Extracting biomolecular interactions using semantic parsing of biomedical text

30th AAAI Conference on Artificial Intelligence, AAAI 2016

Volumn , Issue , 2016, Pages 2718-2726

  Garg, Sahil ^a   Galstyan, Aram ^a   Hermjakob, Ulf ^a   Marcu, Daniel ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; ARTIFICIAL INTELLIGENCE; EXTRACTION; SEMANTICS;

BIOMEDICAL TEXT; BIOMOLECULAR INTERACTIONS; CONCURRENT EXPLOITATION; DEPENDENCY STRUCTURES; INTERACTION EXTRACTION; SEMANTIC PARSING; STATE OF THE ART; TEST CONDITION;

SYNTACTICS;

EID: 85007268680     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (37)

1. Airola, A.; Pyysalo, S.; Bjorne, J.; Pahikkala, T.; Ginter, F.; and Salakoski, T. 2008. All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning. BMC Bioinformatics 9:S2.
2. Andreas, J.; Vlachos, A.; and Clark, S. 2013. Semantic parsing as machine translation. In Proc. of ACL, 47-52.
3. Banarescu, L.; Bonial, C.; Cai, S.; Georgescu, M.; Griffitt, K.; Hermjakob, U.; Knight, K.; Koehn, P.; Palmer, M.; and Schneider, N. 2013. Abstract meaning representation for sembanking. In Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse.
4. Bordes, A.; Glorot, X.; Weston, J.; and Bengio, Y. 2014. A semantic matching energy function for learning with multirelational data. Machine Learning 94:233-259.
5. Borgwardt, K. M.; Gretton, A.; Rasch, M. J.; Kriegel, H.-P.; Schölkopf, B.; and Smola, A. J. 2006. Integrating structured biological data by kernel maximum mean discrepancy. Bioinformatics 22:e49-e57.
6. Bunescu, R.; Ge, R.; Kate, R. J.; Marcotte, E. M.; Mooney, R. J.; Ramani, A. K.; and Wong, Y. W. 2005. Comparative experiments on learning information extractors for proteins and their interactions. Artificial Intelligence in Medicine 139-155.
7. Bunescu, R.; Mooney, R.; Ramani, A.; and Marcotte, E. 2006. Integrating co-occurrence statistics with information extraction for robust retrieval of protein interactions from medline. In Proc. of theWorkshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis.
8. Chang, C.-C., and Lin, C.-J. 2011. Libsvm: A library for support vector machines. ACM Transactions on Intelligent Systems and Technology (TIST) 2:27.
9. Chen, D., and Manning, C. D. 2014. A fast and accurate dependency parser using neural networks. In Proc. of EMNLP, 740-750.
10. Clark, S. 2014. Vector space models of lexical meaning. Handbook of Contemporary Semantics, 2nd Ed. Blackwell.
11. Culotta, A., and Sorensen, J. 2004. Dependency tree kernels for relation extraction. In Proc. of ACL, 423.
12. Demir, E.; Cary, M. P.; Paley, S.; Fukuda, K.; Lemer, C.; Vastrik, I.;Wu, G.; D'Eustachio, P.; Schaefer, C.; Luciano, J.; et al. 2010. The biopax community standard for pathway data sharing. Nature Biotechnology 28:935-942.
13. Demmel, J. W. 1997. Applied numerical linear algebra. Siam.
14. Flanigan, J.; Thomson, S.; Carbonell, J.; Dyer, C.; and Smith, N. A. 2014. A discriminative graph-based parser for the abstract meaning representation. In Proc. of ACL.
15. Gneiting, T. 2002. Compactly supported correlation functions. Journal of Multivariate Analysis 83:493-508.
16. Gretton, A.; Borgwardt, K. M.; Rasch, M. J.; Schölkopf, B.; and Smola, A. 2012. A kernel two-sample test. JMLR 13:723-773.
17. Hahn, M. A. V.-E. G., and Surdeanu, P. T. H. M. 2015. A domain-independent rule-based framework for event extraction. ACL-IJCNLP 2015 127.
18. Hakenberg, J.; Plake, C.; Royer, L.; Strobelt, H.; Leser, U.; and Schroeder, M. 2008. Gene mention normalization and interaction extraction with context models and sentence motifs. Genome Biol 9:S14.
19. Hunter, L.; Lu, Z.; Firby, J.; Baumgartner, W. A.; Johnson, H. L.; Ogren, P. V.; and Cohen, K. B. 2008. Opendmap: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. BMC Bioinformatics 9:78.
20. Kim, B., and Pineau, J. 2013. Maximum mean discrepancy imitation learning. In Proc. of RSS.
21. Krallinger, M.; Leitner, F.; Rodriguez-Penagos, C.; and Valencia, A. 2008. Overview of the protein-protein interaction annotation extraction task of biocreative ii. Genome biology 9:S4.
22. Mallory, E. K.; Zhang, C.; Ŕe, C.; and Altman, R. B. 2015. Large-scale extraction of gene interactions from full-text literature using deepdive. Bioinformatics btv476.
23. McDonald, R.; Pereira, F.; Kulick, S.; Winters, S.; Jin, Y.; and White, P. 2005. Simple algorithms for complex relation extraction with applications to biomedical ie. In Proc. of ACL.
24. Mehdad, Y.; Moschitti, A.; and Zanzotto, F. M. 2010. Syntactic/semantic structures for textual entailment recognition. In Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, 1020-1028.
25. Mikolov, T.; Sutskever, I.; Chen, K.; Corrado, G. S.; and Dean, J. 2013. Distributed representations of words and phrases and their compositionality. In Proc. of NIPS.
26. Mooney, R. J., and Bunescu, R. C. 2005. Subsequence kernels for relation extraction. In Proc. of NIPS, 171-178.
27. Niethammer, W.; De Pillis, J.; and Varga, R. 1984. Convergence of block iterative methods applied to sparse least-squares problems. Linear Algebra and its Applications 58:327-341.
28. Paccanaro, A., and Hinton, G. E. 2000. Learning distributed representations by mapping concepts and relations into a linear space. In Proc. of ICML, 711-718.
29. Pan, S. J.; Kwok, J. T.; and Yang, Q. 2008. Transfer learning via dimensionality reduction. In Proc. of AAAI.
30. Pust, M.; Hermjakob, U.; Knight, K.; Marcu, D.; and May, J. 2015. Using syntax-based machine translation to parse english into abstract meaning representation. In Proc. of EMNLP.
31. Skounakis, M., and Craven, M. 2003. Evidence combination in biomedical natural-language processing. In Proc. of BIOKDD.
32. Srivastava, S.; Hovy, D.; and Hovy, E. H. 2013. A walk-based semantically enriched tree kernel over distributed word representations. In Proc. of EMNLP, 1411-1416.
33. Sutherland, D. J.; Xiong, L.; Póczos, B.; and Schneider, J. 2012. Kernels on sample sets via nonparametric divergence estimates. arXiv preprint arXiv:1202.0302.
34. Tikk, D.; Thomas, P.; Palaga, P.; Hakenberg, J.; and Leser, U. 2010. A comprehensive benchmark of kernel methods to extract protein-protein interactions from literature. PLoS Comput Biol.
35. Wang, Y.; Berant, J.; and Liang, P. 2015. Building a semantic parser overnight. In Proc. of ACL.
36. Wang, Q.; Kulkarni, S. R.; and Verdú, S. 2009. Divergence estimation for multidimensional densities via-nearest-neighbor distances. IEEE Transactions on Information Theory 2392-2405.
37. Zelenko, D.; Aone, C.; and Richardella, A. 2003. Kernel methods for relation extraction. JMLR 3:1083-1106.