnar Ratsch, Takashi Onoda, and Klaus-Robert Muller. 2001. Soft margins for adaboost. Machine Learning, 42(3):287-320.
27. Rune Sætre, Kenji Sagae, and Jun'ichi Tsujii. 2007. Syntactic features for protein-protein interaction extraction. In LBM 2007 short papers.
28. Gabriele Schweikert, Christian Widmer, Bernhard Schölkopf, and Gunnar Rätsch. 2008. An empirical analysis of domain adaptation algorithms for genomic sequence analysis. In NIPS, pages 1433-1440.
29. Jun Yang, Rong Yan, and Alexander G. Hauptmann. 2007. Cross-domain video concept detection using adaptive SVMs. In MULTIMEDIA '07: Proceedings of the 15th international conference on Multimedia, pages 188-197.