Header logo is


2005


no image
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

PDF PostScript PDF [BibTex]

2005


PDF PostScript PDF [BibTex]


no image
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

PDF [BibTex]

PDF [BibTex]


Thumb xl ivc05
Representing cyclic human motion using functional analysis

Ormoneit, D., Black, M. J., Hastie, T., Kjellström, H.

Image and Vision Computing, 23(14):1264-1276, December 2005 (article)

Abstract
We present a robust automatic method for modeling cyclic 3D human motion such as walking using motion-capture data. The pose of the body is represented by a time-series of joint angles which are automatically segmented into a sequence of motion cycles. The mean and the principal components of these cycles are computed using a new algorithm that enforces smooth transitions between the cycles by operating in the Fourier domain. Key to this method is its ability to automatically deal with noise and missing data. A learned walking model is then exploited for Bayesian tracking of 3D human motion.

ps

pdf pdf from publisher DOI [BibTex]

pdf pdf from publisher DOI [BibTex]


no image
Popper, Falsification and the VC-dimension

Corfield, D., Schölkopf, B., Vapnik, V.

(145), Max Planck Institute for Biological Cybernetics, November 2005 (techreport)

ei

PDF [BibTex]

PDF [BibTex]


no image
Kernel methods for dependence testing in LFP-MUA

Gretton, A., Belitski, A., Murayama, Y., Schölkopf, B., Logothetis, N.

35(689.17), 35th Annual Meeting of the Society for Neuroscience (Neuroscience), November 2005 (poster)

Abstract
A fundamental problem in neuroscience is determining whether or not particular neural signals are dependent. The correlation is the most straightforward basis for such tests, but considerable work also focuses on the mutual information (MI), which is capable of revealing dependence of higher orders that the correlation cannot detect. That said, there are other measures of dependence that share with the MI an ability to detect dependence of any order, but which can be easier to compute in practice. We focus in particular on tests based on the functional covariance, which derive from work originally accomplished in 1959 by Renyi. Conceptually, our dependence tests work by computing the covariance between (infinite dimensional) vectors of nonlinear mappings of the observations being tested, and then determining whether this covariance is zero - we call this measure the constrained covariance (COCO). When these vectors are members of universal reproducing kernel Hilbert spaces, we can prove this covariance to be zero only when the variables being tested are independent. The greatest advantage of these tests, compared with the mutual information, is their simplicity – when comparing two signals, we need only take the largest eigenvalue (or the trace) of a product of two matrices of nonlinearities, where these matrices are generally much smaller than the number of observations (and are very simple to construct). We compare the mutual information, the COCO, and the correlation in the context of finding changes in dependence between the LFP and MUA signals in the primary visual cortex of the anaesthetized macaque, during the presentation of dynamic natural stimuli. We demonstrate that the MI and COCO reveal dependence which is not detected by the correlation alone (which we prove by artificially removing all correlation between the signals, and then testing their dependence with COCO and the MI); and that COCO and the MI give results consistent with each other on our data.

ei

Web [BibTex]

Web [BibTex]


no image
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

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


no image
Selective integration of multiple biological data for supervised network inference

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

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

ei

PDF [BibTex]

PDF [BibTex]


no image
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

PDF PDF [BibTex]

PDF PDF [BibTex]


no image
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

PDF [BibTex]

PDF [BibTex]


no image
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

PDF [BibTex]

PDF [BibTex]


no image
Rapid animal detection in natural scenes: Critical features are local

Wichmann, F., Rosas, P., Gegenfurtner, K.

Journal of Vision, 5(8):376, Fifth Annual Meeting of the Vision Sciences Society (VSS), September 2005 (poster)

Abstract
Thorpe et al (Nature 381, 1996) first showed how rapidly human observers are able to classify natural images as to whether they contain an animal or not. Whilst the basic result has been replicated using different response paradigms (yes-no versus forced-choice), modalities (eye movements versus button presses) as well as while measuring neurophysiological correlates (ERPs), it is still unclear which image features support this rapid categorisation. Recently Torralba and Oliva (Network: Computation in Neural Systems, 14, 2003) suggested that simple global image statistics can be used to predict seemingly complex decisions about the absence and/or presence of objects in natural scences. They show that the information contained in a small number (N=16) of spectral principal components (SPC)—principal component analysis (PCA) applied to the normalised power spectra of the images—is sufficient to achieve approximately 80% correct animal detection in natural scenes. Our goal was to test whether human observers make use of the power spectrum when rapidly classifying natural scenes. We measured our subjects' ability to detect animals in natural scenes as a function of presentation time (13 to 167 msec); images were immediately followed by a noise mask. In one condition we used the original images, in the other images whose power spectra were equalised (each power spectrum was set to the mean power spectrum over our ensemble of 1476 images). Thresholds for 75% correct animal detection were in the region of 20–30 msec for all observers, independent of the power spectrum of the images: this result makes it very unlikely that human observers make use of the global power spectrum. Taken together with the results of Gegenfurtner, Braun & Wichmann (Journal of Vision [abstract], 2003), showing the robustness of animal detection to global phase noise, we conclude that humans use local features, like edges and contours, in rapid animal detection.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Correlation of EEG spectral entropy with regional cerebral blood flow during sevoflurane and propofol anaesthesia

Maksimow, A., Kaisti, K., Aalto, S., Mäenpää, M., Jääskeläinen, S., Hinkka, S., Martens, SMM., Särkelä, M., Viertiö-Oja, H., Scheinin, H.

Anaesthesia, 60(9):862-869, September 2005 (article)

Abstract
ENTROPY index monitoring, based on spectral entropy of the electroencephalogram, is a promising new method to measure the depth of anaesthesia. We examined the association between spectral entropy and regional cerebral blood flow in healthy subjects anaesthetised with 2%, 3% and 4% end-expiratory concentrations of sevoflurane and 7.6, 12.5 and 19.0 microg.ml(-1) plasma drug concentrations of propofol. Spectral entropy from the frequency band 0.8-32 Hz was calculated and cerebral blood flow assessed using positron emission tomography and [(15)O]-labelled water at baseline and at each anaesthesia level. Both drugs induced significant reductions in spectral entropy and cortical and global cerebral blood flow. Midfrontal-central spectral entropy was associated with individual frontal and whole brain blood flow values across all conditions, suggesting that this novel measure of anaesthetic depth can depict global changes in neuronal activity induced by the drugs. The cortical areas of the most significant associations were remarkably similar for both drugs.

ei

DOI [BibTex]

DOI [BibTex]


no image
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

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Analyzing microarray data using quantitative association rules

Georgii, E., Richter, L., Rückert, U., Kramer, S.

Bioinformatics, 21(Suppl. 2):123-129, September 2005 (article)

Abstract
Motivation: We tackle the problem of finding regularities in microarray data. Various data mining tools, such as clustering, classification, Bayesian networks and association rules, have been applied so far to gain insight into gene-expression data. Association rule mining techniques used so far work on discretizations of the data and cannot account for cumulative effects. In this paper, we investigate the use of quantitative association rules that can operate directly on numeric data and represent cumulative effects of variables. Technically speaking, this type of quantitative association rules based on half-spaces can find non-axis-parallel regularities. Results: We performed a variety of experiments testing the utility of quantitative association rules for microarray data. First of all, the results should be statistically significant and robust against fluctuations in the data. Next, the approach should be scalable in the number of variables, which is important for such high-dimensional data. Finally, the rules should make sense biologically and be sufficiently different from rules found in regular association rule mining working with discretizations. In all of these dimensions, the proposed approach performed satisfactorily. Therefore, quantitative association rules based on half-spaces should be considered as a tool for the analysis of microarray gene-expression data.

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
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]

Web DOI [BibTex]


no image
Learning an Interest Operator from Eye Movements

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

International Workshop on Bioinspired Information Processing (BIP 2005), 2005, pages: 1, September 2005 (poster)

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
Large Margin Methods for Structured and Interdependent Output Variables

Tsochantaridis, I., Joachims, T., Hofmann, T., Altun, Y.

Journal of Machine Learning Research, 6, pages: 1453-1484, September 2005 (article)

Abstract
Learning general functional dependencies between arbitrary input and output spaces is one of the key challenges in computational intelligence. While recent progress in machine learning has mainly focused on designing flexible and powerful input representations, this paper addresses the complementary issue of designing classification algorithms that can deal with more complex outputs, such as trees, sequences, or sets. More generally, we consider problems involving multiple dependent output variables, structured output spaces, and classification problems with class attributes. In order to accomplish this, we propose to appropriately generalize the well-known notion of a separation margin and derive a corresponding maximum-margin formulation. While this leads to a quadratic program with a potentially prohibitive, i.e. exponential, number of constraints, we present a cutting plane algorithm that solves the optimization problem in polynomial time for a large class of problems. The proposed method has important applications in areas such as computational biology, natural language processing, information retrieval/extraction, and optical character recognition. Experiments from various domains involving different types of output spaces emphasize the breadth and generality of our approach.

ei

PDF [BibTex]

PDF [BibTex]


no image
Classification of natural scenes using global image statistics

Drewes, J., Wichmann, F., Gegenfurtner, K.

Journal of Vision, 5(8):602, Fifth Annual Meeting of the Vision Sciences Society (VSS), September 2005 (poster)

Abstract
The algorithmic classification of complex, natural scenes is generally considered a difficult task due to the large amount of information conveyed by natural images. Work by Simon Thorpe and colleagues showed that humans are capable of detecting animals within novel natural scenes with remarkable speed and accuracy. This suggests that the relevant information for classification can be extracted at comparatively limited computational cost. One hypothesis is that global image statistics such as the amplitude spectrum could underly fast image classification (Johnson & Olshausen, Journal of Vision, 2003; Torralba & Oliva, Network: Comput. Neural Syst., 2003). We used linear discriminant analysis to classify a set of 11.000 images into animal and non-animal images. After applying a DFT to the image, we put the Fourier spectrum into bins (8 orientations with 6 frequency bands each). Using all bins, classification performance on the Fourier spectrum reached 70%. However, performance was similar (67%) when only the high spatial frequency information was used and decreased steadily at lower spatial frequencies, reaching a minimum (50%) for the low spatial frequency information. Similar results were obtained when all bins were used on spatially filtered images. A detailed analysis of the classification weights showed that a relatively high level of performance (67%) could also be obtained when only 2 bins were used, namely the vertical and horizontal orientation at the highest spatial frequency band. Our results show that in the absence of sophisticated machine learning techniques, animal detection in natural scenes is limited to rather modest levels of performance, far below those of human observers. If limiting oneself to global image statistics such as the DFT then mostly information at the highest spatial frequencies is useful for the task. This is analogous to the results obtained with human observers on filtered images (Kirchner et al, VSS 2004).

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
Contact Location Display for Haptic Perception of Curvature and Object Motion

Provancher, W. R., Cutkosky, M. R., Kuchenbecker, K. J., Niemeyer, G.

International Journal of Robotics Research, 24(9):691-702, sep 2005 (article)

hi

[BibTex]

[BibTex]


no image
Gene Expression Profiling of Serum- and Interleukin-1beta-Stimulated Primary Human Adult Articular Chondrocytes - A Molecular Analysis Based on Chondrocytes Isolated from One Donor

Aigner, T., McKenna, L., Zien, A., Fan, Z., Gebhard, P., Zimmer, R.

Cytokine, 31(3):227-240, August 2005 (article)

Abstract
In order to understand the cellular disease mechanisms of osteoarthritic cartilage degeneration it is of primary importance to understand both the anabolic and the catabolic processes going on in parallel in the diseased tissue. In this study, we have applied cDNA-array technology (Clontech) to study gene expression patterns of primary human normal adult articular chondrocytes isolated from one donor cultured under anabolic (serum) and catabolic (IL-1beta) conditions. Significant differences between the different in vitro cultures tested were detected. Overall, serum and IL-1beta significantly altered gene expression levels of 102 and 79 genes, respectively. IL-1beta stimulated the matrix metalloproteinases-1, -3, and -13 as well as members of its intracellular signaling cascade, whereas serum increased the expression of many cartilage matrix genes. Comparative gene expression analysis with previously published in vivo data (normal and osteoarthritic cartilage) showed significant differences of all in vitro s timulations compared to the changes detected in osteoarthritic cartilage in vivo. This investigation allowed us to characterize gene expression profiles of two classical anabolic and catabolic stimuli of human adult articular chondrocytes in vitro. No in vitro model appeared to be adequate to study overall gene expression alterations in osteoarthritic cartilage. Serum stimulated in vitro cultures largely reflected the results that were only consistent with the anabolic activation seen in osteoarthritic chondrocytes. In contrast, IL-1beta did not appear to be a good model for mimicking catabolic gene alterations in degenerating chondrocytes.

ei

Web [BibTex]


no image
A Combinatorial View of Graph Laplacians

Huang, J.

(144), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, August 2005 (techreport)

Abstract
Discussions about different graph Laplacian, mainly normalized and unnormalized versions of graph Laplacian, have been ardent with respect to various methods in clustering and graph based semi-supervised learning. Previous research on graph Laplacians investigated their convergence properties to Laplacian operators on continuous manifolds. There is still no strong proof on convergence for the normalized Laplacian. In this paper, we analyze different variants of graph Laplacians directly from the ways solving the original graph partitioning problem. The graph partitioning problem is a well-known combinatorial NP hard optimization problem. The spectral solutions provide evidence that normalized Laplacian encodes more reasonable considerations for graph partitioning. We also provide some examples to show their differences.

ei

[BibTex]

[BibTex]


no image
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]

Web [BibTex]


no image
Beyond Pairwise Classification and Clustering Using Hypergraphs

Zhou, D., Huang, J., Schölkopf, B.

(143), Max Planck Institute for Biological Cybernetics, August 2005 (techreport)

Abstract
In many applications, relationships among objects of interest are more complex than pairwise. Simply approximating complex relationships as pairwise ones can lead to loss of information. An alternative for these applications is to analyze complex relationships among data directly, without the need to first represent the complex relationships into pairwise ones. A natural way to describe complex relationships is to use hypergraphs. A hypergraph is a graph in which edges can connect more than two vertices. Thus we consider learning from a hypergraph, and develop a general framework which is applicable to classification and clustering for complex relational data. We have applied our framework to real-world web classification problems and obtained encouraging results.

ei

PDF [BibTex]

PDF [BibTex]


no image
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

PDF PostScript Web [BibTex]

PDF PostScript Web [BibTex]


no image
Inlier-based ICA with an application to superimposed images

Meinecke, F., Harmeling, S., Müller, K.

International Journal of Imaging Systems and Technology, 15(1):48-55, July 2005 (article)

Abstract
This paper proposes a new independent component analysis (ICA) method which is able to unmix overcomplete mixtures of sparce or structured signals like speech, music or images. Furthermore, the method is designed to be robust against outliers, which is a favorable feature for ICA algorithms since most of them are extremely sensitive to outliers. Our approach is based on a simple outlier index. However, instead of robustifying an existing algorithm by some outlier rejection technique we show how this index can be used directly to solve the ICA problem for super-Gaussian sources. The resulting inlier-based ICA (IBICA) is outlier-robust by construction and can be used for standard ICA as well as for overcomplete ICA (i.e. more source signals than observed signals).

ei

Web DOI [BibTex]

Web DOI [BibTex]


no image
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

PDF [BibTex]

PDF [BibTex]


no image
Comparative evaluation of Independent Components Analysis algorithms for isolating target-relevant information in brain-signal classification

Hill, N., Schröder, M., Lal, T., Schölkopf, B.

Brain-Computer Interface Technology, 3, pages: 95, June 2005 (poster)

ei

PDF [BibTex]


no image
Generalized Nonnegative Matrix Approximations using Bregman Divergences

Sra, S., Dhillon, I.

Univ. of Texas at Austin, June 2005 (techreport)

ei

[BibTex]

[BibTex]


no image
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

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
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

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
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

PDF [BibTex]

PDF [BibTex]


no image
Measuring Statistical Dependence with Hilbert-Schmidt Norms

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

(140), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, June 2005 (techreport)

Abstract
We propose an independence criterion based on the eigenspectrum of covariance operators in reproducing kernel Hilbert spaces (RKHSs), consisting of an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator (we term this a Hilbert-Schmidt Independence Criterion, or HSIC). This approach has several advantages, compared with previous kernel-based independence criteria. First, the empirical estimate is simpler than any other kernel dependence test, and requires no user-defined regularisation. Second, there is a clearly defined population quantity which the empirical estimate approaches in the large sample limit, with exponential convergence guaranteed between the two: this ensures that independence tests based on HSIC do not suffer from slow learning rates. Finally, we show in the context of independent component analysis (ICA) that the performance of HSIC is competitive with that of previously published kernel-based criteria, and of other recently published ICA methods.

ei

PDF [BibTex]

PDF [BibTex]


no image
Protein function prediction via graph kernels

Borgwardt, KM., Ong, CS., Schönauer, S., Vishwanathan, ., Smola, AJ., Kriegel, H-P.

Bioinformatics, 21(Suppl. 1: ISMB 2005 Proceedings):i47-i56, June 2005 (article)

Abstract
Motivation: Computational approaches to protein function prediction infer protein function by finding proteins with similar sequence, structure, surface clefts, chemical properties, amino acid motifs, interaction partners or phylogenetic profiles. We present a new approach that combines sequential, structural and chemical information into one graph model of proteins. We predict functional class membership of enzymes and non-enzymes using graph kernels and support vector machine classification on these protein graphs. Results: Our graph model, derivable from protein sequence and structure only, is competitive with vector models that require additional protein information, such as the size of surface pockets. If we include this extra information into our graph model, our classifier yields significantly higher accuracy levels than the vector models. Hyperkernels allow us to select and to optimally combine the most relevant node attributes in our protein graphs. We have laid the foundation for a protein function prediction system that integrates protein information from various sources efficiently and effectively.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


no image
Consistency of Kernel Canonical Correlation Analysis

Fukumizu, K., Bach, F., Gretton, A.

(942), Institute of Statistical Mathematics, 4-6-7 Minami-azabu, Minato-ku, Tokyo 106-8569 Japan, June 2005 (techreport)

ei

PDF [BibTex]

PDF [BibTex]


no image
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

PDF Web [BibTex]

PDF Web [BibTex]


no image
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

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


no image
Classification of natural scenes using global image statistics

Drewes, J., Wichmann, F., Gegenfurtner, K.

47, pages: 88, 47. Tagung Experimentell Arbeitender Psychologen, April 2005 (poster)

ei

[BibTex]

[BibTex]


no image
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

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Morphological characterization of molecular complexes present in the synaptic cleft

Lucic, V., Yang, T., Schweikert, G., Förster, F., Baumeister, W.

Structure, 13(3):423-434, March 2005 (article)

Abstract
We obtained tomograms of isolated mammalian excitatory synapses by cryo-electron tomography. This method allows the investigation of biological material in the frozen-hydrated state, without staining, and can therefore provide reliable structural information at the molecular level. We developed an automated procedure for the segmentation of molecular complexes present in the synaptic cleft based on thresholding and connectivity, and calculated several morphological characteristics of these complexes. Extensive lateral connections along the synaptic cleft are shown to form a highly connected structure with a complex topology. Our results are essentially parameter-free, i.e., they do not depend on the choice of certain parameter values (such as threshold). In addition, the results are not sensitive to noise; the same conclusions can be drawn from the analysis of both nondenoised and denoised tomograms.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
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

PDF DOI [BibTex]

PDF DOI [BibTex]


no image
Classification of Natural Scenes using Global Image Statistics

Drewes, J., Wichmann, F., Gegenfurtner, K.

8, pages: 88, 8th T{\"u}bingen Perception Conference (TWK), February 2005 (poster)

Abstract
The algorithmic classification of complex, natural scenes is generally considered a difficult task due to the large amount of information conveyed by natural images. Work by Simon Thorpe and colleagues showed that humans are capable of detecting animals within novel natural scenes with remarkable speed and accuracy. This suggests that the relevant information for classification can be extracted at comparatively limited computational cost. One hypothesis is that global image statistics such as the amplitude spectrum could underly fast image classification (Johnson & Olshausen, Journal of Vision, 2003; Torralba & Oliva, Network: Comput. Neural Syst., 2003). We used linear discriminant analysis to classify a set of 11.000 images into animal and nonanimal images. After applying a DFT to the image, we put the Fourier spectrum of each image into 48 bins (8 orientations with 6 frequency bands). Using all of these bins, classification performance on the Fourier spectrum reached 70%. In an iterative procedure, we then removed the bins whose absence caused the smallest damage to the classification performance (one bin per iteration). Notably, performance stayed at about 70% until less then 6 bins were left. A detailed analysis of the classification weights showed that a comparatively high level of performance (67%) could also be obtained when only 2 bins were used, namely the vertical orientations at the highest spatial frequency band. When using only a single frequency band (8 bins) we found that 67% classification performance could be reached when only the high spatial frequency information was used, which decreased steadily at lower spatial frequencies, reaching a minimum (50%) for the low spatial frequency information. Similar results were obtained when all bins were used on spatially pre-filtered images. Our results show that in the absence of sophisticated machine learning techniques, animal detection in natural scenes is limited to rather modest levels of performance, far below those of human observers. If limiting oneself to global image statistics such as the DFT then mostly information at the highest spatial frequencies is useful for the task. This is analogous to the results obtained with human observers on filtered images (Kirchner et al, VSS 2004).

ei

Web [BibTex]

Web [BibTex]


no image
Efficient Adaptive Sampling of the Psychometric Function by Maximizing Information Gain

Tanner, T., Hill, N., Rasmussen, C., Wichmann, F.

8, pages: 109, (Editors: Bülthoff, H. H., H. A. Mallot, R. Ulrich and F. A. Wichmann), 8th T{\"u}bingen Perception Conference (TWK), February 2005 (poster)

Abstract
A psychometric function can be described by its shape and four parameters: position or threshold, slope or width, false alarm rate or chance level, and miss or lapse rate. Depending on the parameters of interest some points on the psychometric function may be more informative than others. Adaptive methods attempt to place trials on the most informative points based on the data collected in previous trials. We introduce a new adaptive bayesian psychometric method which collects data for any set of parameters with high efficency. It places trials by minimizing the expected entropy [1] of the posterior pdf over a set of possible stimuli. In contrast to most other adaptive methods it is neither limited to threshold measurement nor to forced-choice designs. Nuisance parameters can be included in the estimation and lead to less biased estimates. The method supports block designs which do not harm the performance when a sufficient number of trials are performed. Block designs are useful for control of response bias and short term performance shifts such as adaptation. We present the results of evaluations of the method by computer simulations and experiments with human observers. In the simulations we investigated the role of parametric assumptions, the quality of different point estimates, the effect of dynamic termination criteria and many other settings. [1] Kontsevich, L.L. and Tyler, C.W. (1999): Bayesian adaptive estimation of psychometric slope and threshold. Vis. Res. 39 (16), 2729-2737.

ei

Web [BibTex]

Web [BibTex]


no image
Automatic Classification of Plankton from Digital Images

Sieracki, M., Riseman, E., Balch, W., Benfield, M., Hanson, A., Pilskaln, C., Schultz, H., Sieracki, C., Utgoff, P., Blaschko, M., Holness, G., Mattar, M., Lisin, D., Tupper, B.

ASLO Aquatic Sciences Meeting, 1, pages: 1, February 2005 (poster)

ei

[BibTex]

[BibTex]


no image
Bayesian Inference for Psychometric Functions

Kuss, M., Jäkel, F., Wichmann, F.

8, pages: 106, (Editors: Bülthoff, H. H., H. A. Mallot, R. Ulrich and F. A. Wichmann), 8th T{\"u}bingen Perception Conference (TWK), February 2005 (poster)

Abstract
In psychophysical studies of perception the psychometric function is used to model the relation between the physical stimulus intensity and the observer's ability to detect or discriminate between stimuli of different intensities. We propose the use of Bayesian inference to extract the information contained in experimental data to learn about the parameters of psychometric functions. Since Bayesian inference cannot be performed analytically we use a Markov chain Monte Carlo method to generate samples from the posterior distribution over parameters. These samples can be used to estimate Bayesian confidence intervals and other characteristics of the posterior distribution. We compare our approach with traditional methods based on maximum-likelihood parameter estimation combined with parametric bootstrap techniques for confidence interval estimation. Experiments indicate that Bayesian inference methods are superior to bootstrap-based methods and are thus the method of choice for estimating the psychometric function and its confidence-intervals.

ei

Web [BibTex]

Web [BibTex]


no image
Composite adaptive control with locally weighted statistical learning

Nakanishi, J., Farrell, J. A., Schaal, S.

Neural Networks, 18(1):71-90, January 2005, clmc (article)

Abstract
This paper introduces a provably stable learning adaptive control framework with statistical learning. The proposed algorithm employs nonlinear function approximation with automatic growth of the learning network according to the nonlinearities and the working domain of the control system. The unknown function in the dynamical system is approximated by piecewise linear models using a nonparametric regression technique. Local models are allocated as necessary and their parameters are optimized on-line. Inspired by composite adaptive control methods, the proposed learning adaptive control algorithm uses both the tracking error and the estimation error to update the parameters. We first discuss statistical learning of nonlinear functions, and motivate our choice of the locally weighted learning framework. Second, we begin with a class of first order SISO systems for theoretical development of our learning adaptive control framework, and present a stability proof including a parameter projection method that is needed to avoid potential singularities during adaptation. Then, we generalize our adaptive controller to higher order SISO systems, and discuss further extension to MIMO problems. Finally, we evaluate our theoretical control framework in numerical simulations to illustrate the effectiveness of the proposed learning adaptive controller for rapid convergence and high accuracy of control.

am

link (url) [BibTex]

link (url) [BibTex]


no image
Semi-supervised protein classification using cluster kernels

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

Bioinformatics, 21(15):3241-3247, 2005 (article)

ei

[BibTex]

[BibTex]


no image
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

PDF PDF [BibTex]

PDF PDF [BibTex]


no image
Approximate Inference for Robust Gaussian Process Regression

Kuss, M., Pfingsten, T., Csato, L., Rasmussen, C.

(136), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, 2005 (techreport)

Abstract
Gaussian process (GP) priors have been successfully used in non-parametric Bayesian regression and classification models. Inference can be performed analytically only for the regression model with Gaussian noise. For all other likelihood models inference is intractable and various approximation techniques have been proposed. In recent years expectation-propagation (EP) has been developed as a general method for approximate inference. This article provides a general summary of how expectation-propagation can be used for approximate inference in Gaussian process models. Furthermore we present a case study describing its implementation for a new robust variant of Gaussian process regression. To gain further insights into the quality of the EP approximation we present experiments in which we compare to results obtained by Markov chain Monte Carlo (MCMC) sampling.

ei

PDF [BibTex]

PDF [BibTex]


no image
Global image statistics of natural scenes

Drewes, J., Wichmann, F., Gegenfurtner, K.

Bioinspired Information Processing, 08, pages: 1, 2005 (poster)

ei

[BibTex]

[BibTex]


no image
Graph Kernels for Chemical Informatics

Ralaivola, L., Swamidass, J., Saigo, H., Baldi, P.

Neural Networks, 18(8):1093-1110, 2005 (article)

Abstract
Increased availability of large repositories of chemical compounds is creating new challenges and opportunities for the application of machine learning methods to problems in computational chemistry and chemical informatics. Because chemical compounds are often represented by the graph of their covalent bonds, machine learning methods in this domain must be capable of processing graphical structures with variable size. Here we first briefly review the literature on graph kernels and then introduce three new kernels (Tanimoto, MinMax, Hybrid) based on the idea of molecular fingerprints and counting labeled paths of depth up to d using depthfirst search from each possible vertex. The kernels are applied to three classification problems to predict mutagenicity, toxicity, and anti-cancer activity on three publicly available data sets. The kernels achieve performances at least comparable, and most often superior, to those previously reported in the literature reaching accuracies of 91.5% on the Mutag dataset, 65-67% on the PTC (Predictive Toxicology Challenge) dataset, and 72% on the NCI (National Cancer Institute) dataset. Properties and tradeoffs of these kernels, as well as other proposed kernels that leverage 1D or 3D representations of molecules, are briefly discussed.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]