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86 results (View BibTeX file of all listed publications)

2005

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Kernel Methods for Measuring Independence

Gretton, A., Herbrich, R., Smola, A., Bousquet, O., Schölkopf, B.

Journal of Machine Learning Research, 6, pages: 2075-2129, December 2005 (article)

Abstract
We introduce two new functionals, the constrained covariance and the kernel mutual information, to measure the degree of independence of random variables. These quantities are both based on the covariance between functions of the random variables in reproducing kernel Hilbert spaces (RKHSs). We prove that when the RKHSs are universal, both functionals are zero if and only if the random variables are pairwise independent. We also show that the kernel mutual information is an upper bound near independence on the Parzen window estimate of the mutual information. Analogous results apply for two correlation-based dependence functionals introduced earlier: we show the kernel canonical correlation and the kernel generalised variance to be independence measures for universal kernels, and prove the latter to be an upper bound on the mutual information near independence. The performance of the kernel dependence functionals in measuring independence is verified in the context of independent component analysis.

ei

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2005

ei Gretton, A., Herbrich, R., Smola, A., Bousquet, O., Schölkopf, B. Kernel Methods for Measuring Independence Journal of Machine Learning Research, 6, pages: 2075-2129, December 2005 (article)

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A Unifying View of Sparse Approximate Gaussian Process Regression

Quinonero Candela, J., Rasmussen, C.

Journal of Machine Learning Research, 6, pages: 1935-1959, December 2005 (article)

Abstract
We provide a new unifying view, including all existing proper probabilistic sparse approximations for Gaussian process regression. Our approach relies on expressing the effective prior which the methods are using. This allows new insights to be gained, and highlights the relationship between existing methods. It also allows for a clear theoretically justified ranking of the closeness of the known approximations to the corresponding full GPs. Finally we point directly to designs of new better sparse approximations, combining the best of the existing strategies, within attractive computational constraints.

ei

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ei Quinonero Candela, J., Rasmussen, C. A Unifying View of Sparse Approximate Gaussian Process Regression Journal of Machine Learning Research, 6, pages: 1935-1959, December 2005 (article)

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Maximal Margin Classification for Metric Spaces

Hein, M., Bousquet, O., Schölkopf, B.

Journal of Computer and System Sciences, 71(3):333-359, October 2005 (article)

Abstract
In order to apply the maximum margin method in arbitrary metric spaces, we suggest to embed the metric space into a Banach or Hilbert space and to perform linear classification in this space. We propose several embeddings and recall that an isometric embedding in a Banach space is always possible while an isometric embedding in a Hilbert space is only possible for certain metric spaces. As a result, we obtain a general maximum margin classification algorithm for arbitrary metric spaces (whose solution is approximated by an algorithm of Graepel. Interestingly enough, the embedding approach, when applied to a metric which can be embedded into a Hilbert space, yields the SVM algorithm, which emphasizes the fact that its solution depends on the metric and not on the kernel. Furthermore we give upper bounds of the capacity of the function classes corresponding to both embeddings in terms of Rademacher averages. Finally we compare the capacities of these function classes directly.

ei

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ei Hein, M., Bousquet, O., Schölkopf, B. Maximal Margin Classification for Metric Spaces Journal of Computer and System Sciences, 71(3):333-359, October 2005 (article)

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Selective integration of multiple biological data for supervised network inference

Kato, T., Tsuda, K., Asai, K.

Bioinformatics, 21(10):2488 , October 2005 (article)

ei

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ei Kato, T., Tsuda, K., Asai, K. Selective integration of multiple biological data for supervised network inference Bioinformatics, 21(10):2488 , October 2005 (article)

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Assessing Approximate Inference for Binary Gaussian Process Classification

Kuss, M., Rasmussen, C.

Journal of Machine Learning Research, 6, pages: 1679 , October 2005 (article)

Abstract
Gaussian process priors can be used to define flexible, probabilistic classification models. Unfortunately exact Bayesian inference is analytically intractable and various approximation techniques have been proposed. In this work we review and compare Laplace‘s method and Expectation Propagation for approximate Bayesian inference in the binary Gaussian process classification model. We present a comprehensive comparison of the approximations, their predictive performance and marginal likelihood estimates to results obtained by MCMC sampling. We explain theoretically and corroborate empirically the advantages of Expectation Propagation compared to Laplace‘s method.

ei

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ei Kuss, M., Rasmussen, C. Assessing Approximate Inference for Binary Gaussian Process Classification Journal of Machine Learning Research, 6, pages: 1679 , October 2005 (article)

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Clustering on the Unit Hypersphere using von Mises-Fisher Distributions

Banerjee, A., Dhillon, I., Ghosh, J., Sra, S.

Journal of Machine Learning Research, 6, pages: 1345-1382, September 2005 (article)

Abstract
Several large scale data mining applications, such as text categorization and gene expression analysis, involve high-dimensional data that is also inherently directional in nature. Often such data is L2 normalized so that it lies on the surface of a unit hypersphere. Popular models such as (mixtures of) multi-variate Gaussians are inadequate for characterizing such data. This paper proposes a generative mixture-model approach to clustering directional data based on the von Mises-Fisher (vMF) distribution, which arises naturally for data distributed on the unit hypersphere. In particular, we derive and analyze two variants of the Expectation Maximization (EM) framework for estimating the mean and concentration parameters of this mixture. Numerical estimation of the concentration parameters is non-trivial in high dimensions since it involves functional inversion of ratios of Bessel functions. We also formulate two clustering algorithms corresponding to the variants of EM that we derive. Our approach provides a theoretical basis for the use of cosine similarity that has been widely employed by the information retrieval community, and obtains the spherical kmeans algorithm (kmeans with cosine similarity) as a special case of both variants. Empirical results on clustering of high-dimensional text and gene-expression data based on a mixture of vMF distributions show that the ability to estimate the concentration parameter for each vMF component, which is not present in existing approaches, yields superior results, especially for difficult clustering tasks in high-dimensional spaces.

ei

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ei Banerjee, A., Dhillon, I., Ghosh, J., Sra, S. Clustering on the Unit Hypersphere using von Mises-Fisher Distributions Journal of Machine Learning Research, 6, pages: 1345-1382, September 2005 (article)

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Support Vector Machines for 3D Shape Processing

Steinke, F., Schölkopf, B., Blanz, V.

Computer Graphics Forum, 24(3, EUROGRAPHICS 2005):285-294, September 2005 (article)

Abstract
We propose statistical learning methods for approximating implicit surfaces and computing dense 3D deformation fields. Our approach is based on Support Vector (SV) Machines, which are state of the art in machine learning. It is straightforward to implement and computationally competitive; its parameters can be automatically set using standard machine learning methods. The surface approximation is based on a modified Support Vector regression. We present applications to 3D head reconstruction, including automatic removal of outliers and hole filling. In a second step, we build on our SV representation to compute dense 3D deformation fields between two objects. The fields are computed using a generalized SVMachine enforcing correspondence between the previously learned implicit SV object representations, as well as correspondences between feature points if such points are available. We apply the method to the morphing of 3D heads and other objects.

ei

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ei Steinke, F., Schölkopf, B., Blanz, V. Support Vector Machines for 3D Shape Processing Computer Graphics Forum, 24(3, EUROGRAPHICS 2005):285-294, September 2005 (article)

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Fast Protein Classification with Multiple Networks

Tsuda, K., Shin, H., Schölkopf, B.

Bioinformatics, 21(Suppl. 2):59-65, September 2005 (article)

Abstract
Support vector machines (SVM) have been successfully used to classify proteins into functional categories. Recently, to integrate multiple data sources, a semidefinite programming (SDP) based SVM method was introduced Lanckriet et al (2004). In SDP/SVM, multiple kernel matrices corresponding to each of data sources are combined with weights obtained by solving an SDP. However, when trying to apply SDP/SVM to large problems, the computational cost can become prohibitive, since both converting the data to a kernel matrix for the SVM and solving the SDP are time and memory demanding. Another application-specific drawback arises when some of the data sources are protein networks. A common method of converting the network to a kernel matrix is the diffusion kernel method, which has time complexity of O(n^3), and produces a dense matrix of size n x n. We propose an efficient method of protein classification using multiple protein networks. Available protein networks, such as a physical interaction network or a metabolic network, can be directly incorporated. Vectorial data can also be incorporated after conversion into a network by means of neighbor point connection. Similarly to the SDP/SVM method, the combination weights are obtained by convex optimization. Due to the sparsity of network edges, the computation time is nearly linear in the number of edges of the combined network. Additionally, the combination weights provide information useful for discarding noisy or irrelevant networks. Experiments on function prediction of 3588 yeast proteins show promising results: the computation time is enormously reduced, while the accuracy is still comparable to the SDP/SVM method.

ei

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ei Tsuda, K., Shin, H., Schölkopf, B. Fast Protein Classification with Multiple Networks Bioinformatics, 21(Suppl. 2):59-65, September 2005 (article)

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Iterative Kernel Principal Component Analysis for Image Modeling

Kim, K., Franz, M., Schölkopf, B.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(9):1351-1366, September 2005 (article)

Abstract
In recent years, Kernel Principal Component Analysis (KPCA) has been suggested for various image processing tasks requiring an image model such as, e.g., denoising or compression. The original form of KPCA, however, can be only applied to strongly restricted image classes due to the limited number of training examples that can be processed. We therefore propose a new iterative method for performing KPCA, the Kernel Hebbian Algorithm which iteratively estimates the Kernel Principal Components with only linear order memory complexity. In our experiments, we compute models for complex image classes such as faces and natural images which require a large number of training examples. The resulting image models are tested in single-frame super-resolution and denoising applications. The KPCA model is not specifically tailored to these tasks; in fact, the same model can be used in super-resolution with variable input resolution, or denoising with unknown noise characteristics. In spite of this, both super-resolution a nd denoising performance are comparable to existing methods.

ei

Web DOI [BibTex]

ei Kim, K., Franz, M., Schölkopf, B. Iterative Kernel Principal Component Analysis for Image Modeling IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(9):1351-1366, September 2005 (article)

Web DOI [BibTex]

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Phenotypic characterization of chondrosarcoma-derived cell lines

Schorle, C., Finger, F., Zien, A., Block, J., Gebhard, P., Aigner, T.

Cancer Letters, 226(2):143-154, August 2005 (article)

Abstract
Gene expression profiling of three chondrosarcoma derived cell lines (AD, SM, 105KC) showed an increased proliferative activity and a reduced expression of chondrocytic-typical matrix products compared to primary chondrocytes. The incapability to maintain an adequate matrix synthesis as well as a notable proliferative activity at the same time is comparable to neoplastic chondrosarcoma cells in vivo which cease largely cartilage matrix formation as soon as their proliferative activity increases. Thus, the investigated cell lines are of limited value as substitute of primary chondrocytes but might have a much higher potential to investigate the behavior of neoplastic chondrocytes, i.e. chondrosarcoma biology.

ei

Web [BibTex]

ei Schorle, C., Finger, F., Zien, A., Block, J., Gebhard, P., Aigner, T. Phenotypic characterization of chondrosarcoma-derived cell lines Cancer Letters, 226(2):143-154, August 2005 (article)

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Local Rademacher Complexities

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

The Annals of Statistics, 33(4):1497-1537, August 2005 (article)

Abstract
We propose new bounds on the error of learning algorithms in terms of a data-dependent notion of complexity. The estimates we establish give optimal rates and are based on a local and empirical version of Rademacher averages, in the sense that the Rademacher averages are computed from the data, on a subset of functions with small empirical error. We present some applications to classification and prediction with convex function classes, and with kernel classes in particular.

ei

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ei Bartlett, P., Bousquet, O., Mendelson, S. Local Rademacher Complexities The Annals of Statistics, 33(4):1497-1537, August 2005 (article)

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Learning the Kernel with Hyperkernels

Ong, CS., Smola, A., Williamson, R.

Journal of Machine Learning Research, 6, pages: 1043-1071, July 2005 (article)

Abstract
This paper addresses the problem of choosing a kernel suitable for estimation with a Support Vector Machine, hence further automating machine learning. This goal is achieved by defining a Reproducing Kernel Hilbert Space on the space of kernels itself. Such a formulation leads to a statistical estimation problem similar to the problem of minimizing a regularized risk functional. We state the equivalent representer theorem for the choice of kernels and present a semidefinite programming formulation of the resulting optimization problem. Several recipes for constructing hyperkernels are provided, as well as the details of common machine learning problems. Experimental results for classification, regression and novelty detection on UCI data show the feasibility of our approach.

ei

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ei Ong, CS., Smola, A., Williamson, R. Learning the Kernel with Hyperkernels Journal of Machine Learning Research, 6, pages: 1043-1071, July 2005 (article)

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Image Reconstruction by Linear Programming

Tsuda, K., Rätsch, G.

IEEE Transactions on Image Processing, 14(6):737-744, June 2005 (article)

Abstract
One way of image denoising is to project a noisy image to the subspace of admissible images derived, for instance, by PCA. However, a major drawback of this method is that all pixels are updated by the projection, even when only a few pixels are corrupted by noise or occlusion. We propose a new method to identify the noisy pixels by l1-norm penalization and to update the identified pixels only. The identification and updating of noisy pixels are formulated as one linear program which can be efficiently solved. In particular, one can apply the upsilon trick to directly specify the fraction of pixels to be reconstructed. Moreover, we extend the linear program to be able to exploit prior knowledge that occlusions often appear in contiguous blocks (e.g., sunglasses on faces). The basic idea is to penalize boundary points and interior points of the occluded area differently. We are also able to show the upsilon property for this extended LP leading to a method which is easy to use. Experimental results demonstrate the power of our approach.

ei

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ei Tsuda, K., Rätsch, G. Image Reconstruction by Linear Programming IEEE Transactions on Image Processing, 14(6):737-744, June 2005 (article)

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RASE: recognition of alternatively spliced exons in C.elegans

Rätsch, G., Sonnenburg, S., Schölkopf, B.

Bioinformatics, 21(Suppl. 1):i369-i377, June 2005 (article)

ei

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ei Rätsch, G., Sonnenburg, S., Schölkopf, B. RASE: recognition of alternatively spliced exons in C.elegans Bioinformatics, 21(Suppl. 1):i369-i377, June 2005 (article)

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Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection

Tsuda, K., Rätsch, G., Warmuth, M.

Journal of Machine Learning Research, 6, pages: 995-1018, June 2005 (article)

Abstract
We address the problem of learning a symmetric positive definite matrix. The central issue is to design parameter updates that preserve positive definiteness. Our updates are motivated with the von Neumann divergence. Rather than treating the most general case, we focus on two key applications that exemplify our methods: on-line learning with a simple square loss, and finding a symmetric positive definite matrix subject to linear constraints. The updates generalize the exponentiated gradient (EG) update and AdaBoost, respectively: the parameter is now a symmetric positive definite matrix of trace one instead of a probability vector (which in this context is a diagonal positive definite matrix with trace one). The generalized updates use matrix logarithms and exponentials to preserve positive definiteness. Most importantly, we show how the derivation and the analyses of the original EG update and AdaBoost generalize to the non-diagonal case. We apply the resulting matrix exponentiated gradient (MEG) update and DefiniteBoost to the problem of learning a kernel matrix from distance measurements.

ei

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ei Tsuda, K., Rätsch, G., Warmuth, M. Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection Journal of Machine Learning Research, 6, pages: 995-1018, June 2005 (article)

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Texture and haptic cues in slant discrimination: Reliability-based cue weighting without statistically optimal cue combination

Rosas, P., Wagemans, J., Ernst, M., Wichmann, F.

Journal of the Optical Society of America A, 22(5):801-809, May 2005 (article)

Abstract
A number of models of depth cue combination suggest that the final depth percept results from a weighted average of independent depth estimates based on the different cues available. The weight of each cue in such an average is thought to depend on the reliability of each cue. In principle, such a depth estimation could be statistically optimal in the sense of producing the minimum variance unbiased estimator that can be constructed from the available information. Here we test such models using visual and haptic depth information. Different texture types produce differences in slant discrimination performance, providing a means for testing a reliability-sensitive cue combination model using texture as one of the cues to slant. Our results show that the weights for the cues were generally sensitive to their reliability, but fell short of statistically optimal combination—we find reliability-based re-weighting, but not statistically optimal cue combination.

ei

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ei Rosas, P., Wagemans, J., Ernst, M., Wichmann, F. Texture and haptic cues in slant discrimination: Reliability-based cue weighting without statistically optimal cue combination Journal of the Optical Society of America A, 22(5):801-809, May 2005 (article)

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Bayesian inference for psychometric functions

Kuss, M., Jäkel, F., Wichmann, F.

Journal of Vision, 5(5):478-492, May 2005 (article)

Abstract
In psychophysical studies, the psychometric function is used to model the relation between physical stimulus intensity and the observer’s ability to detect or discriminate between stimuli of different intensities. In this study, we propose the use of Bayesian inference to extract the information contained in experimental data to estimate the parameters of psychometric functions. Because Bayesian inference cannot be performed analytically, we describe how a Markov chain Monte Carlo method can be used to generate samples from the posterior distribution over parameters. These samples are used to estimate Bayesian confidence intervals and other characteristics of the posterior distribution. In addition, we discuss the parameterization of psychometric functions and the role of prior distributions in the analysis. The proposed approach is exemplified using artificially generated data and in a case study for real experimental data. Furthermore, we compare our approach with traditional methods based on maximum likelihood parameter estimation combined with bootstrap techniques for confidence interval estimation and find the Bayesian approach to be superior.

ei

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ei Kuss, M., Jäkel, F., Wichmann, F. Bayesian inference for psychometric functions Journal of Vision, 5(5):478-492, May 2005 (article)

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A gene expression map of Arabidopsis thaliana development

Schmid, M., Davison, T., Henz, S., Pape, U., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., Lohmann, J.

Nature Genetics, 37(5):501-506, April 2005 (article)

Abstract
Regulatory regions of plant genes tend to be more compact than those of animal genes, but the complement of transcription factors encoded in plant genomes is as large or larger than that found in those of animals. Plants therefore provide an opportunity to study how transcriptional programs control multicellular development. We analyzed global gene expression during development of the reference plant Arabidopsis thaliana in samples covering many stages, from embryogenesis to senescence, and diverse organs. Here, we provide a first analysis of this data set, which is part of the AtGenExpress expression atlas. We observed that the expression levels of transcription factor genes and signal transduction components are similar to those of metabolic genes. Examining the expression patterns of large gene families, we found that they are often more similar than would be expected by chance, indicating that many gene families have been co-opted for specific developmental processes.

ei

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ei Schmid, M., Davison, T., Henz, S., Pape, U., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., Lohmann, J. A gene expression map of Arabidopsis thaliana development Nature Genetics, 37(5):501-506, April 2005 (article)

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Experimentally optimal v in support vector regression for different noise models and parameter settings

Chalimourda, A., Schölkopf, B., Smola, A.

Neural Networks, 18(2):205-205, March 2005 (article)

ei

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ei Chalimourda, A., Schölkopf, B., Smola, A. Experimentally optimal v in support vector regression for different noise models and parameter settings Neural Networks, 18(2):205-205, March 2005 (article)

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Invariance of Neighborhood Relation under Input Space to Feature Space Mapping

Shin, H., Cho, S.

Pattern Recognition Letters, 26(6):707-718, 2005 (article)

Abstract
If the training pattern set is large, it takes a large memory and a long time to train support vector machine (SVM). Recently, we proposed neighborhood property based pattern selection algorithm (NPPS) which selects only the patterns that are likely to be near the decision boundary ahead of SVM training [Proc. of the 7th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Lecture Notes in Artificial Intelligence (LNAI 2637), Seoul, Korea, pp. 376–387]. NPPS tries to identify those patterns that are likely to become support vectors in feature space. Preliminary reports show its effectiveness: SVM training time was reduced by two orders of magnitude with almost no loss in accuracy for various datasets. It has to be noted, however, that decision boundary of SVM and support vectors are all defined in feature space while NPPS described above operates in input space. If neighborhood relation in input space is not preserved in feature space, NPPS may not always be effective. In this paper, we sh ow that the neighborhood relation is invariant under input to feature space mapping. The result assures that the patterns selected by NPPS in input space are likely to be located near decision boundary in feature space.

ei

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ei Shin, H., Cho, S. Invariance of Neighborhood Relation under Input Space to Feature Space Mapping Pattern Recognition Letters, 26(6):707-718, 2005 (article)

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Theory of Classification: A Survey of Some Recent Advances

Boucheron, S., Bousquet, O., Lugosi, G.

ESAIM: Probability and Statistics, 9, pages: 323 , 2005 (article)

Abstract
The last few years have witnessed important new developments in the theory and practice of pattern classification. We intend to survey some of the main new ideas that have lead to these important recent developments.

ei

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ei Boucheron, S., Bousquet, O., Lugosi, G. Theory of Classification: A Survey of Some Recent Advances ESAIM: Probability and Statistics, 9, pages: 323 , 2005 (article)

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Support Vector Machines and Kernel Algorithms

Schölkopf, B., Smola, A.

In Encyclopedia of Biostatistics (2nd edition), Vol. 8, 8, pages: 5328-5335, (Editors: P Armitage and T Colton), John Wiley & Sons, NY USA, 2005 (inbook)

ei

[BibTex]

ei Schölkopf, B., Smola, A. Support Vector Machines and Kernel Algorithms In Encyclopedia of Biostatistics (2nd edition), Vol. 8, 8, pages: 5328-5335, (Editors: P Armitage and T Colton), John Wiley & Sons, NY USA, 2005 (inbook)

[BibTex]

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Moment Inequalities for Functions of Independent Random Variables

Boucheron, S., Bousquet, O., Lugosi, G., Massart, P.

To appear in Annals of Probability, 33, pages: 514-560, 2005 (article)

Abstract
A general method for obtaining moment inequalities for functions of independent random variables is presented. It is a generalization of the entropy method which has been used to derive concentration inequalities for such functions cite{BoLuMa01}, and is based on a generalized tensorization inequality due to Lata{l}a and Oleszkiewicz cite{LaOl00}. The new inequalities prove to be a versatile tool in a wide range of applications. We illustrate the power of the method by showing how it can be used to effortlessly re-derive classical inequalities including Rosenthal and Kahane-Khinchine-type inequalities for sums of independent random variables, moment inequalities for suprema of empirical processes, and moment inequalities for Rademacher chaos and $U$-statistics. Some of these corollaries are apparently new. In particular, we generalize Talagrands exponential inequality for Rademacher chaos of order two to any order. We also discuss applications for other complex functions of independent random variables, such as suprema of boolean polynomials which include, as special cases, subgraph counting problems in random graphs.

ei

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ei Boucheron, S., Bousquet, O., Lugosi, G., Massart, P. Moment Inequalities for Functions of Independent Random Variables To appear in Annals of Probability, 33, pages: 514-560, 2005 (article)

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Visual perception I: Basic principles

Wagemans, J., Wichmann, F., de Beeck, H.

In Handbook of Cognition, pages: 3-47, (Editors: Lamberts, K. , R. Goldstone), Sage, London, 2005 (inbook)

ei

[BibTex]

ei Wagemans, J., Wichmann, F., de Beeck, H. Visual perception I: Basic principles In Handbook of Cognition, pages: 3-47, (Editors: Lamberts, K. , R. Goldstone), Sage, London, 2005 (inbook)

[BibTex]

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A tutorial on v-support vector machines

Chen, P., Lin, C., Schölkopf, B.

Applied Stochastic Models in Business and Industry, 21(2):111-136, 2005 (article)

Abstract
We briefly describe the main ideas of statistical learning theory, support vector machines (SVMs), and kernel feature spaces. We place particular emphasis on a description of the so-called -SVM, including details of the algorithm and its implementation, theoretical results, and practical applications. Copyright © 2005 John Wiley & Sons, Ltd.

ei

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ei Chen, P., Lin, C., Schölkopf, B. A tutorial on v-support vector machines Applied Stochastic Models in Business and Industry, 21(2):111-136, 2005 (article)

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Robust EEG Channel Selection Across Subjects for Brain Computer Interfaces

Schröder, M., Lal, T., Hinterberger, T., Bogdan, M., Hill, J., Birbaumer, N., Rosenstiel, W., Schölkopf, B.

EURASIP Journal on Applied Signal Processing, 2005(19, Special Issue: Trends in Brain Computer Interfaces):3103-3112, (Editors: Vesin, J. M., T. Ebrahimi), 2005 (article)

Abstract
Most EEG-based Brain Computer Interface (BCI) paradigms come along with specific electrode positions, e.g.~for a visual based BCI electrode positions close to the primary visual cortex are used. For new BCI paradigms it is usually not known where task relevant activity can be measured from the scalp. For individual subjects Lal et.~al showed that recording positions can be found without the use of prior knowledge about the paradigm used. However it remains unclear to what extend their method of Recursive Channel Elimination (RCE) can be generalized across subjects. In this paper we transfer channel rankings from a group of subjects to a new subject. For motor imagery tasks the results are promising, although cross-subject channel selection does not quite achieve the performance of channel selection on data of single subjects. Although the RCE method was not provided with prior knowledge about the mental task, channels that are well known to be important (from a physiological point of view) were consistently selected whereas task-irrelevant channels were reliably disregarded.

ei

Web DOI [BibTex]

ei Schröder, M., Lal, T., Hinterberger, T., Bogdan, M., Hill, J., Birbaumer, N., Rosenstiel, W., Schölkopf, B. Robust EEG Channel Selection Across Subjects for Brain Computer Interfaces EURASIP Journal on Applied Signal Processing, 2005(19, Special Issue: Trends in Brain Computer Interfaces):3103-3112, (Editors: Vesin, J. M., T. Ebrahimi), 2005 (article)

Web DOI [BibTex]

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Geckobot and waalbot: Small-scale wall climbing robots

Unver, O., Murphy, M., Sitti, M.

In Infotech@ Aerospace, pages: 6940, 2005 (incollection)

pi

[BibTex]

pi Unver, O., Murphy, M., Sitti, M. Geckobot and waalbot: Small-scale wall climbing robots In Infotech@ Aerospace, pages: 6940, 2005 (incollection)

[BibTex]

2004

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On the representation, learning and transfer of spatio-temporal movement characteristics

Ilg, W., Bakir, GH., Mezger, J., Giese, M.

International Journal of Humanoid Robotics, 1(4):613-636, December 2004 (article)

ei

[BibTex]

2004

ei Ilg, W., Bakir, GH., Mezger, J., Giese, M. On the representation, learning and transfer of spatio-temporal movement characteristics International Journal of Humanoid Robotics, 1(4):613-636, December 2004 (article)

[BibTex]

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Insect-inspired estimation of egomotion

Franz, MO., Chahl, JS., Krapp, HG.

Neural Computation, 16(11):2245-2260, November 2004 (article)

Abstract
Tangential neurons in the fly brain are sensitive to the typical optic flow patterns generated during egomotion. In this study, we examine whether a simplified linear model based on the organization principles in tangential neurons can be used to estimate egomotion from the optic flow. We present a theory for the construction of an estimator consisting of a linear combination of optic flow vectors that incorporates prior knowledge both about the distance distribution of the environment, and about the noise and egomotion statistics of the sensor. The estimator is tested on a gantry carrying an omnidirectional vision sensor. The experiments show that the proposed approach leads to accurate and robust estimates of rotation rates, whereas translation estimates are of reasonable quality, albeit less reliable.

ei

PDF PostScript Web DOI [BibTex]

ei Franz, MO., Chahl, JS., Krapp, HG. Insect-inspired estimation of egomotion Neural Computation, 16(11):2245-2260, November 2004 (article)

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Efficient face detection by a cascaded support-vector machine expansion

Romdhani, S., Torr, P., Schölkopf, B., Blake, A.

Proceedings of The Royal Society of London A, 460(2501):3283-3297, A, November 2004 (article)

Abstract
We describe a fast system for the detection and localization of human faces in images using a nonlinear ‘support-vector machine‘. We approximate the decision surface in terms of a reduced set of expansion vectors and propose a cascaded evaluation which has the property that the full support-vector expansion is only evaluated on the face-like parts of the image, while the largest part of typical images is classified using a single expansion vector (a simpler and more efficient classifier). As a result, only three reduced-set vectors are used, on average, to classify an image patch. Hence, the cascaded evaluation, presented in this paper, offers a thirtyfold speed-up over an evaluation using the full set of reduced-set vectors, which is itself already thirty times faster than classification using all the support vectors.

ei

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ei Romdhani, S., Torr, P., Schölkopf, B., Blake, A. Efficient face detection by a cascaded support-vector machine expansion Proceedings of The Royal Society of London A, 460(2501):3283-3297, A, November 2004 (article)

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Kernel Methods in Computational Biology

Schölkopf, B., Tsuda, K., Vert, J.

pages: 410, Computational Molecular Biology, MIT Press, Cambridge, MA, USA, August 2004 (book)

Abstract
Modern machine learning techniques are proving to be extremely valuable for the analysis of data in computational biology problems. One branch of machine learning, kernel methods, lends itself particularly well to the difficult aspects of biological data, which include high dimensionality (as in microarray measurements), representation as discrete and structured data (as in DNA or amino acid sequences), and the need to combine heterogeneous sources of information. This book provides a detailed overview of current research in kernel methods and their applications to computational biology. Following three introductory chapters—an introduction to molecular and computational biology, a short review of kernel methods that focuses on intuitive concepts rather than technical details, and a detailed survey of recent applications of kernel methods in computational biology—the book is divided into three sections that reflect three general trends in current research. The first part presents different ideas for the design of kernel functions specifically adapted to various biological data; the second part covers different approaches to learning from heterogeneous data; and the third part offers examples of successful applications of support vector machine methods.

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Web [BibTex]

ei Schölkopf, B., Tsuda, K., Vert, J. Kernel Methods in Computational Biology pages: 410, Computational Molecular Biology, MIT Press, Cambridge, MA, USA, August 2004 (book)

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Learning kernels from biological networks by maximizing entropy

Tsuda, K., Noble, W.

Bioinformatics, 20(Suppl. 1):i326-i333, August 2004 (article)

Abstract
Motivation: The diffusion kernel is a general method for computing pairwise distances among all nodes in a graph, based on the sum of weighted paths between each pair of nodes. This technique has been used successfully, in conjunction with kernel-based learning methods, to draw inferences from several types of biological networks. Results: We show that computing the diffusion kernel is equivalent to maximizing the von Neumann entropy, subject to a global constraint on the sum of the Euclidean distances between nodes. This global constraint allows for high variance in the pairwise distances. Accordingly, we propose an alternative, locally constrained diffusion kernel, and we demonstrate that the resulting kernel allows for more accurate support vector machine prediction of protein functional classifications from metabolic and protein–protein interaction networks.

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ei Tsuda, K., Noble, W. Learning kernels from biological networks by maximizing entropy Bioinformatics, 20(Suppl. 1):i326-i333, August 2004 (article)

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Masking effect produced by Mach bands on the detection of narrow bars of random polarity

Henning, GB., Hoddinott, KT., Wilson-Smith, ZJ., Hill, NJ.

Journal of the Optical Society of America, 21(8):1379-1387, A, August 2004 (article)

ei

[BibTex]

ei Henning, GB., Hoddinott, KT., Wilson-Smith, ZJ., Hill, NJ. Masking effect produced by Mach bands on the detection of narrow bars of random polarity Journal of the Optical Society of America, 21(8):1379-1387, A, August 2004 (article)

[BibTex]

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Support Vector Channel Selection in BCI

Lal, T., Schröder, M., Hinterberger, T., Weston, J., Bogdan, M., Birbaumer, N., Schölkopf, B.

IEEE Transactions on Biomedical Engineering, 51(6):1003-1010, June 2004 (article)

Abstract
Designing a Brain Computer Interface (BCI) system one can choose from a variety of features that may be useful for classifying brain activity during a mental task. For the special case of classifying EEG signals we propose the usage of the state of the art feature selection algorithms Recursive Feature Elimination and Zero-Norm Optimization which are based on the training of Support Vector Machines (SVM). These algorithms can provide more accurate solutions than standard filter methods for feature selection. We adapt the methods for the purpose of selecting EEG channels. For a motor imagery paradigm we show that the number of used channels can be reduced significantly without increasing the classification error. The resulting best channels agree well with the expected underlying cortical activity patterns during the mental tasks. Furthermore we show how time dependent task specific information can be visualized.

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DOI [BibTex]

ei Lal, T., Schröder, M., Hinterberger, T., Weston, J., Bogdan, M., Birbaumer, N., Schölkopf, B. Support Vector Channel Selection in BCI IEEE Transactions on Biomedical Engineering, 51(6):1003-1010, June 2004 (article)

DOI [BibTex]

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Distance-Based Classification with Lipschitz Functions

von Luxburg, U., Bousquet, O.

Journal of Machine Learning Research, 5, pages: 669-695, June 2004 (article)

Abstract
The goal of this article is to develop a framework for large margin classification in metric spaces. We want to find a generalization of linear decision functions for metric spaces and define a corresponding notion of margin such that the decision function separates the training points with a large margin. It will turn out that using Lipschitz functions as decision functions, the inverse of the Lipschitz constant can be interpreted as the size of a margin. In order to construct a clean mathematical setup we isometrically embed the given metric space into a Banach space and the space of Lipschitz functions into its dual space. To analyze the resulting algorithm, we prove several representer theorems. They state that there always exist solutions of the Lipschitz classifier which can be expressed in terms of distance functions to training points. We provide generalization bounds for Lipschitz classifiers in terms of the Rademacher complexities of some Lipschitz function classes. The generality of our approach can be seen from the fact that several well-known algorithms are special cases of the Lipschitz classifier, among them the support vector machine, the linear programming machine, and the 1-nearest neighbor classifier.

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ei von Luxburg, U., Bousquet, O. Distance-Based Classification with Lipschitz Functions Journal of Machine Learning Research, 5, pages: 669-695, June 2004 (article)

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Distributed Command Execution

Stark, S., Berlin, M.

In BSD Hacks: 100 industrial-strength tips & tools, pages: 152-152, (Editors: Lavigne, Dru), O’Reilly, Beijing, May 2004 (inbook)

Abstract
Often you want to execute a command not only on one computer, but on several at once. For example, you might want to report the current statistics on a group of managed servers or update all of your web servers at once.

ei

[BibTex]

ei Stark, S., Berlin, M. Distributed Command Execution In BSD Hacks: 100 industrial-strength tips & tools, pages: 152-152, (Editors: Lavigne, Dru), O’Reilly, Beijing, May 2004 (inbook)

[BibTex]

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cDNA-Microarray Technology in Cartilage Research - Functional Genomics of Osteoarthritis [in German]

Aigner, T., Finger, F., Zien, A., Bartnik, E.

Zeitschrift f{\"u}r Orthop{\"a}die und ihre Grenzgebiete, 142(2):241-247, April 2004 (article)

Abstract
Functional genomics represents a new challenging approach in order to analyze complex diseases such as osteoarthritis on a molecular level. The characterization of the molecular changes of the cartilage cells, the chondrocytes, enables a better understanding of the pathomechanisms of the disease. In particular, the identification and characterization of new target molecules for therapeutic intervention is of interest. Also, potential molecular markers for diagnosis and monitoring of osteoarthritis contribute to a more appropriate patient management. The DNA-microarray technology complements (but does not replace) biochemical and biological research in new disease-relevant genes. Large-scale functional genomics will identify molecular networks such as yet identified players in the anabolic-catabolic balance of articular cartilage as well as disease-relevant intracellular signaling cascades so far rather unknown in articular chondrocytes. However, at the moment it is also important to recognize the limitations of the microarray technology in order to avoid over-interpretation of the results. This might lead to misleading results and prevent to a significant extent a proper use of the potential of this technology in the field of osteoarthritis.

ei

[BibTex]

ei Aigner, T., Finger, F., Zien, A., Bartnik, E. cDNA-Microarray Technology in Cartilage Research - Functional Genomics of Osteoarthritis [in German] Zeitschrift f{\"u}r Orthop{\"a}die und ihre Grenzgebiete, 142(2):241-247, April 2004 (article)

[BibTex]

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A Compression Approach to Support Vector Model Selection

von Luxburg, U., Bousquet, O., Schölkopf, B.

Journal of Machine Learning Research, 5, pages: 293-323, April 2004 (article)

Abstract
In this paper we investigate connections between statistical learning theory and data compression on the basis of support vector machine (SVM) model selection. Inspired by several generalization bounds we construct "compression coefficients" for SVMs which measure the amount by which the training labels can be compressed by a code built from the separating hyperplane. The main idea is to relate the coding precision to geometrical concepts such as the width of the margin or the shape of the data in the feature space. The so derived compression coefficients combine well known quantities such as the radius-margin term R^2/rho^2, the eigenvalues of the kernel matrix, and the number of support vectors. To test whether they are useful in practice we ran model selection experiments on benchmark data sets. As a result we found that compression coefficients can fairly accurately predict the parameters for which the test error is minimized.

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PDF [BibTex]

ei von Luxburg, U., Bousquet, O., Schölkopf, B. A Compression Approach to Support Vector Model Selection Journal of Machine Learning Research, 5, pages: 293-323, April 2004 (article)

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Experimentally optimal v in support vector regression for different noise models and parameter settings

Chalimourda, A., Schölkopf, B., Smola, A.

Neural Networks, 17(1):127-141, January 2004 (article)

Abstract
In Support Vector (SV) regression, a parameter ν controls the number of Support Vectors and the number of points that come to lie outside of the so-called var epsilon-insensitive tube. For various noise models and SV parameter settings, we experimentally determine the values of ν that lead to the lowest generalization error. We find good agreement with the values that had previously been predicted by a theoretical argument based on the asymptotic efficiency of a simplified model of SV regression. As a side effect of the experiments, valuable information about the generalization behavior of the remaining SVM parameters and their dependencies is gained. The experimental findings are valid even for complex ‘real-world’ data sets. Based on our results on the role of the ν-SVM parameters, we discuss various model selection methods.

ei

PDF DOI [BibTex]

ei Chalimourda, A., Schölkopf, B., Smola, A. Experimentally optimal v in support vector regression for different noise models and parameter settings Neural Networks, 17(1):127-141, January 2004 (article)

PDF DOI [BibTex]

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Protein ranking: from local to global structure in the protein similarity network

Weston, J., Elisseeff, A., Zhou, D., Leslie, C., Noble, W.

Proceedings of the National Academy of Science, 101(17):6559-6563, 2004 (article)

Abstract
Biologists regularly search databases of DNA or protein sequences for evolutionary or functional relationships to a given query sequence. We describe a ranking algorithm that exploits the entire network structure of similarity relationships among proteins in a sequence database by performing a diffusion operation on a pre-computed, weighted network. The resulting ranking algorithm, evaluated using a human-curated database of protein structures, is efficient and provides significantly better rankings than a local network search algorithm such as PSI-BLAST.

ei

Web [BibTex]

ei Weston, J., Elisseeff, A., Zhou, D., Leslie, C., Noble, W. Protein ranking: from local to global structure in the protein similarity network Proceedings of the National Academy of Science, 101(17):6559-6563, 2004 (article)

Web [BibTex]

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Gaussian Processes in Machine Learning

Rasmussen, CE.

In 3176, pages: 63-71, Lecture Notes in Computer Science, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, 2004, Copyright by Springer (inbook)

Abstract
We give a basic introduction to Gaussian Process regression models. We focus on understanding the role of the stochastic process and how it is used to define a distribution over functions. We present the simple equations for incorporating training data and examine how to learn the hyperparameters using the marginal likelihood. We explain the practical advantages of Gaussian Process and end with conclusions and a look at the current trends in GP work.

ei

PDF PostScript [BibTex]

ei Rasmussen, CE. Gaussian Processes in Machine Learning In 3176, pages: 63-71, Lecture Notes in Computer Science, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, 2004, Copyright by Springer (inbook)

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Statistical Performance of Support Vector Machines

Blanchard, G., Bousquet, O., Massart, P.

2004 (article)

ei

PostScript [BibTex]

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Asymptotic Properties of the Fisher Kernel

Tsuda, K., Akaho, S., Kawanabe, M., Müller, K.

Neural Computation, 16(1):115-137, 2004 (article)

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ei Tsuda, K., Akaho, S., Kawanabe, M., Müller, K. Asymptotic Properties of the Fisher Kernel Neural Computation, 16(1):115-137, 2004 (article)

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Some observations on the effects of slant and texture type on slant-from-texture

Rosas, P., Wichmann, F., Wagemans, J.

Vision Research, 44(13):1511-1535, 2004 (article)

Abstract
We measure the performance of five subjects in a slant-discrimination task for differently textured planes. As textures we used uniform lattices, randomly displaced lattices, circles (polka dots), Voronoi tessellations, plaids, 1/f noise, “coherent” noise and a leopard skin-like texture. Our results show: (1) Improving performance with larger slants for all textures. (2) Thus, following from (1), cases of “non-symmetrical” performance around a particular orientation. (3) For orientations sufficiently slanted, the different textures do not elicit major differences in performance, (4) while for orientations closer to the vertical plane there are marked differences between them. (5) These differences allow a rank-order of textures to be formed according to their “helpfulness”– that is, how easy the discrimination task is when a particular texture is mapped on the plane. Polka dots tend to allow the best slant discrimination performance, noise patterns the worst. Two additional experiments were conducted to test the generality of the obtained rank-order. First, the tilt of the planes was rotated to break the axis of gravity present in the original discrimination experiment. Second, the task was changed to a slant report task via probe adjustment. The results of both control experiments confirmed the texture-based rank-order previously obtained. We comment on the importance of these results for depth perception research in general, and in particular the implications our results have for studies of cue combination (sensor fusion) using texture as one of the cues involved.

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ei Rosas, P., Wichmann, F., Wagemans, J. Some observations on the effects of slant and texture type on slant-from-texture Vision Research, 44(13):1511-1535, 2004 (article)

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Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data

Tsuda, K., Uda, S., Kin, T., Asai, K.

Neural Processing Letters, 19, pages: 63-72, 2004 (article)

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PDF [BibTex]

ei Tsuda, K., Uda, S., Kin, T., Asai, K. Minimizing the Cross Validation Error to Mix Kernel Matrices of Heterogeneous Biological Data Neural Processing Letters, 19, pages: 63-72, 2004 (article)

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A Tutorial on Support Vector Regression

Smola, A., Schölkopf, B.

Statistics and Computing, 14(3):199-222, 2004 (article)

ei

Web [BibTex]

ei Smola, A., Schölkopf, B. A Tutorial on Support Vector Regression Statistics and Computing, 14(3):199-222, 2004 (article)

Web [BibTex]

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Protein Classification via Kernel Matrix Completion

Kin, T., Kato, T., Tsuda, K.

In pages: 261-274, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

ei

PDF [BibTex]

ei Kin, T., Kato, T., Tsuda, K. Protein Classification via Kernel Matrix Completion In pages: 261-274, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

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Bayesian analysis of the Scatterometer Wind Retrieval Inverse Problem: Some New Approaches

Cornford, D., Csato, L., Evans, D., Opper, M.

Journal of the Royal Statistical Society B, 66, pages: 1-17, 3, 2004 (article)

Abstract
The retrieval of wind vectors from satellite scatterometer observations is a non-linear inverse problem.A common approach to solving inverse problems is to adopt a Bayesian framework and to infer the posterior distribution of the parameters of interest given the observations by using a likelihood model relating the observations to the parameters, and a prior distribution over the parameters.We show how Gaussian process priors can be used efficiently with a variety of likelihood models, using local forward (observation) models and direct inverse models for the scatterometer.We present an enhanced Markov chain Monte Carlo method to sample from the resulting multimodal posterior distribution.We go on to show how the computational complexity of the inference can be controlled by using a sparse, sequential Bayes algorithm for estimation with Gaussian processes.This helps to overcome the most serious barrier to the use of probabilistic, Gaussian process methods in remote sensing inverse problems, which is the prohibitively large size of the data sets.We contrast the sampling results with the approximations that are found by using the sparse, sequential Bayes algorithm.

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ei Cornford, D., Csato, L., Evans, D., Opper, M. Bayesian analysis of the Scatterometer Wind Retrieval Inverse Problem: Some New Approaches Journal of the Royal Statistical Society B, 66, pages: 1-17, 3, 2004 (article)

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Feature Selection for Support Vector Machines Using Genetic Algorithms

Fröhlich, H., Chapelle, O., Schölkopf, B.

International Journal on Artificial Intelligence Tools (Special Issue on Selected Papers from the 15th IEEE International Conference on Tools with Artificial Intelligence 2003), 13(4):791-800, 2004 (article)

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Web [BibTex]

ei Fröhlich, H., Chapelle, O., Schölkopf, B. Feature Selection for Support Vector Machines Using Genetic Algorithms International Journal on Artificial Intelligence Tools (Special Issue on Selected Papers from the 15th IEEE International Conference on Tools with Artificial Intelligence 2003), 13(4):791-800, 2004 (article)

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Introduction to Statistical Learning Theory

Bousquet, O., Boucheron, S., Lugosi, G.

In Lecture Notes in Artificial Intelligence 3176, pages: 169-207, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

ei

PDF [BibTex]

ei Bousquet, O., Boucheron, S., Lugosi, G. Introduction to Statistical Learning Theory In Lecture Notes in Artificial Intelligence 3176, pages: 169-207, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

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