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2002


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k-NN based Pattern Selection for Support Vector Classifiers

Shin, H., Cho, S.

In Proc. of the Korean Industrial Engineers Conference, pages: 645-651, Korean Industrial Engineers Conference, May 2002 (inproceedings)

[BibTex]

2002

[BibTex]


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Microarrays: How Many Do You Need?

Zien, A., Fluck, J., Zimmer, R., Lengauer, T.

In RECOMB 2002, pages: 321-330, ACM Press, New York, NY, USA, Sixth Annual International Conference on Research in Computational Molecular Biology, April 2002 (inproceedings)

Abstract
We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. Current knowlegde seems to suffice for the construction of models that are realistic with respect to searches for individual differentially expressed genes. Such models allow to investigate the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class; the fold changes in expression; the detection sensitivity of the microarrays; and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at http://cartan.gmd.de/~zien/classsize/ for fine tuning simulations to their particular actualities. Since the situation can be assumed to be very similar for large scale proteomics and metabolomics studies, our methods and results might also apply there.

Web DOI [BibTex]

Web DOI [BibTex]


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Pattern Selection for Support Vector Classifiers

Shin, H., Cho, S.

In Ideal 2002, pages: 97-103, (Editors: Yin, H. , N. Allinson, R. Freeman, J. Keane, S. Hubbard), Springer, Berlin, Germany, Third International Conference on Intelligent Data Engineering and Automated Learning, January 2002 (inproceedings)

Abstract
SVMs tend to take a very long time to train with a large data set. If "redundant" patterns are identified and deleted in pre-processing, the training time could be reduced significantly. We propose a k-nearest neighbors(k-NN) based pattern selection method. The method tries to select the patterns that are near the decision boundary and that are correctly labeled. The simulations over synthetic data sets showed promising results: (1) By converting a non-separable problem to a separable one, the search for an optimal error tolerance parameter became unnecessary. (2) SVM training time decreased by two orders of magnitude without any loss of accuracy. (3) The redundant SVs were substantially reduced.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Training invariant support vector machines

DeCoste, D., Schölkopf, B.

Machine Learning, 46(1-3):161-190, January 2002 (article)

Abstract
Practical experience has shown that in order to obtain the best possible performance, prior knowledge about invariances of a classification problem at hand ought to be incorporated into the training procedure. We describe and review all known methods for doing so in support vector machines, provide experimental results, and discuss their respective merits. One of the significant new results reported in this work is our recent achievement of the lowest reported test error on the well-known MNIST digit recognition benchmark task, with SVM training times that are also significantly faster than previous SVM methods.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Model Selection for Small Sample Regression

Chapelle, O., Vapnik, V., Bengio, Y.

Machine Learning, 48(1-3):9-23, 2002 (article)

Abstract
Model selection is an important ingredient of many machine learning algorithms, in particular when the sample size in small, in order to strike the right trade-off between overfitting and underfitting. Previous classical results for linear regression are based on an asymptotic analysis. We present a new penalization method for performing model selection for regression that is appropriate even for small samples. Our penalization is based on an accurate estimator of the ratio of the expected training error and the expected generalization error, in terms of the expected eigenvalues of the input covariance matrix.

PostScript [BibTex]

PostScript [BibTex]


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The leave-one-out kernel

Tsuda, K., Kawanabe, M.

In Artificial Neural Networks -- ICANN 2002, 2415, pages: 727-732, LNCS, (Editors: Dorronsoro, J. R.), Artificial Neural Networks -- ICANN, 2002 (inproceedings)

PDF [BibTex]

PDF [BibTex]


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Contrast discrimination with sinusoidal gratings of different spatial frequency

Bird, C., Henning, G., Wichmann, F.

Journal of the Optical Society of America A, 19(7), pages: 1267-1273, 2002 (article)

Abstract
The detectability of contrast increments was measured as a function of the contrast of a masking or “pedestal” grating at a number of different spatial frequencies ranging from 2 to 16 cycles per degree of visual angle. The pedestal grating always had the same orientation, spatial frequency and phase as the signal. The shape of the contrast increment threshold versus pedestal contrast (TvC) functions depend of the performance level used to define the “threshold,” but when both axes are normalized by the contrast corresponding to 75% correct detection at each frequency, the (TvC) functions at a given performance level are identical. Confidence intervals on the slope of the rising part of the TvC functions are so wide that it is not possible with our data to reject Weber’s Law.

PDF [BibTex]

PDF [BibTex]


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A Bennett Concentration Inequality and Its Application to Suprema of Empirical Processes

Bousquet, O.

C. R. Acad. Sci. Paris, Ser. I, 334, pages: 495-500, 2002 (article)

Abstract
We introduce new concentration inequalities for functions on product spaces. They allow to obtain a Bennett type deviation bound for suprema of empirical processes indexed by upper bounded functions. The result is an improvement on Rio's version \cite{Rio01b} of Talagrand's inequality \cite{Talagrand96} for equidistributed variables.

PDF PostScript [BibTex]


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Numerical evolution of axisymmetric, isolated systems in general relativity

Frauendiener, J., Hein, M.

Physical Review D, 66, pages: 124004-124004, 2002 (article)

Abstract
We describe in this article a new code for evolving axisymmetric isolated systems in general relativity. Such systems are described by asymptotically flat space-times, which have the property that they admit a conformal extension. We are working directly in the extended conformal manifold and solve numerically Friedrich's conformal field equations, which state that Einstein's equations hold in the physical space-time. Because of the compactness of the conformal space-time the entire space-time can be calculated on a finite numerical grid. We describe in detail the numerical scheme, especially the treatment of the axisymmetry and the boundary.

GZIP [BibTex]

GZIP [BibTex]


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Marginalized kernels for biological sequences

Tsuda, K., Kin, T., Asai, K.

Bioinformatics, 18(Suppl 1):268-275, 2002 (article)

PDF [BibTex]

PDF [BibTex]


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Localized Rademacher Complexities

Bartlett, P., Bousquet, O., Mendelson, S.

In Proceedings of the 15th annual conference on Computational Learning Theory, pages: 44-58, Proceedings of the 15th annual conference on Computational Learning Theory, 2002 (inproceedings)

Abstract
We investigate the behaviour of global and local Rademacher averages. We present new error bounds which are based on the local averages and indicate how data-dependent local averages can be estimated without {it a priori} knowledge of the class at hand.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Film Cooling: A Comparative Study of Different Heaterfoil Configurations for Liquid Crystals Experiments

Vogel, G., Graf, ABA., Weigand, B.

In ASME TURBO EXPO 2002, Amsterdam, GT-2002-30552, ASME TURBO EXPO, Amsterdam, 2002 (inproceedings)

PDF [BibTex]

PDF [BibTex]


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Stability and Generalization

Bousquet, O., Elisseeff, A.

Journal of Machine Learning Research, 2, pages: 499-526, 2002 (article)

Abstract
We define notions of stability for learning algorithms and show how to use these notions to derive generalization error bounds based on the empirical error and the leave-one-out error. The methods we use can be applied in the regression framework as well as in the classification one when the classifier is obtained by thresholding a real-valued function. We study the stability properties of large classes of learning algorithms such as regularization based algorithms. In particular we focus on Hilbert space regularization and Kullback-Leibler regularization. We demonstrate how to apply the results to SVM for regression and classification.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Subspace information criterion for non-quadratic regularizers – model selection for sparse regressors

Tsuda, K., Sugiyama, M., Müller, K.

IEEE Trans Neural Networks, 13(1):70-80, 2002 (article)

PDF [BibTex]

PDF [BibTex]


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Modeling splicing sites with pairwise correlations

Arita, M., Tsuda, K., Asai, K.

Bioinformatics, 18(Suppl 2):27-34, 2002 (article)

PDF [BibTex]

PDF [BibTex]


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Perfusion Quantification using Gaussian Process Deconvolution

Andersen, IK., Szymkowiak, A., Rasmussen, CE., Hanson, LG., Marstrand, JR., Larsson, HBW., Hansen, LK.

Magnetic Resonance in Medicine, (48):351-361, 2002 (article)

Abstract
The quantification of perfusion using dynamic susceptibility contrast MR imaging requires deconvolution to obtain the residual impulse-response function (IRF). Here, a method using a Gaussian process for deconvolution, GPD, is proposed. The fact that the IRF is smooth is incorporated as a constraint in the method. The GPD method, which automatically estimates the noise level in each voxel, has the advantage that model parameters are optimized automatically. The GPD is compared to singular value decomposition (SVD) using a common threshold for the singular values and to SVD using a threshold optimized according to the noise level in each voxel. The comparison is carried out using artificial data as well as using data from healthy volunteers. It is shown that GPD is comparable to SVD variable optimized threshold when determining the maximum of the IRF, which is directly related to the perfusion. GPD provides a better estimate of the entire IRF. As the signal to noise ratio increases or the time resolution of the measurements increases, GPD is shown to be superior to SVD. This is also found for large distribution volumes.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Tracking a Small Set of Experts by Mixing Past Posteriors

Bousquet, O., Warmuth, M.

Journal of Machine Learning Research, 3, pages: 363-396, (Editors: Long, P.), 2002 (article)

Abstract
In this paper, we examine on-line learning problems in which the target concept is allowed to change over time. In each trial a master algorithm receives predictions from a large set of n experts. Its goal is to predict almost as well as the best sequence of such experts chosen off-line by partitioning the training sequence into k+1 sections and then choosing the best expert for each section. We build on methods developed by Herbster and Warmuth and consider an open problem posed by Freund where the experts in the best partition are from a small pool of size m. Since k >> m, the best expert shifts back and forth between the experts of the small pool. We propose algorithms that solve this open problem by mixing the past posteriors maintained by the master algorithm. We relate the number of bits needed for encoding the best partition to the loss bounds of the algorithms. Instead of paying log n for choosing the best expert in each section we first pay log (n choose m) bits in the bounds for identifying the pool of m experts and then log m bits per new section. In the bounds we also pay twice for encoding the boundaries of the sections.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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A femoral arteriovenous shunt facilitates arterial whole blood sampling in animals

Weber, B., Burger, C., Biro, P., Buck, A.

Eur J Nucl Med Mol Imaging, 29, pages: 319-323, 2002 (article)

[BibTex]

[BibTex]


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Some Local Measures of Complexity of Convex Hulls and Generalization Bounds

Bousquet, O., Koltchinskii, V., Panchenko, D.

In Proceedings of the 15th annual conference on Computational Learning Theory, Proceedings of the 15th annual conference on Computational Learning Theory, 2002 (inproceedings)

Abstract
We investigate measures of complexity of function classes based on continuity moduli of Gaussian and Rademacher processes. For Gaussian processes, we obtain bounds on the continuity modulus on the convex hull of a function class in terms of the same quantity for the class itself. We also obtain new bounds on generalization error in terms of localized Rademacher complexities. This allows us to prove new results about generalization performance for convex hulls in terms of characteristics of the base class. As a byproduct, we obtain a simple proof of some of the known bounds on the entropy of convex hulls.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Contrast discrimination with pulse-trains in pink noise

Henning, G., Bird, C., Wichmann, F.

Journal of the Optical Society of America A, 19(7), pages: 1259-1266, 2002 (article)

Abstract
Detection performance was measured with sinusoidal and pulse-train gratings. Although the 2.09-c/deg pulse-train, or line gratings, contained at least 8 harmonics all at equal contrast, they were no more detectable than their most detectable component. The addition of broadband pink noise designed to equalize the detectability of the components of the pulse train made the pulse train about a factor of four more detectable than any of its components. However, in contrast-discrimination experiments, with a pedestal or masking grating of the same form and phase as the signal and 15% contrast, the noise did not affect the discrimination performance of the pulse train relative to that obtained with its sinusoidal components. We discuss the implications of these observations for models of early vision in particular the implications for possible sources of internal noise.

PDF [BibTex]

PDF [BibTex]


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A kernel approach for learning from almost orthogonal patterns

Schölkopf, B., Weston, J., Eskin, E., Leslie, C., Noble, W.

In Principles of Data Mining and Knowledge Discovery, Lecture Notes in Computer Science, 2430/2431, pages: 511-528, Lecture Notes in Computer Science, (Editors: T Elomaa and H Mannila and H Toivonen), Springer, Berlin, Germany, 13th European Conference on Machine Learning (ECML) and 6th European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD'2002), 2002 (inproceedings)

PostScript DOI [BibTex]

PostScript DOI [BibTex]


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Choosing Multiple Parameters for Support Vector Machines

Chapelle, O., Vapnik, V., Bousquet, O., Mukherjee, S.

Machine Learning, 46(1):131-159, 2002 (article)

Abstract
The problem of automatically tuning multiple parameters for pattern recognition Support Vector Machines (SVM) is considered. This is done by minimizing some estimates of the generalization error of SVMs using a gradient descent algorithm over the set of parameters. Usual methods for choosing parameters, based on exhaustive search become intractable as soon as the number of parameters exceeds two. Some experimental results assess the feasibility of our approach for a large number of parameters (more than 100) and demonstrate an improvement of generalization performance.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Infinite Mixtures of Gaussian Process Experts

Rasmussen, CE., Ghahramani, Z.

In (Editors: Dietterich, Thomas G.; Becker, Suzanna; Ghahramani, Zoubin), 2002 (inproceedings)

Abstract
We present an extension to the Mixture of Experts (ME) model, where the individual experts are Gaussian Process (GP) regression models. Using a input-dependent adaptation of the Dirichlet Process, we implement a gating network for an infinite number of Experts. Inference in this model may be done efficiently using a Markov Chain relying on Gibbs sampling. The model allows the effective covariance function to vary with the inputs, and may handle large datasets -- thus potentially overcoming two of the biggest hurdles with GP models. Simulations show the viability of this approach.

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Marginalized kernels for RNA sequence data analysis

Kin, T., Tsuda, K., Asai, K.

In Genome Informatics 2002, pages: 112-122, (Editors: Lathtop, R. H.; Nakai, K.; Miyano, S.; Takagi, T.; Kanehisa, M.), Genome Informatics, 2002, (Best Paper Award) (inproceedings)

Web [BibTex]

Web [BibTex]


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Luminance Artifacts on CRT Displays

Wichmann, F.

In IEEE Visualization, pages: 571-574, (Editors: Moorhead, R.; Gross, M.; Joy, K. I.), IEEE Visualization, 2002 (inproceedings)

Abstract
Most visualization panels today are still built around cathode-ray tubes (CRTs), certainly on personal desktops at work and at home. Whilst capable of producing pleasing images for common applications ranging from email writing to TV and DVD presentation, it is as well to note that there are a number of nonlinear transformations between input (voltage) and output (luminance) which distort the digital and/or analogue images send to a CRT. Some of them are input-independent and hence easy to fix, e.g. gamma correction, but others, such as pixel interactions, depend on the content of the input stimulus and are thus harder to compensate for. CRT-induced image distortions cause problems not only in basic vision research but also for applications where image fidelity is critical, most notably in medicine (digitization of X-ray images for diagnostic purposes) and in forms of online commerce, such as the online sale of images, where the image must be reproduced on some output device which will not have the same transfer function as the customer's CRT. I will present measurements from a number of CRTs and illustrate how some of their shortcomings may be problematic for the aforementioned applications.

[BibTex]

[BibTex]