Abstract
In this paper we analyze Support Vector Machine (SVM) algorithm to the problem of chemical compounds screening with a desired activity, definition of hits. The support vector machine transforms the input data in an (unknown) high dimensional feature space and the kernel technique is applied to calculate the inner-product of feature data.The problem of automatically tuning multiple parameters for pattern recognition SVMs using our new introduced kernel for chemical compounds is considered. This is done by simple eigen analysis method which is applied to the matrix of the same dimension as the kernel matrix to find the structure of feature data, and to find the kernel parameter accordingly. We characterize distribution of data by the principle component analysis method.
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References
Burden, F.R.: Molecular Identification Number For Substructure Searches. Journal of Chemical Information and Computer Sciences 29, 225–227 (1989)
Cortes, C., Vapnik, V.: Support-vector networks. Machine Learning 20(3), 273–297 (1995)
dtp.nci.nih.gov. Dtp aids antiviral screen dataset
Graham, W.R.: Virtual screening using grid computing: the screensaver project. Nature Reviews: Drug Discovery 1, 551–554 (2002)
Froehlich, H., Wegner, J.K., Zell, A.: QSAR Comb. Sci. 23, 311–318 (2004)
Chung, K.-M., Kao, W.-C., Sun, T., Wang, L.-L., Lin, C.-J.: Radious margin bounds for support vector machines with Gaussian kernel. Neural Computation 15, 2643–2681 (2003)
Kozak, K., Kozak, M., Stapor, K.: Kernels for Chemical Compounds in Biological Screening. In: Beliczynski, B., Dzielinski, A., Iwanowski, M., Ribeiro, B. (eds.) ICANNGA 2007. LNCS, vol. 4432, pp. 327–337. Springer, Heidelberg (2007)
Pearlman, R.S., Smith, K.M.: Novel software tools for chemical diversity. Perspectives in Drug Discovery and Design, 9/10/11, 339–353 (1998)
Debnath, R., Takahashi, H.: Generalization of kernel PCA and automatic parameter tuning. Neural Information Processing 5(3) (December 2004)
Keerthi, S.S., Lin, C.-J.: Asymptotic behaviours of support vector machines with Gaussian kernel. Neural Computation 15, 1667–1689 (2003)
Kramer, S., De Raedt, L., Helma, C.: Molecular feature mining in hiv data. In: 7th International Conference on Knowledge Discovery and Data Mining (2001)
Schoelkopf, B., Smola, A.J.: Learning with kernels. MIT Press, Cambridge (2002)
Vapnik, V.N.: Stasistical Learning Theory. Wiley, New York (1998)
Vapnik, V., Chapelle, O.: Bounds on error expectation for support vector machines. Neural computation 12(9), 2013–2036 (2000)
Westfall, P.H., Young, S.S.: Resampling-based multiple testing: Examples and methods for p-value adjustment. John Wiley & Sons, Chichester (1993)
Boser, Y., Guyon, I., Vapnik, V.: A training algorithm for optimal margin classifiers. In: Fifth Annual Workshop on Computational Learning Theory, Pittsburg (1992)
“exactRankTests”: Exact Distributions for Rank and Permutation Tests, http://cran.r-project.org/src/contrib/Descriptions/exactRankTests.html.
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Kozak, K., Stapor, K. (2008). Classes of Kernels for Hit Definition in Compound Screening. In: Rutkowski, L., Tadeusiewicz, R., Zadeh, L.A., Zurada, J.M. (eds) Artificial Intelligence and Soft Computing – ICAISC 2008. ICAISC 2008. Lecture Notes in Computer Science(), vol 5097. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69731-2_59
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DOI: https://doi.org/10.1007/978-3-540-69731-2_59
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-69572-1
Online ISBN: 978-3-540-69731-2
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