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2009


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Efficient Bregman Range Search

Cayton, L.

In Advances in Neural Information Processing Systems 22, pages: 243-251, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
We develop an algorithm for efficient range search when the notion of dissimilarity is given by a Bregman divergence. The range search task is to return all points in a potentially large database that are within some specified distance of a query. It arises in many learning algorithms such as locally-weighted regression, kernel density estimation, neighborhood graph-based algorithms, and in tasks like outlier detection and information retrieval. In metric spaces, efficient range search-like algorithms based on spatial data structures have been deployed on a variety of statistical tasks. Here we describe an algorithm for range search for an arbitrary Bregman divergence. This broad class of dissimilarity measures includes the relative entropy, Mahalanobis distance, Itakura-Saito divergence, and a variety of matrix divergences. Metric methods cannot be directly applied since Bregman divergences do not in general satisfy the triangle inequality. We derive geometric properties of Bregman divergences that yield an efficient algorithm for range search based on a recently proposed space decomposition for Bregman divergences.

ei

PDF Web [BibTex]

2009


PDF Web [BibTex]


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Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases

Djuranovic, S., Hartmann, MD., Habeck, M., Ursinus, A., Zwickl, P., Martin, J., Lupas, AN., Zeth, K.

Molecular Cell, 34(5):580-590, 2009 (article)

Abstract
The proteasome forms the core of the protein quality control system in archaea and eukaryotes and also occurs in one bacterial lineage, the Actinobacteria. Access to its proteolytic compartment is controlled by AAA ATPases, whose N-terminal domains (N domains) are thought to mediate substrate recognition. The N domains of an archaeal proteasomal ATPase, Archaeoglobus fulgidus PAN, and of its actinobacterial homolog, Rhodococcus erythropolis ARC, form hexameric rings, whose subunits consist of an N-terminal coiled coil and a C-terminal OB domain. In ARC-N, the OB domains are duplicated and form separate rings. PAN-N and ARC-N can act as chaperones, preventing the aggregation of heterologous proteins in vitro, and this activity is preserved in various chimeras, even when these include coiled coils and OB domains from unrelated proteins. The structures suggest a molecular mechanism for substrate processing based on concerted radial motions of the coiled coils relative to the OB rings.

ei

DOI [BibTex]

DOI [BibTex]


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Discussion of: Brownian Distance Covariance

Gretton, A., Fukumizu, K., Sriperumbudur, B.

The Annals of Applied Statistics, 3(4):1285-1294, 2009 (article)

ei

[BibTex]

[BibTex]


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Kernel Choice and Classifiability for RKHS Embeddings of Probability Distributions

Sriperumbudur, B., Fukumizu, K., Gretton, A., Lanckriet, G., Schölkopf, B.

In Advances in Neural Information Processing Systems 22, pages: 1750-1758, (Editors: Y Bengio and D Schuurmans and J Lafferty and C Williams and A Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
Embeddings of probability measures into reproducing kernel Hilbert spaces have been proposed as a straightforward and practical means of representing and comparing probabilities. In particular, the distance between embeddings (the maximum mean discrepancy, or MMD) has several key advantages over many classical metrics on distributions, namely easy computability, fast convergence and low bias of finite sample estimates. An important requirement of the embedding RKHS is that it be characteristic: in this case, the MMD between two distributions is zero if and only if the distributions coincide. Three new results on the MMD are introduced in the present study. First, it is established that MMD corresponds to the optimal risk of a kernel classifier, thus forming a natural link between the distance between distributions and their ease of classification. An important consequence is that a kernel must be characteristic to guarantee classifiability between distributions in the RKHS. Second, the class of characteristic kernels is broadened to incorporate all strictly positive definite kernels: these include non-translation invariant kernels and kernels on non-compact domains. Third, a generalization of the MMD is proposed for families of kernels, as the supremum over MMDs on a class of kernels (for instance the Gaussian kernels with different bandwidths). This extension is necessary to obtain a single distance measure if a large selection or class of characteristic kernels is potentially appropriate. This generalization is reasonable, given that it corresponds to the problem of learning the kernel by minimizing the risk of the corresponding kernel classifier. The generalized MMD is shown to have consistent finite sample estimates, and its performance is demonstrated on a homogeneity testing example.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Nonlinear directed acyclic structure learning with weakly additive noise models

Tillman, R., Gretton, A., Spirtes, P.

In Advances in Neural Information Processing Systems 22, pages: 1847-1855, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
The recently proposed emph{additive noise model} has advantages over previous structure learning algorithms, when attempting to recover some true data generating mechanism, since it (i) does not assume linearity or Gaussianity and (ii) can recover a unique DAG rather than an equivalence class. However, its original extension to the multivariate case required enumerating all possible DAGs, and for some special distributions, e.g. linear Gaussian, the model is invertible and thus cannot be used for structure learning. We present a new approach which combines a PC style search using recent advances in kernel measures of conditional dependence with local searches for additive noise models in substructures of the equivalence class. This results in a more computationally efficient approach that is useful for arbitrary distributions even when additive noise models are invertible. Experiments with synthetic and real data show that this method is more accurate than previous methods when data are nonlinear and/or non-Gaussian.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Graphical models for decoding in BCI visual speller systems

Martens, S., Farquhar, J., Hill, J., Schölkopf, B.

In pages: 470-473, IEEE, 4th International IEEE EMBS Conference on Neural Engineering (NER), 2009 (inproceedings)

ei

DOI [BibTex]

DOI [BibTex]


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A Fast, Consistent Kernel Two-Sample Test

Gretton, A., Fukumizu, K., Harchaoui, Z., Sriperumbudur, B.

In Advances in Neural Information Processing Systems 22, pages: 673-681, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
A kernel embedding of probability distributions into reproducing kernel Hilbert spaces (RKHS) has recently been proposed, which allows the comparison of two probability measures P and Q based on the distance between their respective embeddings: for a sufficiently rich RKHS, this distance is zero if and only if P and Q coincide. In using this distance as a statistic for a test of whether two samples are from different distributions, a major difficulty arises in computing the significance threshold, since the empirical statistic has as its null distribution (where P = Q) an infinite weighted sum of x2 random variables. Prior finite sample approximations to the null distribution include using bootstrap resampling, which yields a consistent estimate but is computationally costly; and fitting a parametric model with the low order moments of the test statistic, which can work well in practice but has no consistency or accuracy guarantees. The main result of the present work is a novel estimate of the null distribution, computed from the eigenspectrum of the Gram matrix on the aggregate sample from P and Q, and having lower computational cost than the bootstrap. A proof of consistency of this estimate is provided. The performance of the null distribution estimate is compared with the bootstrap and parametric approaches on an artificial example, high dimensional multivariate data, and text.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Augmenting Feature-driven fMRI Analyses: Semi-supervised learning and resting state activity

Blaschko, M., Shelton, J., Bartels, A.

In Advances in Neural Information Processing Systems 22, pages: 126-134, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
Resting state activity is brain activation that arises in the absence of any task, and is usually measured in awake subjects during prolonged fMRI scanning sessions where the only instruction given is to close the eyes and do nothing. It has been recognized in recent years that resting state activity is implicated in a wide variety of brain function. While certain networks of brain areas have different levels of activation at rest and during a task, there is nevertheless significant similarity between activations in the two cases. This suggests that recordings of resting state activity can be used as a source of unlabeled data to augment discriminative regression techniques in a semi-supervised setting. We evaluate this setting empirically yielding three main results: (i) regression tends to be improved by the use of Laplacian regularization even when no additional unlabeled data are available, (ii) resting state data seem to have a similar marginal distribution to that recorded during the execution of a visual processing task implying largely similar types of activation, and (iii) this source of information can be broadly exploited to improve the robustness of empirical inference in fMRI studies, an inherently data poor domain.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Non-linear System Identification: Visual Saliency Inferred from Eye-Movement Data

Wichmann, F., Kienzle, W., Schölkopf, B., Franz, M.

Journal of Vision, 9(8):article 32, 2009 (article)

Abstract
For simple visual patterns under the experimenter's control we impose which information, or features, an observer can use to solve a given perceptual task. For natural vision tasks, however, there are typically a multitude of potential features in a given visual scene which the visual system may be exploiting when analyzing it: edges, corners, contours, etc. Here we describe a novel non-linear system identification technique based on modern machine learning methods that allows the critical features an observer uses to be inferred directly from the observer's data. The method neither requires stimuli to be embedded in noise nor is it limited to linear perceptive fields (classification images). We demonstrate our technique by deriving the critical image features observers fixate in natural scenes (bottom-up visual saliency). Unlike previous studies where the relevant structure is determined manually—e.g. by selecting Gabors as visual filters—we do not make any assumptions in this regard, but numerically infer number and properties them from the eye-movement data. We show that center-surround patterns emerge as the optimal solution for predicting saccade targets from local image structure. The resulting model, a one-layer feed-forward network with contrast gain-control, is surprisingly simple compared to previously suggested saliency models. Nevertheless, our model is equally predictive. Furthermore, our findings are consistent with neurophysiological hardware in the superior colliculus. Bottom-up visual saliency may thus not be computed cortically as has been thought previously.

ei

Web DOI [BibTex]


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mGene.web: a web service for accurate computational gene finding

Schweikert, G., Behr, J., Zien, A., Zeller, G., Ong, C., Sonnenburg, S., Rätsch, G.

Nucleic Acids Research, 37, pages: W312-6, 2009 (article)

Abstract
We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp).

ei

DOI [BibTex]

DOI [BibTex]


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Fast subtree kernels on graphs

Shervashidze, N., Borgwardt, K.

In Advances in Neural Information Processing Systems 22, pages: 1660-1668, (Editors: Bengio, Y. , D. Schuurmans, J. Lafferty, C. Williams, A. Culotta), Curran, Red Hook, NY, USA, 23rd Annual Conference on Neural Information Processing Systems (NIPS), 2009 (inproceedings)

Abstract
In this article, we propose fast subtree kernels on graphs. On graphs with n nodes and m edges and maximum degree d, these kernels comparing subtrees of height h can be computed in O(mh), whereas the classic subtree kernel by Ramon & G{\"a}rtner scales as O(n24dh). Key to this efficiency is the observation that the Weisfeiler-Lehman test of isomorphism from graph theory elegantly computes a subtree kernel as a byproduct. Our fast subtree kernels can deal with labeled graphs, scale up easily to large graphs and outperform state-of-the-art graph kernels on several classification benchmark datasets in terms of accuracy and runtime.

ei

PDF Web [BibTex]

PDF Web [BibTex]

2003


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Concentration Inequalities for Sub-Additive Functions Using the Entropy Method

Bousquet, O.

Stochastic Inequalities and Applications, 56, pages: 213-247, Progress in Probability, (Editors: Giné, E., C. Houdré and D. Nualart), November 2003 (article)

Abstract
We obtain exponential concentration inequalities for sub-additive functions of independent random variables under weak conditions on the increments of those functions, like the existence of exponential moments for these increments. As a consequence of these general inequalities, we obtain refinements of Talagrand's inequality for empirical processes and new bounds for randomized empirical processes. These results are obtained by further developing the entropy method introduced by Ledoux.

ei

PostScript [BibTex]

2003


PostScript [BibTex]


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On the Complexity of Learning the Kernel Matrix

Bousquet, O., Herrmann, D.

In Advances in Neural Information Processing Systems 15, pages: 399-406, (Editors: Becker, S. , S. Thrun, K. Obermayer), The MIT Press, Cambridge, MA, USA, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

Abstract
We investigate data based procedures for selecting the kernel when learning with Support Vector Machines. We provide generalization error bounds by estimating the Rademacher complexities of the corresponding function classes. In particular we obtain a complexity bound for function classes induced by kernels with given eigenvectors, i.e., we allow to vary the spectrum and keep the eigenvectors fix. This bound is only a logarithmic factor bigger than the complexity of the function class induced by a single kernel. However, optimizing the margin over such classes leads to overfitting. We thus propose a suitable way of constraining the class. We use an efficient algorithm to solve the resulting optimization problem, present preliminary experimental results, and compare them to an alignment-based approach.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Cluster Kernels for Semi-Supervised Learning

Chapelle, O., Weston, J., Schölkopf, B.

In Advances in Neural Information Processing Systems 15, pages: 585-592, (Editors: S Becker and S Thrun and K Obermayer), MIT Press, Cambridge, MA, USA, 16th Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

Abstract
We propose a framework to incorporate unlabeled data in kernel classifier, based on the idea that two points in the same cluster are more likely to have the same label. This is achieved by modifying the eigenspectrum of the kernel matrix. Experimental results assess the validity of this approach.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Mismatch String Kernels for SVM Protein Classification

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

In Advances in Neural Information Processing Systems 15, pages: 1417-1424, (Editors: Becker, S. , S. Thrun, K. Obermayer), MIT Press, Cambridge, MA, USA, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

Abstract
We introduce a class of string kernels, called mismatch kernels, for use with support vector machines (SVMs) in a discriminative approach to the protein classification problem. These kernels measure sequence similarity based on shared occurrences of k-length subsequences, counted with up to m mismatches, and do not rely on any generative model for the positive training sequences. We compute the kernels efficiently using a mismatch tree data structure and report experiments on a benchmark SCOP dataset, where we show that the mismatch kernel used with an SVM classifier performs as well as the Fisher kernel, the most successful method for remote homology detection, while achieving considerable computational savings.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Kernel Dependency Estimation

Weston, J., Chapelle, O., Elisseeff, A., Schölkopf, B., Vapnik, V.

In Advances in Neural Information Processing Systems 15, pages: 873-880, (Editors: S Becker and S Thrun and K Obermayer), MIT Press, Cambridge, MA, USA, 16th Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Linear Combinations of Optic Flow Vectors for Estimating Self-Motion: a Real-World Test of a Neural Model

Franz, MO., Chahl, JS.

In Advances in Neural Information Processing Systems 15, pages: 1319-1326, (Editors: Becker, S., S. Thrun and K. Obermayer), MIT Press, Cambridge, MA, USA, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

Abstract
The tangential neurons in the fly brain are sensitive to the typical optic flow patterns generated during self-motion. In this study, we examine whether a simplified linear model of these neurons can be used to estimate self-motion 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 self-motion 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 turn out to be less reliable.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Clustering with the Fisher score

Tsuda, K., Kawanabe, M., Müller, K.

In Advances in Neural Information Processing Systems 15, pages: 729-736, (Editors: Becker, S. , S. Thrun, K. Obermayer), MIT Press, Cambridge, MA, USA, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS), October 2003 (inproceedings)

Abstract
Recently the Fisher score (or the Fisher kernel) is increasingly used as a feature extractor for classification problems. The Fisher score is a vector of parameter derivatives of loglikelihood of a probabilistic model. This paper gives a theoretical analysis about how class information is preserved in the space of the Fisher score, which turns out that the Fisher score consists of a few important dimensions with class information and many nuisance dimensions. When we perform clustering with the Fisher score, K-Means type methods are obviously inappropriate because they make use of all dimensions. So we will develop a novel but simple clustering algorithm specialized for the Fisher score, which can exploit important dimensions. This algorithm is successfully tested in experiments with artificial data and real data (amino acid sequences).

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Marginalized Kernels between Labeled Graphs

Kashima, H., Tsuda, K., Inokuchi, A.

In 20th International Conference on Machine Learning, pages: 321-328, (Editors: Faucett, T. and N. Mishra), 20th International Conference on Machine Learning, August 2003 (inproceedings)

ei

PDF [BibTex]

PDF [BibTex]


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Sparse Gaussian Processes: inference, subspace identification and model selection

Csato, L., Opper, M.

In Proceedings, pages: 1-6, (Editors: Van der Hof, , Wahlberg), The Netherlands, 13th IFAC Symposium on System Identifiaction, August 2003, electronical version; Index ThA02-2 (inproceedings)

Abstract
Gaussian Process (GP) inference is a probabilistic kernel method where the GP is treated as a latent function. The inference is carried out using the Bayesian online learning and its extension to the more general iterative approach which we call TAP/EP learning. Sparsity is introduced in this context to make the TAP/EP method applicable to large datasets. We address the prohibitive scaling of the number of parameters by defining a subset of the training data that is used as the support the GP, thus the number of required parameters is independent of the training set, similar to the case of ``Support--‘‘ or ``Relevance--Vectors‘‘. An advantage of the full probabilistic treatment is that allows the computation of the marginal data likelihood or evidence, leading to hyper-parameter estimation within the GP inference. An EM algorithm to choose the hyper-parameters is proposed. The TAP/EP learning is the E-step and the M-step then updates the hyper-parameters. Due to the sparse E-step the resulting algorithm does not involve manipulation of large matrices. The presented algorithm is applicable to a wide variety of likelihood functions. We present results of applying the algorithm on classification and nonstandard regression problems for artificial and real datasets.

ei

PDF GZIP [BibTex]

PDF GZIP [BibTex]


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Adaptive, Cautious, Predictive control with Gaussian Process Priors

Murray-Smith, R., Sbarbaro, D., Rasmussen, CE., Girard, A.

In Proceedings of the 13th IFAC Symposium on System Identification, pages: 1195-1200, (Editors: Van den Hof, P., B. Wahlberg and S. Weiland), Proceedings of the 13th IFAC Symposium on System Identification, August 2003 (inproceedings)

Abstract
Nonparametric Gaussian Process models, a Bayesian statistics approach, are used to implement a nonlinear adaptive control law. Predictions, including propagation of the state uncertainty are made over a k-step horizon. The expected value of a quadratic cost function is minimised, over this prediction horizon, without ignoring the variance of the model predictions. The general method and its main features are illustrated on a simulation example.

ei

PDF [BibTex]

PDF [BibTex]


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On the Representation, Learning and Transfer of Spatio-Temporal Movement Characteristics

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

In Humanoids Proceedings, pages: 0-0, Humanoids Proceedings, July 2003, electronical version (inproceedings)

Abstract
In this paper we present a learning-based approach for the modelling of complex movement sequences. Based on the method of Spatio-Temporal Morphable Models (STMMS. We derive a hierarchical algorithm that, in a first step, identifies automatically movement elements in movement sequences based on a coarse spatio-temporal description, and in a second step models these movement primitives by approximation through linear combinations of learned example movement trajectories. We describe the different steps of the algorithm and show how it can be applied for modelling and synthesis of complex sequences of human movements that contain movement elements with variable style. The proposed method is demonstrated on different applications of movement representation relevant for imitation learning of movement styles in humanoid robotics.

ei

PDF [BibTex]

PDF [BibTex]


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Statistical Learning Theory, Capacity and Complexity

Schölkopf, B.

Complexity, 8(4):87-94, July 2003 (article)

Abstract
We give an exposition of the ideas of statistical learning theory, followed by a discussion of how a reinterpretation of the insights of learning theory could potentially also benefit our understanding of a certain notion of complexity.

ei

Web DOI [BibTex]


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Dealing with large Diagonals in Kernel Matrices

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

Annals of the Institute of Statistical Mathematics, 55(2):391-408, June 2003 (article)

Abstract
In kernel methods, all the information about the training data is contained in the Gram matrix. If this matrix has large diagonal values, which arises for many types of kernels, then kernel methods do not perform well: We propose and test several methods for dealing with this problem by reducing the dynamic range of the matrix while preserving the positive definiteness of the Hessian of the quadratic programming problem that one has to solve when training a Support Vector Machine, which is a common kernel approach for pattern recognition.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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The em Algorithm for Kernel Matrix Completion with Auxiliary Data

Tsuda, K., Akaho, S., Asai, K.

Journal of Machine Learning Research, 4, pages: 67-81, May 2003 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Constructing Descriptive and Discriminative Non-linear Features: Rayleigh Coefficients in Kernel Feature Spaces

Mika, S., Rätsch, G., Weston, J., Schölkopf, B., Smola, A., Müller, K.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 25(5):623-628, May 2003 (article)

Abstract
We incorporate prior knowledge to construct nonlinear algorithms for invariant feature extraction and discrimination. Employing a unified framework in terms of a nonlinearized variant of the Rayleigh coefficient, we propose nonlinear generalizations of Fisher‘s discriminant and oriented PCA using support vector kernel functions. Extensive simulations show the utility of our approach.

ei

DOI [BibTex]

DOI [BibTex]


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A case based comparison of identification with neural network and Gaussian process models.

Kocijan, J., Banko, B., Likar, B., Girard, A., Murray-Smith, R., Rasmussen, CE.

In Proceedings of the International Conference on Intelligent Control Systems and Signal Processing ICONS 2003, 1, pages: 137-142, (Editors: Ruano, E.A.), Proceedings of the International Conference on Intelligent Control Systems and Signal Processing ICONS, April 2003 (inproceedings)

Abstract
In this paper an alternative approach to black-box identification of non-linear dynamic systems is compared with the more established approach of using artificial neural networks. The Gaussian process prior approach is a representative of non-parametric modelling approaches. It was compared on a pH process modelling case study. The purpose of modelling was to use the model for control design. The comparison revealed that even though Gaussian process models can be effectively used for modelling dynamic systems caution has to be axercised when signals are selected.

ei

PDF [BibTex]

PDF [BibTex]


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On-Line One-Class Support Vector Machines. An Application to Signal Segmentation

Gretton, A., Desobry, ..

In IEEE ICASSP Vol. 2, pages: 709-712, IEEE ICASSP, April 2003 (inproceedings)

Abstract
In this paper, we describe an efficient algorithm to sequentially update a density support estimate obtained using one-class support vector machines. The solution provided is an exact solution, which proves to be far more computationally attractive than a batch approach. This deterministic technique is applied to the problem of audio signal segmentation, with simulations demonstrating the computational performance gain on toy data sets, and the accuracy of the segmentation on audio signals.

ei

PostScript [BibTex]

PostScript [BibTex]


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The Kernel Mutual Information

Gretton, A., Herbrich, R., Smola, A.

In IEEE ICASSP Vol. 4, pages: 880-883, IEEE ICASSP, April 2003 (inproceedings)

Abstract
We introduce a new contrast function, the kernel mutual information (KMI), to measure the degree of independence of continuous random variables. This contrast function provides an approximate upper bound on the mutual information, as measured near independence, and is based on a kernel density estimate of the mutual information between a discretised approximation of the continuous random variables. We show that Bach and Jordan‘s kernel generalised variance (KGV) is also an upper bound on the same kernel density estimate, but is looser. Finally, we suggest that the addition of a regularising term in the KGV causes it to approach the KMI, which motivates the introduction of this regularisation.

ei

PostScript [BibTex]

PostScript [BibTex]


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Tractable Inference for Probabilistic Data Models

Csato, L., Opper, M., Winther, O.

Complexity, 8(4):64-68, April 2003 (article)

Abstract
We present an approximation technique for probabilistic data models with a large number of hidden variables, based on ideas from statistical physics. We give examples for two nontrivial applications. © 2003 Wiley Periodicals, Inc.

ei

PDF GZIP Web [BibTex]

PDF GZIP Web [BibTex]


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Feature selection and transduction for prediction of molecular bioactivity for drug design

Weston, J., Perez-Cruz, F., Bousquet, O., Chapelle, O., Elisseeff, A., Schölkopf, B.

Bioinformatics, 19(6):764-771, April 2003 (article)

Abstract
Motivation: In drug discovery a key task is to identify characteristics that separate active (binding) compounds from inactive (non-binding) ones. An automated prediction system can help reduce resources necessary to carry out this task. Results: Two methods for prediction of molecular bioactivity for drug design are introduced and shown to perform well in a data set previously studied as part of the KDD (Knowledge Discovery and Data Mining) Cup 2001. The data is characterized by very few positive examples, a very large number of features (describing three-dimensional properties of the molecules) and rather different distributions between training and test data. Two techniques are introduced specifically to tackle these problems: a feature selection method for unbalanced data and a classifier which adapts to the distribution of the the unlabeled test data (a so-called transductive method). We show both techniques improve identification performance and in conjunction provide an improvement over using only one of the techniques. Our results suggest the importance of taking into account the characteristics in this data which may also be relevant in other problems of a similar type.

ei

Web [BibTex]


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Use of the Zero-Norm with Linear Models and Kernel Methods

Weston, J., Elisseeff, A., Schölkopf, B., Tipping, M.

Journal of Machine Learning Research, 3, pages: 1439-1461, March 2003 (article)

Abstract
We explore the use of the so-called zero-norm of the parameters of linear models in learning. Minimization of such a quantity has many uses in a machine learning context: for variable or feature selection, minimizing training error and ensuring sparsity in solutions. We derive a simple but practical method for achieving these goals and discuss its relationship to existing techniques of minimizing the zero-norm. The method boils down to implementing a simple modification of vanilla SVM, namely via an iterative multiplicative rescaling of the training data. Applications we investigate which aid our discussion include variable and feature selection on biological microarray data, and multicategory classification.

ei

PDF PostScript PDF [BibTex]

PDF PostScript PDF [BibTex]


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Hierarchical Spatio-Temporal Morphable Models for Representation of complex movements for Imitation Learning

Ilg, W., Bakir, GH., Franz, MO., Giese, M.

In 11th International Conference on Advanced Robotics, (2):453-458, (Editors: Nunes, U., A. de Almeida, A. Bejczy, K. Kosuge and J.A.T. Machado), 11th International Conference on Advanced Robotics, January 2003 (inproceedings)

ei

PDF [BibTex]

PDF [BibTex]


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An Introduction to Variable and Feature Selection.

Guyon, I., Elisseeff, A.

Journal of Machine Learning, 3, pages: 1157-1182, 2003 (article)

ei

[BibTex]

[BibTex]


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Feature Selection for Support Vector Machines by Means of Genetic Algorithms

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

In 15th IEEE International Conference on Tools with AI, pages: 142-148, 15th IEEE International Conference on Tools with AI, 2003 (inproceedings)

ei

[BibTex]

[BibTex]


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Propagation of Uncertainty in Bayesian Kernel Models - Application to Multiple-Step Ahead Forecasting

Quiñonero-Candela, J., Girard, A., Larsen, J., Rasmussen, CE.

In IEEE International Conference on Acoustics, Speech and Signal Processing, 2, pages: 701-704, IEEE International Conference on Acoustics, Speech and Signal Processing, 2003 (inproceedings)

Abstract
The object of Bayesian modelling is the predictive distribution, which in a forecasting scenario enables improved estimates of forecasted values and their uncertainties. In this paper we focus on reliably estimating the predictive mean and variance of forecasted values using Bayesian kernel based models such as the Gaussian Process and the Relevance Vector Machine. We derive novel analytic expressions for the predictive mean and variance for Gaussian kernel shapes under the assumption of a Gaussian input distribution in the static case, and of a recursive Gaussian predictive density in iterative forecasting. The capability of the method is demonstrated for forecasting of time-series and compared to approximate methods.

ei

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Unsupervised Clustering of Images using their Joint Segmentation

Seldin, Y., Starik, S., Werman, M.

In The 3rd International Workshop on Statistical and Computational Theories of Vision (SCTV 2003), pages: 1-24, 3rd International Workshop on Statistical and Computational Theories of Vision (SCTV), 2003 (inproceedings)

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Kernel Methods and Their Applications to Signal Processing

Bousquet, O., Perez-Cruz, F.

In Proceedings. (ICASSP ‘03), Special Session on Kernel Methods, pages: 860 , ICASSP, 2003 (inproceedings)

Abstract
Recently introduced in Machine Learning, the notion of kernels has drawn a lot of interest as it allows to obtain non-linear algorithms from linear ones in a simple and elegant manner. This, in conjunction with the introduction of new linear classification methods such as the Support Vector Machines has produced significant progress. The successes of such algorithms is now spreading as they are applied to more and more domains. Many Signal Processing problems, by their non-linear and high-dimensional nature may benefit from such techniques. We give an overview of kernel methods and their recent applications.

ei

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Predictive control with Gaussian process models

Kocijan, J., Murray-Smith, R., Rasmussen, CE., Likar, B.

In Proceedings of IEEE Region 8 Eurocon 2003: Computer as a Tool, pages: 352-356, (Editors: Zajc, B. and M. Tkal), Proceedings of IEEE Region 8 Eurocon: Computer as a Tool, 2003 (inproceedings)

Abstract
This paper describes model-based predictive control based on Gaussian processes.Gaussian process models provide a probabilistic non-parametric modelling approach for black-box identification of non-linear dynamic systems. It offers more insight in variance of obtained model response, as well as fewer parameters to determine than other models. The Gaussian processes can highlight areas of the input space where prediction quality is poor, due to the lack of data or its complexity, by indicating the higher variance around the predicted mean. This property is used in predictive control, where optimisation of control signal takes the variance information into account. The predictive control principle is demonstrated on a simulated example of nonlinear system.

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PDF PostScript [BibTex]

PDF PostScript [BibTex]


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New Approaches to Statistical Learning Theory

Bousquet, O.

Annals of the Institute of Statistical Mathematics, 55(2):371-389, 2003 (article)

Abstract
We present new tools from probability theory that can be applied to the analysis of learning algorithms. These tools allow to derive new bounds on the generalization performance of learning algorithms and to propose alternative measures of the complexity of the learning task, which in turn can be used to derive new learning algorithms.

ei

PostScript [BibTex]

PostScript [BibTex]


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Distance-based classification with Lipschitz functions

von Luxburg, U., Bousquet, O.

In Learning Theory and Kernel Machines, Proceedings of the 16th Annual Conference on Computational Learning Theory, pages: 314-328, (Editors: Schölkopf, B. and M.K. Warmuth), Learning Theory and Kernel Machines, Proceedings of the 16th Annual Conference on Computational Learning Theory, 2003 (inproceedings)

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. Our approach leads to a general large margin algorithm for classification in metric spaces. To analyze this algorithm, we first prove a representer theorem. It states that there exists a solution which can be expressed as linear combination of distances to sets of training points. Then we analyze the Rademacher complexity of some Lipschitz function classes. The generality of the Lipschitz approach can be seen from the fact that several well-known algorithms are special cases of the Lipschitz algorithm, among them the support vector machine, the linear programming machine, and the 1-nearest neighbor classifier.

ei

PDF PostScript [BibTex]

PDF PostScript [BibTex]