Publications | Empirical Inference - Max Planck Institute for Intelligent Systems

156 results (View BibTeX file of all listed publications)

2003

Quantitative Cerebral Blood Flow Measurements in the Rat Using a Beta-Probe and H215O

Weber, B., Spaeth, N., Wyss, M., Wild, D., Burger, C., Stanley, R., Buck, A.

Journal of Cerebral Blood Flow and Metabolism, 23(12):1455-1460, December 2003 (article)

Abstract

Beta-probes are a relatively new tool for tracer kinetic studies in animals. They are highly suited to evaluate new positron emission tomography tracers or measure physiologic parameters at rest and after some kind of stimulation or intervention. In many of these experiments, the knowledge of CBF is highly important. Thus, the purpose of this study was to evaluate the method of CBF measurements using a beta-probe and H215O. CBF was measured in the barrel cortex of eight rats at baseline and after acetazolamide challenge. Trigeminal nerve stimulation was additionally performed in five animals. In each category, three injections of 250 to 300 MBq H215O were performed at 10-minute intervals. Data were analyzed using a standard one-tissue compartment model (K1 = CBF, k2 = CBF/p, where p is the partition coefficient). Values for K1 were 0.35 plusminus 0.09, 0.58 plusminus 0.16, and 0.49 plusminus 0.03 mL dot min-1 dot mL-1 at rest, after acetazolamide challenge, and during trigeminal nerve stimulation, respectively. The corresponding values for k2 were 0.55 plusminus 0.12, 0.94 plusminus 0.16, and 0.85 plusminus 0.12 min-7, and for p were 0.64 plusminus 0.05, 0.61 plusminus 0.07, and 0.59 plusminus 0.06.The standard deviation of the difference between two successive experiments, a measure for the reproducibility of the method, was 10.1%, 13.0%, and 5.7% for K1, k2, and p, respectively. In summary, beta-probes in conjunction with H215O allow the reproducible quantitative measurement of CBF, although some systematic underestimation seems to occur, probably because of partial volume effects.

PDF DOI [BibTex]

2003

Weber, B., Spaeth, N., Wyss, M., Wild, D., Burger, C., Stanley, R., Buck, A. Quantitative Cerebral Blood Flow Measurements in the Rat Using a Beta-Probe and H215O Journal of Cerebral Blood Flow and Metabolism, 23(12):1455-1460, December 2003 (article)

PDF DOI [BibTex]

Blind separation of post-nonlinear mixtures using linearizing transformations and temporal decorrelation

Ziehe, A., Kawanabe, M., Harmeling, S., Müller, K.

Journal of Machine Learning Research, 4(7-8):1319-1338, November 2003 (article)

Abstract

We propose two methods that reduce the post-nonlinear blind source separation problem (PNL-BSS) to a linear BSS problem. The first method is based on the concept of maximal correlation: we apply the alternating conditional expectation (ACE) algorithm--a powerful technique from non-parametric statistics--to approximately invert the componentwise nonlinear functions. The second method is a Gaussianizing transformation, which is motivated by the fact that linearly mixed signals before nonlinear transformation are approximately Gaussian distributed. This heuristic, but simple and efficient procedure works as good as the ACE method. Using the framework provided by ACE, convergence can be proven. The optimal transformations obtained by ACE coincide with the sought-after inverse functions of the nonlinearities. After equalizing the nonlinearities, temporal decorrelation separation (TDSEP) allows us to recover the source signals. Numerical simulations testing "ACE-TD" and "Gauss-TD" on realistic examples are performed with excellent results.

PDF PDF DOI [BibTex]

Ziehe, A., Kawanabe, M., Harmeling, S., Müller, K. Blind separation of post-nonlinear mixtures using linearizing transformations and temporal decorrelation Journal of Machine Learning Research, 4(7-8):1319-1338, November 2003 (article)

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Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy

Becker, A., Chen, J., Zien, A., Sochivko, D., Normann, S., Schramm, J., Elger, C., Wiestler, O., Blumcke, I.

European Journal of Neuroscience, 18(10):2792-2802, November 2003 (article)

Abstract

Epileptic activity evokes profound alterations of hippocampal organization and function. Genomic responses may reflect immediate consequences of excitatory stimulation as well as sustained molecular processes related to neuronal plasticity and structural remodeling. Using oligonucleotide microarrays with 8799 sequences, we determined subregional gene expression profiles in rats subjected to pilocarpine-induced epilepsy (U34A arrays, Affymetrix, Santa Clara, CA, USA; P < 0.05, twofold change, n = 3 per stage). Patterns of gene expression corresponded to distinct stages of epilepsy development. The highest number of differentially expressed genes (dentate gyrus, approx. 400 genes and CA1, approx. 700 genes) was observed 3 days after status epilepticus. The majority of up-regulated genes was associated with mechanisms of cellular stress and injury - 14 days after status epilepticus, numerous transcription factors and genes linked to cytoskeletal and synaptic reorganization were differentially expressed and, in the stage of chronic spontaneous seizures, distinct changes were observed in the transcription of genes involved in various neurotransmission pathways and between animals with low vs. high seizure frequency. A number of genes (n = 18) differentially expressed during the chronic epileptic stage showed corresponding expression patterns in hippocampal subfields of patients with pharmacoresistant temporal lobe epilepsy (n = 5 temporal lobe epilepsy patients; U133A microarrays, Affymetrix; covering 22284 human sequences). These data provide novel insights into the molecular mechanisms of epileptogenesis and seizure-associated cellular and structural remodeling of the hippocampus.

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Becker, A., Chen, J., Zien, A., Sochivko, D., Normann, S., Schramm, J., Elger, C., Wiestler, O., Blumcke, I. Correlated stage- and subfield-associated hippocampal gene expression patterns in experimental and human temporal lobe epilepsy European Journal of Neuroscience, 18(10):2792-2802, November 2003 (article)

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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.

PostScript [BibTex]

Bousquet, O. Concentration Inequalities for Sub-Additive Functions Using the Entropy Method Stochastic Inequalities and Applications, 56, pages: 213-247, Progress in Probability, (Editors: Giné, E., C. Houdré and D. Nualart), November 2003 (article)

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YKL-39 (chitinase 3-like protein 2), but not YKL-40 (chitinase 3-like protein 1), is up regulated in osteoarthritic chondrocytes

Knorr, T., Obermayr, F., Bartnik, E., Zien, A., Aigner, T.

Annals of the Rheumatic Diseases, 62(10):995-998, October 2003 (article)

Abstract

OBJECTIVE: To investigate quantitatively the mRNA expression levels of YKL-40, an established marker of rheumatoid and osteoarthritic cartilage degeneration in synovial fluid and serum, and a closely related molecule YKL-39, in articular chondrocytes. METHODS: cDNA array and online quantitative polymerase chain reaction (PCR) were used to measure mRNA expression levels of YKL-39 and YKL-40 in chondrocytes in normal, early degenerative, and late stage osteoarthritic cartilage samples. RESULTS: Expression analysis showed high levels of both proteins in normal articular chondrocytes, with lower levels of YKL-39 than YKL-40. Whereas YKL-40 was significantly down regulated in late stage osteoarthritic chondrocytes, YKL-39 was significantly up regulated. In vitro both YKLs were down regulated by interleukin 1beta. CONCLUSIONS: The up regulation of YKL-39 in osteoarthritic cartilage suggests that YKL-39 may be a more accurate marker of chondrocyte activation than YKL-40, although it has yet to be established as a suitable marker in synovial fluid and serum. The decreased expression of YKL-40 by osteoarthritic chondrocytes is surprising as increased levels have been reported in rheumatoid and osteoarthritic synovial fluid, where it may derive from activated synovial cells or osteophytic tissue or by increased matrix destruction in the osteoarthritic joint. YKL-39 and YKL-40 are potentially interesting marker molecules for arthritic joint disease because they are abundantly expressed by both normal and osteoarthritic chondrocytes.

[BibTex]

Knorr, T., Obermayr, F., Bartnik, E., Zien, A., Aigner, T. YKL-39 (chitinase 3-like protein 2), but not YKL-40 (chitinase 3-like protein 1), is up regulated in osteoarthritic chondrocytes Annals of the Rheumatic Diseases, 62(10):995-998, October 2003 (article)

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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.

Web DOI [BibTex]

Schölkopf, B. Statistical Learning Theory, Capacity and Complexity Complexity, 8(4):87-94, July 2003 (article)

Web DOI [BibTex]

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.

PDF DOI [BibTex]

Weston, J., Schölkopf, B., Eskin, E., Leslie, C., Noble, W. Dealing with large Diagonals in Kernel Matrices Annals of the Institute of Statistical Mathematics, 55(2):391-408, June 2003 (article)

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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)

PDF [BibTex]

Tsuda, K., Akaho, S., Asai, K. The em Algorithm for Kernel Matrix Completion with Auxiliary Data Journal of Machine Learning Research, 4, pages: 67-81, May 2003 (article)

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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.

DOI [BibTex]

Mika, S., Rätsch, G., Weston, J., Schölkopf, B., Smola, A., Müller, K. Constructing Descriptive and Discriminative Non-linear Features: Rayleigh Coefficients in Kernel Feature Spaces IEEE Transactions on Pattern Analysis and Machine Intelligence, 25(5):623-628, May 2003 (article)

DOI [BibTex]

Kernel-based nonlinear blind source separation

Harmeling, S., Ziehe, A., Kawanabe, M., Müller, K.

Neural Computation, 15(5):1089-1124, May 2003 (article)

Abstract

We propose kTDSEP, a kernel-based algorithm for nonlinear blind source separation (BSS). It combines complementary research fields: kernel feature spaces and BSS using temporal information. This yields an efficient algorithm for nonlinear BSS with invertible nonlinearity. Key assumptions are that the kernel feature space is chosen rich enough to approximate the nonlinearity and that signals of interest contain temporal information. Both assumptions are fulfilled for a wide set of real-world applications. The algorithm works as follows: First, the data are (implicitly) mapped to a high (possibly infinite)dimensional kernel feature space. In practice, however, the data form a smaller submanifold in feature spaceeven smaller than the number of training data pointsa fact that has already been used by, for example, reduced set techniques for support vector machines. We propose to adapt to this effective dimension as a preprocessing step and to construct an orthonormal basis of this submanifold. The latter dimension-reduction step is essential for making the subsequent application of BSS methods computationally and numerically tractable. In the reduced space, we use a BSS algorithm that is based on second-order temporal decorrelation. Finally, we propose a selection procedure to obtain the original sources from the extracted nonlinear components automatically. Experiments demonstrate the excellent performance and efficiency of our kTDSEP algorithm for several problems of nonlinear BSS and for more than two sources.

PDF Web DOI [BibTex]

Harmeling, S., Ziehe, A., Kawanabe, M., Müller, K. Kernel-based nonlinear blind source separation Neural Computation, 15(5):1089-1124, May 2003 (article)

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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.

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Csato, L., Opper, M., Winther, O. Tractable Inference for Probabilistic Data Models Complexity, 8(4):64-68, April 2003 (article)

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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.

Web [BibTex]

Weston, J., Perez-Cruz, F., Bousquet, O., Chapelle, O., Elisseeff, A., Schölkopf, B. Feature selection and transduction for prediction of molecular bioactivity for drug design Bioinformatics, 19(6):764-771, April 2003 (article)

Web [BibTex]

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.

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Weston, J., Elisseeff, A., Schölkopf, B., Tipping, M. Use of the Zero-Norm with Linear Models and Kernel Methods Journal of Machine Learning Research, 3, pages: 1439-1461, March 2003 (article)

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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)

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Guyon, I., Elisseeff, A. An Introduction to Variable and Feature Selection. Journal of Machine Learning, 3, pages: 1157-1182, 2003 (article)

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Dynamics of a rigid body in a Stokes fluid

Gonzalez, O., Graf, ABA., Maddocks, JH.

Journal of Fluid Mechanics, 2003 (article) Accepted

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Gonzalez, O., Graf, ABA., Maddocks, JH. Dynamics of a rigid body in a Stokes fluid Journal of Fluid Mechanics, 2003 (article) Accepted

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A novel transient heater-foil technique for liquid crystal experiments on film cooled surfaces

Vogel, G., Graf, ABA., von Wolfersdorf, J., Weigand, B.

ASME Journal of Turbomachinery, 125, pages: 529-537, 2003 (article)

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Vogel, G., Graf, ABA., von Wolfersdorf, J., Weigand, B. A novel transient heater-foil technique for liquid crystal experiments on film cooled surfaces ASME Journal of Turbomachinery, 125, pages: 529-537, 2003 (article)

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Microarrays: How Many Do You Need?

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

Journal of Computational Biology, 10(3-4):653-667, 2003 (article)

Abstract

We estimate the number of microarrays that is required in order to gain reliable results from a common type of study: the pairwise comparison of different classes of samples. We show that current knowledge allows for the construction of models that look realistic with respect to searches for individual differentially expressed genes and derive prototypical parameters from real data sets. Such models allow investigation of the dependence of the required number of samples on the relevant parameters: the biological variability of the samples within each class, the fold changes in expression that are desired to be detected, the detection sensitivity of the microarrays, and the acceptable error rates of the results. We supply experimentalists with general conclusions as well as a freely accessible Java applet at www.scai.fhg.de/special/bio/howmanyarrays/ for fine tuning simulations to their particular settings.

Web [BibTex]

Zien, A., Fluck, J., Zimmer, R., Lengauer, T. Microarrays: How Many Do You Need? Journal of Computational Biology, 10(3-4):653-667, 2003 (article)

Web [BibTex]

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.

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Bousquet, O. New Approaches to Statistical Learning Theory Annals of the Institute of Statistical Mathematics, 55(2):371-389, 2003 (article)

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Gene expression in chondrocytes assessed with use of microarrays

Aigner, T., Zien, A., Hanisch, D., Zimmer, R.

Journal of Bone and Joint Surgery, 85(Suppl 2):117-123, 2003 (article)

[BibTex]

Aigner, T., Zien, A., Hanisch, D., Zimmer, R. Gene expression in chondrocytes assessed with use of microarrays Journal of Bone and Joint Surgery, 85(Suppl 2):117-123, 2003 (article)

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2002

Optimized Support Vector Machines for Nonstationary Signal Classification

Davy, M., Gretton, A., Doucet, A., Rayner, P.

IEEE Signal Processing Letters, 9(12):442-445, December 2002 (article)

Abstract

This letter describes an efficient method to perform nonstationary signal classification. A support vector machine (SVM) algorithm is introduced and its parameters optimised in a principled way. Simulations demonstrate that our low complexity method outperforms state-of-the-art nonstationary signal classification techniques.

PostScript Web DOI [BibTex]

2002

Davy, M., Gretton, A., Doucet, A., Rayner, P. Optimized Support Vector Machines for Nonstationary Signal Classification IEEE Signal Processing Letters, 9(12):442-445, December 2002 (article)

PostScript Web DOI [BibTex]

A New Discriminative Kernel from Probabilistic Models

Tsuda, K., Kawanabe, M., Rätsch, G., Sonnenburg, S., Müller, K.

Neural Computation, 14(10):2397-2414, October 2002 (article)

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Tsuda, K., Kawanabe, M., Rätsch, G., Sonnenburg, S., Müller, K. A New Discriminative Kernel from Probabilistic Models Neural Computation, 14(10):2397-2414, October 2002 (article)

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Functional Genomics of Osteoarthritis

Aigner, T., Bartnik, E., Zien, A., Zimmer, R.

Pharmacogenomics, 3(5):635-650, September 2002 (article)

Web [BibTex]

Aigner, T., Bartnik, E., Zien, A., Zimmer, R. Functional Genomics of Osteoarthritis Pharmacogenomics, 3(5):635-650, September 2002 (article)

Web [BibTex]

Constructing Boosting algorithms from SVMs: an application to one-class classification.

Rätsch, G., Mika, S., Schölkopf, B., Müller, K.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 24(9):1184-1199, September 2002 (article)

Abstract

We show via an equivalence of mathematical programs that a support vector (SV) algorithm can be translated into an equivalent boosting-like algorithm and vice versa. We exemplify this translation procedure for a new algorithmone-class leveragingstarting from the one-class support vector machine (1-SVM). This is a first step toward unsupervised learning in a boosting framework. Building on so-called barrier methods known from the theory of constrained optimization, it returns a function, written as a convex combination of base hypotheses, that characterizes whether a given test point is likely to have been generated from the distribution underlying the training data. Simulations on one-class classification problems demonstrate the usefulness of our approach.

DOI [BibTex]

Rätsch, G., Mika, S., Schölkopf, B., Müller, K. Constructing Boosting algorithms from SVMs: an application to one-class classification. IEEE Transactions on Pattern Analysis and Machine Intelligence, 24(9):1184-1199, September 2002 (article)

DOI [BibTex]

Co-Clustering of Biological Networks and Gene Expression Data

Hanisch, D., Zien, A., Zimmer, R., Lengauer, T.

Bioinformatics, (Suppl 1):145S-154S, 18, July 2002 (article)

Abstract

Motivation: Large scale gene expression data are often analysed by clustering genes based on gene expression data alone, though a priori knowledge in the form of biological networks is available. The use of this additional information promises to improve exploratory analysis considerably. Results: We propose constructing a distance function which combines information from expression data and biological networks. Based on this function, we compute a joint clustering of genes and vertices of the network. This general approach is elaborated for metabolic networks. We define a graph distance function on such networks and combine it with a correlation-based distance function for gene expression measurements. A hierarchical clustering and an associated statistical measure is computed to arrive at a reasonable number of clusters. Our method is validated using expression data of the yeast diauxic shift. The resulting clusters are easily interpretable in terms of the biochemical network and the gene expression data and suggest that our method is able to automatically identify processes that are relevant under the measured conditions.

Web [BibTex]

Hanisch, D., Zien, A., Zimmer, R., Lengauer, T. Co-Clustering of Biological Networks and Gene Expression Data Bioinformatics, (Suppl 1):145S-154S, 18, July 2002 (article)

Web [BibTex]

Confidence measures for protein fold recognition

Sommer, I., Zien, A., von Ohsen, N., Zimmer, R., Lengauer, T.

Bioinformatics, 18(6):802-812, June 2002 (article)

[BibTex]

Sommer, I., Zien, A., von Ohsen, N., Zimmer, R., Lengauer, T. Confidence measures for protein fold recognition Bioinformatics, 18(6):802-812, June 2002 (article)

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The contributions of color to recognition memory for natural scenes

Wichmann, F., Sharpe, L., Gegenfurtner, K.

Journal of Experimental Psychology: Learning, Memory and Cognition, 28(3):509-520, May 2002 (article)

Abstract

The authors used a recognition memory paradigm to assess the influence of color information on visual memory for images of natural scenes. Subjects performed 5-10% better for colored than for black-and-white images independent of exposure duration. Experiment 2 indicated little influence of contrast once the images were suprathreshold, and Experiment 3 revealed that performance worsened when images were presented in color and tested in black and white, or vice versa, leading to the conclusion that the surface property color is part of the memory representation. Experiments 4 and 5 exclude the possibility that the superior recognition memory for colored images results solely from attentional factors or saliency. Finally, the recognition memory advantage disappears for falsely colored images of natural scenes: The improvement in recognition memory depends on the color congruence of presented images with learned knowledge about the color gamut found within natural scenes. The results can be accounted for within a multiple memory systems framework.

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Wichmann, F., Sharpe, L., Gegenfurtner, K. The contributions of color to recognition memory for natural scenes Journal of Experimental Psychology: Learning, Memory and Cognition, 28(3):509-520, May 2002 (article)

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Training invariant support vector machines

DeCoste, D., Schölkopf, B.

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

Abstract

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

PDF DOI [BibTex]

DeCoste, D., Schölkopf, B. Training invariant support vector machines Machine Learning, 46(1-3):161-190, January 2002 (article)

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Model Selection for Small Sample Regression

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

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

Abstract

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

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Chapelle, O., Vapnik, V., Bengio, Y. Model Selection for Small Sample Regression Machine Learning, 48(1-3):9-23, 2002 (article)

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Contrast discrimination with sinusoidal gratings of different spatial frequency

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

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

Abstract

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

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Bird, C., Henning, G., Wichmann, F. Contrast discrimination with sinusoidal gratings of different spatial frequency Journal of the Optical Society of America A, 19(7), pages: 1267-1273, 2002 (article)

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

Bousquet, O.

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

Abstract

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

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Bousquet, O. A Bennett Concentration Inequality and Its Application to Suprema of Empirical Processes C. R. Acad. Sci. Paris, Ser. I, 334, pages: 495-500, 2002 (article)

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Numerical evolution of axisymmetric, isolated systems in general relativity

Frauendiener, J., Hein, M.

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

Abstract

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

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Frauendiener, J., Hein, M. Numerical evolution of axisymmetric, isolated systems in general relativity Physical Review D, 66, pages: 124004-124004, 2002 (article)

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Marginalized kernels for biological sequences

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

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

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Tsuda, K., Kin, T., Asai, K. Marginalized kernels for biological sequences Bioinformatics, 18(Suppl 1):268-275, 2002 (article)

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Support Vector Machines and Kernel Methods: The New Generation of Learning Machines

Cristianini, N., Schölkopf, B.

AI Magazine, 23(3):31-41, 2002 (article)

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Cristianini, N., Schölkopf, B. Support Vector Machines and Kernel Methods: The New Generation of Learning Machines AI Magazine, 23(3):31-41, 2002 (article)

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Stability and Generalization

Bousquet, O., Elisseeff, A.

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

Abstract

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

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Bousquet, O., Elisseeff, A. Stability and Generalization Journal of Machine Learning Research, 2, pages: 499-526, 2002 (article)

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

Tsuda, K., Sugiyama, M., Müller, K.

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

PDF [BibTex]

Tsuda, K., Sugiyama, M., Müller, K. Subspace information criterion for non-quadratic regularizers – model selection for sparse regressors IEEE Trans Neural Networks, 13(1):70-80, 2002 (article)

PDF [BibTex]

Modeling splicing sites with pairwise correlations

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

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

PDF [BibTex]

Arita, M., Tsuda, K., Asai, K. Modeling splicing sites with pairwise correlations Bioinformatics, 18(Suppl 2):27-34, 2002 (article)

PDF [BibTex]

Perfusion Quantification using Gaussian Process Deconvolution

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

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

Abstract

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

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Andersen, IK., Szymkowiak, A., Rasmussen, CE., Hanson, LG., Marstrand, JR., Larsson, HBW., Hansen, LK. Perfusion Quantification using Gaussian Process Deconvolution Magnetic Resonance in Medicine, (48):351-361, 2002 (article)

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Tracking a Small Set of Experts by Mixing Past Posteriors

Bousquet, O., Warmuth, M.

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

Abstract

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

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Bousquet, O., Warmuth, M. Tracking a Small Set of Experts by Mixing Past Posteriors Journal of Machine Learning Research, 3, pages: 363-396, (Editors: Long, P.), 2002 (article)

PDF PostScript [BibTex]

A femoral arteriovenous shunt facilitates arterial whole blood sampling in animals

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

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

[BibTex]

Weber, B., Burger, C., Biro, P., Buck, A. A femoral arteriovenous shunt facilitates arterial whole blood sampling in animals Eur J Nucl Med Mol Imaging, 29, pages: 319-323, 2002 (article)

[BibTex]

Contrast discrimination with pulse-trains in pink noise

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

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

Abstract

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

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Henning, G., Bird, C., Wichmann, F. Contrast discrimination with pulse-trains in pink noise Journal of the Optical Society of America A, 19(7), pages: 1259-1266, 2002 (article)

PDF [BibTex]

Choosing Multiple Parameters for Support Vector Machines

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

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

Abstract

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

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Chapelle, O., Vapnik, V., Bousquet, O., Mukherjee, S. Choosing Multiple Parameters for Support Vector Machines Machine Learning, 46(1):131-159, 2002 (article)

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White matter glucose metabolism during intracortical electrostimulation: a quantitative [(18)F]Fluorodeoxyglucose autoradiography study in the rat

Weber, B., Fouad, K., Burger, C., Buck, A.

Neuroimage, 16, pages: 993-998, 2002 (article)

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Weber, B., Fouad, K., Burger, C., Buck, A. White matter glucose metabolism during intracortical electrostimulation: a quantitative [(18)F]Fluorodeoxyglucose autoradiography study in the rat Neuroimage, 16, pages: 993-998, 2002 (article)

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1998

Book Review: An Introduction to Fuzzy Logic for Practical Applications

Peters, J.

K{\"u}nstliche Intelligenz (KI), 98(4):60-60, November 1998 (article)

[BibTex]

1998

Peters, J. Book Review: An Introduction to Fuzzy Logic for Practical Applications K{\"u}nstliche Intelligenz (KI), 98(4):60-60, November 1998 (article)

[BibTex]

Where did I take that snapshot? Scene-based homing by image matching

Franz, M., Schölkopf, B., Bülthoff, H.

Biological Cybernetics, 79(3):191-202, October 1998 (article)

Abstract

In homing tasks, the goal is often not marked by visible objects but must be inferred from the spatial relation to the visual cues in the surrounding scene. The exact computation of the goal direction would require knowledge about the distances to visible landmarks, information, which is not directly available to passive vision systems. However, if prior assumptions about typical distance distributions are used, a snapshot taken at the goal suffices to compute the goal direction from the current view. We show that most existing approaches to scene-based homing implicitly assume an isotropic landmark distribution. As an alternative, we propose a homing scheme that uses parameterized displacement fields. These are obtained from an approximation that incorporates prior knowledge about perspective distortions of the visual environment. A mathematical analysis proves that both approximations do not prevent the schemes from approaching the goal with arbitrary accuracy, but lead to different errors in the computed goal direction. Mobile robot experiments are used to test the theoretical predictions and to demonstrate the practical feasibility of the new approach.

PDF PDF DOI [BibTex]

Franz, M., Schölkopf, B., Bülthoff, H. Where did I take that snapshot? Scene-based homing by image matching Biological Cybernetics, 79(3):191-202, October 1998 (article)

PDF PDF DOI [BibTex]

On a Kernel-Based Method for Pattern Recognition, Regression, Approximation, and Operator Inversion

Smola, A., Schölkopf, B.

Algorithmica, 22(1-2):211-231, September 1998 (article)

Abstract

We present a kernel-based framework for pattern recognition, regression estimation, function approximation, and multiple operator inversion. Adopting a regularization-theoretic framework, the above are formulated as constrained optimization problems. Previous approaches such as ridge regression, support vector methods, and regularization networks are included as special cases. We show connections between the cost function and some properties up to now believed to apply to support vector machines only. For appropriately chosen cost functions, the optimal solution of all the problems described above can be found by solving a simple quadratic programming problem.

PDF DOI [BibTex]

Smola, A., Schölkopf, B. On a Kernel-Based Method for Pattern Recognition, Regression, Approximation, and Operator Inversion Algorithmica, 22(1-2):211-231, September 1998 (article)

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The moon tilt illusion

Schölkopf, B.

Perception, 27(10):1229-1232, August 1998 (article)

Abstract

Besides the familiar moon illusion [eg Hershenson, 1989 The Moon illusion (Hillsdale, NJ: Lawrence Erlbaum Associates)], wherein the moon appears bigger when it is close to the horizon, there is a less known illusion which causes the moon‘s illuminated side to appear turned away from the direction of the sun. An experiment documenting the effect is described, and a possible explanation is put forward.

Web DOI [BibTex]

Schölkopf, B. The moon tilt illusion Perception, 27(10):1229-1232, August 1998 (article)

Web DOI [BibTex]

Characterization of the oligomerization defects of two p53 mutants found in families with Li-Fraumeni and Li-Fraumeni-like syndrome.

Davison, T., Yin, P., Nie, E., Kay, C., CH, ..

Oncogene, 17(5):651-656, August 1998 (article)

Abstract

Recently two germline mutations in the oligomerization domain of p53 have been identified in patients with Li-Fraumeni and Li-Fraumeni-like Syndromes. We have used biophysical and biochemical methods to characterize these two mutants in order to better understand their functional defects and the role of the p53 oligomerization domain (residues 325-355) in oncogenesis. We find that residues 310-360 of the L344P mutant are monomeric, apparently unfolded and cannot interact with wild-type (WT) p53. The full length L344P protein is unable to bind sequence specifically to DNA and is therefore an inactive, but not a dominant negative mutant. R337C, on the other hand, can form dimers and tetramers, can hetero-oligomerize with WTp53 and can bind to a p53 consensus element. However, the thermal stability of R337C is much lower than that of WTp53 and at physiological temperatures more than half of this mutant is less than tetrameric. Thus, the R337C mutant retains some functional activity yet leads to a predisposition to cancer, suggesting that even partial inactivation of p53 oligomerization is sufficient for accelerated tumour progression.

Web [BibTex]

Davison, T., Yin, P., Nie, E., Kay, C., CH, .. Characterization of the oligomerization defects of two p53 mutants found in families with Li-Fraumeni and Li-Fraumeni-like syndrome. Oncogene, 17(5):651-656, August 1998 (article)

Web [BibTex]

Nonlinear Component Analysis as a Kernel Eigenvalue Problem

Schölkopf, B., Smola, A., Müller, K.

Neural Computation, 10(5):1299-1319, July 1998 (article)

Abstract

A new method for performing a nonlinear form of principal component analysis is proposed. By the use of integral operator kernel functions, one can efficiently compute principal components in high-dimensional feature spaces, related to input space by some nonlinear map—for instance, the space of all possible five-pixel products in 16 × 16 images. We give the derivation of the method and present experimental results on polynomial feature extraction for pattern recognition.

Web DOI [BibTex]

Schölkopf, B., Smola, A., Müller, K. Nonlinear Component Analysis as a Kernel Eigenvalue Problem Neural Computation, 10(5):1299-1319, July 1998 (article)

Web DOI [BibTex]

SVMs — a practical consequence of learning theory

Schölkopf, B.

IEEE Intelligent Systems and their Applications, 13(4):18-21, July 1998 (article)

Abstract

My first exposure to Support Vector Machines came this spring when heard Sue Dumais present impressive results on text categorization using this analysis technique. This issue's collection of essays should help familiarize our readers with this interesting new racehorse in the Machine Learning stable. Bernhard Scholkopf, in an introductory overview, points out that a particular advantage of SVMs over other learning algorithms is that it can be analyzed theoretically using concepts from computational learning theory, and at the same time can achieve good performance when applied to real problems. Examples of these real-world applications are provided by Sue Dumais, who describes the aforementioned text-categorization problem, yielding the best results to date on the Reuters collection, and Edgar Osuna, who presents strong results on application to face detection. Our fourth author, John Platt, gives us a practical guide and a new technique for implementing the algorithm efficiently.

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Schölkopf, B. SVMs — a practical consequence of learning theory IEEE Intelligent Systems and their Applications, 13(4):18-21, July 1998 (article)

PDF Web DOI [BibTex]

Support vector machines

Hearst, M., Dumais, S., Osman, E., Platt, J., Schölkopf, B.

IEEE Intelligent Systems and their Applications, 13(4):18-28, July 1998 (article)

Abstract

PDF Web DOI [BibTex]

Hearst, M., Dumais, S., Osman, E., Platt, J., Schölkopf, B. Support vector machines IEEE Intelligent Systems and their Applications, 13(4):18-28, July 1998 (article)

PDF Web DOI [BibTex]

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