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2000


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Identification of Drug Target Proteins

Zien, A., Küffner, R., Mevissen, T., Zimmer, R., Lengauer, T.

ERCIM News, 43, pages: 16-17, October 2000 (article)

Web [BibTex]

2000

Web [BibTex]


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Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites

Zien, A., Rätsch, G., Mika, S., Schölkopf, B., Lengauer, T., Müller, K.

Bioinformatics, 16(9):799-807, September 2000 (article)

Abstract
Motivation: In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS). Results: The task of finding TIS can be modeled as a classification problem. We demonstrate the applicability of support vector machines for this task, and show how to incorporate prior biological knowledge by engineering an appropriate kernel function. With the described techniques the recognition performance can be improved by 26% over leading existing approaches. We provide evidence that existing related methods (e.g. ESTScan) could profit from advanced TIS recognition.

Web DOI [BibTex]

Web DOI [BibTex]


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A Meanfield Approach to the Thermodynamics of a Protein-Solvent System with Application to the Oligomerization of the Tumour Suppressor p53.

Noolandi, J., Davison, TS., Vokel, A., Nie, F., Kay, C., Arrowsmith, C.

Proceedings of the National Academy of Sciences of the United States of America, 97(18):9955-9960, August 2000 (article)

Web [BibTex]

Web [BibTex]


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New Support Vector Algorithms

Schölkopf, B., Smola, A., Williamson, R., Bartlett, P.

Neural Computation, 12(5):1207-1245, May 2000 (article)

Abstract
We propose a new class of support vector algorithms for regression and classification. In these algorithms, a parameter {nu} lets one effectively control the number of support vectors. While this can be useful in its own right, the parameterization has the additional benefit of enabling us to eliminate one of the other free parameters of the algorithm: the accuracy parameter {epsilon} in the regression case, and the regularization constant C in the classification case. We describe the algorithms, give some theoretical results concerning the meaning and the choice of {nu}, and report experimental results.

Web DOI [BibTex]

Web DOI [BibTex]


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Bounds on Error Expectation for Support Vector Machines

Vapnik, V., Chapelle, O.

Neural Computation, 12(9):2013-2036, 2000 (article)

Abstract
We introduce the concept of span of support vectors (SV) and show that the generalization ability of support vector machines (SVM) depends on this new geometrical concept. We prove that the value of the span is always smaller (and can be much smaller) than the diameter of the smallest sphere containing th e support vectors, used in previous bounds. We also demonstate experimentally that the prediction of the test error given by the span is very accurate and has direct application in model selection (choice of the optimal parameters of the SVM)

GZIP [BibTex]

GZIP [BibTex]

1997


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Comparing support vector machines with Gaussian kernels to radial basis function classifiers

Schölkopf, B., Sung, K., Burges, C., Girosi, F., Niyogi, P., Poggio, T., Vapnik, V.

IEEE Transactions on Signal Processing, 45(11):2758-2765, November 1997 (article)

Abstract
The support vector (SV) machine is a novel type of learning machine, based on statistical learning theory, which contains polynomial classifiers, neural networks, and radial basis function (RBF) networks as special cases. In the RBF case, the SV algorithm automatically determines centers, weights, and threshold that minimize an upper bound on the expected test error. The present study is devoted to an experimental comparison of these machines with a classical approach, where the centers are determined by X-means clustering, and the weights are computed using error backpropagation. We consider three machines, namely, a classical RBF machine, an SV machine with Gaussian kernel, and a hybrid system with the centers determined by the SV method and the weights trained by error backpropagation. Our results show that on the United States postal service database of handwritten digits, the SV machine achieves the highest recognition accuracy, followed by the hybrid system. The SV approach is thus not only theoretically well-founded but also superior in a practical application.

Web DOI [BibTex]

1997

Web DOI [BibTex]


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ATM-dependent telomere loss in aging human diploid fibroblasts and DNA damage lead to the post-translational activation of p53 protein involving poly(ADP-ribose) polymerase.

Vaziri, H., MD, .., RC, .., Davison, T., YS, .., CH, .., GG, .., Benchimol, S.

The European Molecular Biology Organization Journal, 16(19):6018-6033, 1997 (article)

Web [BibTex]

Web [BibTex]