Feature selection for pairwise scoring kernels with applications to protein subcellular localization

ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings

Volumn 2, Issue , 2007, Pages

  Kung, Sun Yuan ^a   Mak, Man Wai ^b  

^a Princeton University   (United States)

^b HONG KONG POLYTECHNIC UNIVERSITY   (Hong Kong)

Author keywords

Feature selection; Kernel methods; Pairwise scoring; Subcellular localization; SVM

Indexed keywords

CLASSIFICATION (OF INFORMATION); DNA SEQUENCES; INDEXING (OF INFORMATION); PROTEINS; SET THEORY; SUPPORT VECTOR MACHINES;

KERNEL METHODS; PAIRWISE SCORING; SUBCELLULAR LOCALIZATION;

FEATURE EXTRACTION;

EID: 34547525054     PISSN: 15206149     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICASSP.2007.366299     Document Type: Conference Paper

References (13)

1. L. Liao and W. S. Noble, "Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships," J. Comput. Biol., vol. 10, no. 6, pp, 857-868, 2003.
2. J. K. Kim, G. P. S. Raghava, S. Y. Bang, and S. Choi, "Prediction of subcellular localization of proteins using pairwise sequence alignment and support vector machine," Pattern Recog. Lett., vol. 27, no. 9, pp. 996-1001, 2006.
3. J, Guo, M. W. Mak, and S. Y Kung, "Eukaryotic protein subcellular localization based on local pairwise profile alignment SVM," in 2006 IEEE International Workshop on Machine Learning for Signal Processing (MLSP '06), 2006, pp. 391-396.
4. R. Kuang, E. le, K. Wang, K. Wang, M. Siddiqi, Y. Freund, and C. Leslie, "Profile-based string kernels for remote homology detection and motif extraction," J. Bioinfom. Comput. Biol., vol. 3, pp. 527-550, 2005.
5. M. W. Mak and S. Y. Kung, "A solution to the curse of dimensionality problem in pairwise scoring techniques," in Int. Conf. on Neural Information Processing, 2006, pp. 314-323.
6. I. Guyon, J. Weston, S. Bamhill, and V. Vapnik, "Gene selection for cancer classification using support vector machines," Machine Learning, vol. 46, pp. 389422, 2002.
7. X. G. Zhang, X. Lu, Q. Shi, X. Q. Xu, H. C. E. Leung, L. N. Harris, J. D. Iglehart, A. Miron, J. S. Liu, and W. H. Wong, "Recursive SVM feature selection and sample classification for mass-spectrometry and microarray data," BMC Bioinformatics, vol. 7, no. 197, 2006.
8. http://www.expasy.org/sprot," .
9. S. F. Altschul, T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, "Gapped BLAST and PSI-BLAST: A new generation of protein database search programs," Nucleic Acids Res., vol. 25, pp. 3389-3402, 1997.
10. T. F. Smith and M. S. Waterman, "Comparison of biosequences," Adv. Appl. Math., vol. 2, pp. 482-489, 1981.
11. O. Gotoh, "An improved algorithm for matching biological sequences," J. Mol. Biol., vol. 162, pp. 705-708, 1982.
12. A. Reinhardt and T. Hubbard, "Using neural networks for prediction of the subcellular location of proteins," Nucleic Acids Res., vol. 26, pp. 2230-2236, 1998.
13. Y. Huang and Y. D. Li, "Prediction of protein subcellular locations using fuzzy K-NN method," Bioinformatics, vol. 20, no. 1, pp. 21-28, 2004.