Abstract
As biological sequences and various annotation data grow rapidly in public databases, the classification problems become larger and more complicated. New classifier designs are necessitated. Besides, how to incorporate some explicit domain knowledge into learning methods is also a big issue. In this paper, we adopt a modular classifier, min-max modular support vector machine (M3-SVM) to solve protein subcellular localization problem, and use the domain knowledge of taxonomy information to guide the task decomposition. Experimental results show that M3-SVM can maintain the overall accuracy and improve location average accuracy compared with traditional SVMs. The taxonomy decomposition is superior to other decomposition methods on a majority of the classes. The results also demonstrate a speedup on training time of M3-SVM compared with traditional SVMs.
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References
Collobert, R., Bengio, S., Bengio, Y.: A parallel mixture of SVMs for very large scale problems (2002)
Cao, L.J., Keerthi, S.S., Ong, C.J., Zhang, J.Q., Periyathamby, U., Fu, X.J., Lee, H.P.: Parallel sequential minimal optimization for the training of support vector machines. IEEE Trans Neural Network 2006, 1039–1049 (2004)
Platt, J.C.: Fast training of support vector machines using sequential minimal optimization. Advances in kernel methods: support vector learning table of contents, 185–208 (1999)
Lu, B.L., Wang, K.A., Utiyama, M., Isahara, H.: A part-versus-part method for massively parallel training of support vector machines. In: Proceedings of IEEE International Joint Conference on Neural Networks, vol. 1, pp. 735–740 (2004)
Lu, B.L., Ito, M.: Task decomposition and module combination based on class relations: a modular neural network for pattern classification. IEEE Transactions on Neural Networks 10(5), 1244–1256 (1999)
Cedano, J., Aloy, P., Perez-Pons, J.A., Querol, E.: Relation between amino acid composition and cellular location of proteins. Journal of Molecular Biology 266(3), 594–600 (1997)
Hua, S., Sun, Z.: Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17(8), 721–728 (2001)
Park, K.J., Kanehisa, M.: Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics 19(13), 1656–1663 (2003)
Liu, F.Y., Wu, K., Zhao, H., Lu, B.L.: Fast text categorization with a min-max modular support vector machine. In: Proceedings of IEEE International Joint Conference on Neural Networks, pp. 570–575 (2005)
Wen, Y.M., Lu, B.L., Zhao, H.: Equal clustering makes min-max modular support vector machine more efficient. In: Proceedings of the 12th International Conference on Neural Information Processing, pp. 77–82 (2006)
Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M., Estreicher, A., Gasteiger, E., Martin, M., Michoud, K., O’Donovan, C., Phan, I., et al.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Research 31(1), 365–370 (2003)
Chang, C., Lin, C.: LIBSVM: a library for support vector machines. Software 80, 604–611 (2001), http://www.csie.ntu.edu.tw/cjlin/libsvm
Pierleoni, A., Martelli, P.L., Fariselli, P., Casadio, R.: BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22(14), 408–416 (2006)
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Yang, Y., Lu, BL. (2008). Incorporating Domain Knowledge into a Min-Max Modular Support Vector Machine for Protein Subcellular Localization. In: Ishikawa, M., Doya, K., Miyamoto, H., Yamakawa, T. (eds) Neural Information Processing. ICONIP 2007. Lecture Notes in Computer Science, vol 4985. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69162-4_86
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DOI: https://doi.org/10.1007/978-3-540-69162-4_86
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