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2008


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Learning resolved velocity control

Peters, J.

2008 IEEE International Conference on Robotics and Automation (ICRA), May 2008 (talk)

Web [BibTex]

2008

Web [BibTex]


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Relating the Thermodynamic Arrow of Time to the Causal Arrow

Allahverdyan, A., Janzing, D.

Journal of Statistical Mechanics, 2008(P04001):1-21, April 2008 (article)

Abstract
Consider a Hamiltonian system that consists of a slow subsystem S and a fast subsystem F. The autonomous dynamics of S is driven by an effective Hamiltonian, but its thermodynamics is unexpected. We show that a well-defined thermodynamic arrow of time (second law) emerges for S whenever there is a well-defined causal arrow from S to F and the back-action is negligible. This is because the back-action of F on S is described by a non-globally Hamiltonian Born–Oppenheimer term that violates the Liouville theorem, and makes the second law inapplicable to S. If S and F are mixing, under the causal arrow condition they are described by microcanonical distributions P(S) and P(S|F). Their structure supports a causal inference principle proposed recently in machine learning.

Web DOI [BibTex]

Web DOI [BibTex]


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Generalization and Similarity in Exemplar Models of Categorization: Insights from Machine Learning

Jäkel, F., Schölkopf, B., Wichmann, F.

Psychonomic Bulletin and Review, 15(2):256-271, April 2008 (article)

Abstract
Exemplar theories of categorization depend on similarity for explaining subjects’ ability to generalize to new stimuli. A major criticism of exemplar theories concerns their lack of abstraction mechanisms and thus, seemingly, generalization ability. Here, we use insights from machine learning to demonstrate that exemplar models can actually generalize very well. Kernel methods in machine learning are akin to exemplar models and very successful in real-world applications. Their generalization performance depends crucially on the chosen similaritymeasure. While similarity plays an important role in describing generalization behavior it is not the only factor that controls generalization performance. In machine learning, kernel methods are often combined with regularization techniques to ensure good generalization. These same techniques are easily incorporated in exemplar models. We show that the Generalized Context Model (Nosofsky, 1986) and ALCOVE (Kruschke, 1992) are closely related to a statistical model called kernel logistic regression. We argue that generalization is central to the enterprise of understanding categorization behavior and suggest how insights from machine learning can offer some guidance. Keywords: kernel, similarity, regularization, generalization, categorization.

PDF Web DOI [BibTex]


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Bayesian methods for protein structure determination

Habeck, M.

Machine Learning in Structural Bioinformatics, April 2008 (talk)

Web [BibTex]

Web [BibTex]


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Manifold-valued Thin-plate Splines with Applications in Computer Graphics

Steinke, F., Hein, M., Peters, J., Schölkopf, B.

Computer Graphics Forum, 27(2):437-448, April 2008 (article)

Abstract
We present a generalization of thin-plate splines for interpolation and approximation of manifold-valued data, and demonstrate its usefulness in computer graphics with several applications from different fields. The cornerstone of our theoretical framework is an energy functional for mappings between two Riemannian manifolds which is independent of parametrization and respects the geometry of both manifolds. If the manifolds are Euclidean, the energy functional reduces to the classical thin-plate spline energy. We show how the resulting optimization problems can be solved efficiently in many cases. Our example applications range from orientation interpolation and motion planning in animation over geometric modelling tasks to color interpolation.

PDF AVI Web DOI [BibTex]


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Data-driven efficient score tests for deconvolution hypotheses

Langovoy, M.

Inverse Problems, 24(2):1-17, April 2008 (article)

Abstract
We consider testing statistical hypotheses about densities of signals in deconvolution models. A new approach to this problem is proposed. We constructed score tests for the deconvolution density testing with the known noise density and efficient score tests for the case of unknown density. The tests are incorporated with model selection rules to choose reasonable model dimensions automatically by the data. Consistency of the tests is proved.

PDF DOI [BibTex]


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The Metric Nearness Problem

Brickell, J., Dhillon, I., Sra, S., Tropp, J.

SIAM Journal on Matrix Analysis and Applications, 30(1):375-396, April 2008 (article)

Abstract
Metric nearness refers to the problem of optimally restoring metric properties to distance measurements that happen to be nonmetric due to measurement errors or otherwise. Metric data can be important in various settings, for example, in clustering, classification, metric-based indexing, query processing, and graph theoretic approximation algorithms. This paper formulates and solves the metric nearness problem: Given a set of pairwise dissimilarities, find a “nearest” set of distances that satisfy the properties of a metric—principally the triangle inequality. For solving this problem, the paper develops efficient triangle fixing algorithms that are based on an iterative projection method. An intriguing aspect of the metric nearness problem is that a special case turns out to be equivalent to the all pairs shortest paths problem. The paper exploits this equivalence and develops a new algorithm for the latter problem using a primal-dual method. Applications to graph clustering are provided as an illustratio n. We include experiments that demonstrate the computational superiority of triangle fixing over general purpose convex programming software. Finally, we conclude by suggesting various useful extensions and generalizations to metric nearness.

Web DOI [BibTex]

Web DOI [BibTex]


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Bayesian Inference and Optimal Design for the Sparse Linear Model

Seeger, MW.

Journal of Machine Learning Research, 9, pages: 759-813, April 2008 (article)

Abstract
The linear model with sparsity-favouring prior on the coefficients has important applications in many different domains. In machine learning, most methods to date search for maximum a posteriori sparse solutions and neglect to represent posterior uncertainties. In this paper, we address problems of Bayesian optimal design (or experiment planning), for which accurate estimates of uncertainty are essential. To this end, we employ expectation propagation approximate inference for the linear model with Laplace prior, giving new insight into numerical stability properties and proposing a robust algorithm. We also show how to estimate model hyperparameters by empirical Bayesian maximisation of the marginal likelihood, and propose ideas in order to scale up the method to very large underdetermined problems. We demonstrate the versatility of our framework on the application of gene regulatory network identification from micro-array expression data, where both the Laplace prior and the active experimental design approach are shown to result in significant improvements. We also address the problem of sparse coding of natural images, and show how our framework can be used for compressive sensing tasks.

PDF PDF [BibTex]

PDF PDF [BibTex]


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Consistency of Spectral Clustering

von Luxburg, U., Belkin, M., Bousquet, O.

Annals of Statistics, 36(2):555-586, April 2008 (article)

Abstract
Consistency is a key property of statistical algorithms when the data is drawn from some underlying probability distribution. Surprisingly, despite decades of work, little is known about consistency of most clustering algorithms. In this paper we investigate consistency of the popular family of spectral clustering algorithms, which clusters the data with the help of eigenvectors of graph Laplacian matrices. We develop new methods to establish that for increasing sample size, those eigenvectors converge to the eigenvectors of certain limit operators. As a result we can prove that one of the two major classes of spectral clustering (normalized clustering) converges under very general conditions, while the other (unnormalized clustering) is only consistent under strong additional assumptions, which are not always satisfied in real data. We conclude that our analysis provides strong evidence for the superiority of normalized spectral clustering.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Plant Classification from Bat-Like Echolocation Signals

Yovel, Y., Franz, MO., Stilz, P., Schnitzler, H-U.

PLoS Computational Biology, 4(3, e1000032):1-13, March 2008 (article)

Abstract
Classification of plants according to their echoes is an elementary component of bat behavior that plays an important role in spatial orientation and food acquisition. Vegetation echoes are, however, highly complex stochastic signals: from an acoustical point of view, a plant can be thought of as a three-dimensional array of leaves reflecting the emitted bat call. The received echo is therefore a superposition of many reflections. In this work we suggest that the classification of these echoes might not be such a troublesome routine for bats as formerly thought. We present a rather simple approach to classifying signals from a large database of plant echoes that were created by ensonifying plants with a frequency-modulated bat-like ultrasonic pulse. Our algorithm uses the spectrogram of a single echo from which it only uses features that are undoubtedly accessible to bats. We used a standard machine learning algorithm (SVM) to automatically extract suitable linear combinations of time and frequency cues from the spectrograms such that classification with high accuracy is enabled. This demonstrates that ultrasonic echoes are highly informative about the species membership of an ensonified plant, and that this information can be extracted with rather simple, biologically plausible analysis. Thus, our findings provide a new explanatory basis for the poorly understood observed abilities of bats in classifying vegetation and other complex objects.

Web DOI [BibTex]

Web DOI [BibTex]


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Causal Reasoning by Evaluating the Complexity of Conditional Densities with Kernel Methods

Sun, X., Janzing, D., Schölkopf, B.

Neurocomputing, 71(7-9):1248-1256, March 2008 (article)

Abstract
We propose a method to quantify the complexity of conditional probability measures by a Hilbert space seminorm of the logarithm of its density. The concept of reproducing kernel Hilbert spaces (RKHSs) is a flexible tool to define such a seminorm by choosing an appropriate kernel. We present several examples with artificial data sets where our kernel-based complexity measure is consistent with our intuitive understanding of complexity of densities. The intention behind the complexity measure is to provide a new approach to inferring causal directions. The idea is that the factorization of the joint probability measure P(effect, cause) into P(effect|cause)P(cause) leads typically to "simpler" and "smoother" terms than the factorization into P(cause|effect)P(effect). Since the conventional constraint-based approach of causal discovery is not able to determine the causal direction between only two variables, our inference principle can in particular be useful when combined with other existing methods. We provide several simple examples with real-world data where the true causal directions indeed lead to simpler (conditional) densities.

Web DOI [BibTex]


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Natural Actor-Critic

Peters, J., Schaal, S.

Neurocomputing, 71(7-9):1180-1190, March 2008 (article)

Abstract
In this paper, we suggest a novel reinforcement learning architecture, the Natural Actor-Critic. The actor updates are achieved using stochastic policy gradients em- ploying Amari’s natural gradient approach, while the critic obtains both the natural policy gradient and additional parameters of a value function simultaneously by lin- ear regression. We show that actor improvements with natural policy gradients are particularly appealing as these are independent of coordinate frame of the chosen policy representation, and can be estimated more efficiently than regular policy gra- dients. The critic makes use of a special basis function parameterization motivated by the policy-gradient compatible function approximation. We show that several well-known reinforcement learning methods such as the original Actor-Critic and Bradtke’s Linear Quadratic Q-Learning are in fact Natural Actor-Critic algorithms. Empirical evaluations illustrate the effectiveness of our techniques in comparison to previous methods, and also demonstrate their applicability for learning control on an anthropomorphic robot arm.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Inferring Spike Trains From Local Field Potentials

Rasch, M., Gretton, A., Murayama, Y., Maass, W., Logothetis, N.

Journal of Neurophysiology, 99(3):1461-1476, March 2008 (article)

Abstract
We investigated whether it is possible to infer spike trains solely on the basis of the underlying local field potentials (LFPs). Using support vector machines and linear regression models, we found that in the primary visual cortex (V1) of monkeys, spikes can indeed be inferred from LFPs, at least with moderate success. Although there is a considerable degree of variation across electrodes, the low-frequency structure in spike trains (in the 100-ms range) can be inferred with reasonable accuracy, whereas exact spike positions are not reliably predicted. Two kinds of features of the LFP are exploited for prediction: the frequency power of bands in the high gamma-range (40–90 Hz) and information contained in lowfrequency oscillations ( 10 Hz), where both phase and power modulations are informative. Information analysis revealed that both features code (mainly) independent aspects of the spike-to-LFP relationship, with the low-frequency LFP phase coding for temporally clustered spiking activity. Although both features and prediction quality are similar during seminatural movie stimuli and spontaneous activity, prediction performance during spontaneous activity degrades much more slowly with increasing electrode distance. The general trend of data obtained with anesthetized animals is qualitatively mirrored in that of a more limited data set recorded in V1 of non-anesthetized monkeys. In contrast to the cortical field potentials, thalamic LFPs (e.g., LFPs derived from recordings in the dorsal lateral geniculate nucleus) hold no useful information for predicting spiking activity.

Web DOI [BibTex]

Web DOI [BibTex]


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Poisson Geometry of Parabolic Bundles on Elliptic Curves

Balduzzi, D.

International Journal of Mathematics , 19(3):339-367, March 2008 (article)

Abstract
The moduli space of G-bundles on an elliptic curve with additional flag structure admits a Poisson structure. The bivector can be defined using double loop group, loop group and sheaf cohomology constructions. We investigate the links between these methods and for the case SL2 perform explicit computations, describing the bracket and its leaves in detail.

Web DOI [BibTex]

Web DOI [BibTex]


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ISD: A Software Package for Bayesian NMR Structure Calculation

Rieping, W., Nilges, M., Habeck, M.

Bioinformatics, 24(8):1104-1105, February 2008 (article)

Abstract
SUMMARY: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The Inferential Structure Determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology. AVAILABILITY: The program is available at http://www.bioc.cam.ac.uk/isd

Web DOI [BibTex]

Web DOI [BibTex]


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Probabilistic Structure Calculation

Nilges, M., Habeck, M., Rieping, W.

Comptes Rendus Chimie, 11(4-5):356-369, February 2008 (article)

Abstract
Molecular structures are usually calculated from experimental data with some method of energy minimisation or non-linear optimisation. Key aims of a structure calculation are to estimate the coordinate uncertainty, and to provide a meaningful measure of the quality of the fit to the data. We discuss approaches to optimally combine prior information and experimental data and the connection to probability theory. We analyse the appropriate statistics for NOEs and NOE-derived distances, and the related question of restraint potentials. Finally, we will discuss approaches to determine the appropriate weight on the experimental evidence and to obtain in this way an estimate of the data quality from the structure calculation. Whereas objective estimates of coordinates and their uncertainties can only be obtained by a full Bayesian treatment of the problem, standard structure calculation methods continue to play an important role. To obtain the full benefit of these methods, they should be founded on a rigorous Baye sian analysis.

Web DOI [BibTex]

Web DOI [BibTex]


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Fast Projection-based Methods for the Least Squares Nonnegative Matrix Approximation Problem

Kim, D., Sra, S., Dhillon, I.

Statistical Analysis and Data Mining, 1(1):38-51, February 2008 (article)

Abstract
Nonnegative matrix approximation (NNMA) is a popular matrix decomposition technique that has proven to be useful across a diverse variety of fields with applications ranging from document analysis and image processing to bioinformatics and signal processing. Over the years, several algorithms for NNMA have been proposed, e.g. Lee and Seung‘s multiplicative updates, alternating least squares (ALS), and gradient descent-based procedures. However, most of these procedures suffer from either slow convergence, numerical instability, or at worst, serious theoretical drawbacks. In this paper, we develop a new and improved algorithmic framework for the least-squares NNMA problem, which is not only theoretically well-founded, but also overcomes many deficiencies of other methods. Our framework readily admits powerful optimization techniques and as concrete realizations we present implementations based on the Newton, BFGS and conjugate gradient methods. Our algorithms provide numerical resu lts supe rior to both Lee and Seung‘s method as well as to the alternating least squares heuristic, which was reported to work well in some situations but has no theoretical guarantees[1]. Our approach extends naturally to include regularization and box-constraints without sacrificing convergence guarantees. We present experimental results on both synthetic and real-world datasets that demonstrate the superiority of our methods, both in terms of better approximations as well as computational efficiency.

Web DOI [BibTex]

Web DOI [BibTex]


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Optimization Techniques for Semi-Supervised Support Vector Machines

Chapelle, O., Sindhwani, V., Keerthi, S.

Journal of Machine Learning Research, 9, pages: 203-233, February 2008 (article)

Abstract
Due to its wide applicability, the problem of semi-supervised classification is attracting increasing attention in machine learning. Semi-Supervised Support Vector Machines (S3VMs) are based on applying the margin maximization principle to both labeled and unlabeled examples. Unlike SVMs, their formulation leads to a non-convex optimization problem. A suite of algorithms have recently been proposed for solving S3VMs. This paper reviews key ideas in this literature. The performance and behavior of various S3VMs algorithms is studied together, under a common experimental setting.

PDF [BibTex]

PDF [BibTex]


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A Unifying Probabilistic Framework for Analyzing Residual Dipolar Couplings

Habeck, M., Nilges, M., Rieping, W.

Journal of Biomolecular NMR, 40(2):135-144, February 2008 (article)

Abstract
Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Contour-propagation Algorithms for Semi-automated Reconstruction of Neural Processes

Macke, J., Maack, N., Gupta, R., Denk, W., Schölkopf, B., Borst, A.

Journal of Neuroscience Methods, 167(2):349-357, January 2008 (article)

Abstract
A new technique, ”Serial Block Face Scanning Electron Microscopy” (SBFSEM), allows for automatic sectioning and imaging of biological tissue with a scanning electron microscope. Image stacks generated with this technology have a resolution sufficient to distinguish different cellular compartments, including synaptic structures, which should make it possible to obtain detailed anatomical knowledge of complete neuronal circuits. Such an image stack contains several thousands of images and is recorded with a minimal voxel size of 10-20nm in the x and y- and 30nm in z-direction. Consequently, a tissue block of 1mm3 (the approximate volume of the Calliphora vicina brain) will produce several hundred terabytes of data. Therefore, highly automated 3D reconstruction algorithms are needed. As a first step in this direction we have developed semiautomated segmentation algorithms for a precise contour tracing of cell membranes. These algorithms were embedded into an easy-to-operate user interface, which allows direct 3D observation of the extracted objects during the segmentation of image stacks. Compared to purely manual tracing, processing time is greatly accelerated.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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A Quantum-Statistical-Mechanical Extension of Gaussian Mixture Model

Tanaka, K., Tsuda, K.

Journal of Physics: Conference Series, 95(012023):1-9, January 2008 (article)

Abstract
We propose an extension of Gaussian mixture models in the statistical-mechanical point of view. The conventional Gaussian mixture models are formulated to divide all points in given data to some kinds of classes. We introduce some quantum states constructed by superposing conventional classes in linear combinations. Our extension can provide a new algorithm in classifications of data by means of linear response formulas in the statistical mechanics.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Minimal Nonlinear Distortion Principle for Nonlinear Independent Component Analysis

Zhang, K., Chan, L.

Journal of Machine Learning Research, 9, pages: 2455-2487, 2008 (article)

Abstract
It is well known that solutions to the nonlinear independent component analysis (ICA) problem are highly non-unique. In this paper we propose the "minimal nonlinear distortion" (MND) principle for tackling the ill-posedness of nonlinear ICA problems. MND prefers the nonlinear ICA solution with the estimated mixing procedure as close as possible to linear, among all possible solutions. It also helps to avoid local optima in the solutions. To achieve MND, we exploit a regularization term to minimize the mean square error between the nonlinear mixing mapping and the best-fitting linear one. The effect of MND on the inherent trivial and non-trivial indeterminacies in nonlinear ICA solutions is investigated. Moreover, we show that local MND is closely related to the smoothness regularizer penalizing large curvature, which provides another useful regularization condition for nonlinear ICA. Experiments on synthetic data show the usefulness of the MND principle for separating various nonlinear mixtures. Finally, as an application, we use nonlinear ICA with MND to separate daily returns of a set of stocks in Hong Kong, and the linear causal relations among them are successfully discovered. The resulting causal relations give some interesting insights into the stock market. Such a result can not be achieved by linear ICA. Simulation studies also verify that when doing causality discovery, sometimes one should not ignore the nonlinear distortion in the data generation procedure, even if it is weak.

Web [BibTex]

Web [BibTex]


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Transport processes in networks with scattering ramification nodes

Radl, A.

Journal of Applied Functional Analysis, 3, pages: 461-483, 2008 (article)

Web [BibTex]

Web [BibTex]


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Learning to control in operational space

Peters, J., Schaal, S.

International Journal of Robotics Research, 27, pages: 197-212, 2008, clmc (article)

Abstract
One of the most general frameworks for phrasing control problems for complex, redundant robots is operational space control. However, while this framework is of essential importance for robotics and well-understood from an analytical point of view, it can be prohibitively hard to achieve accurate control in face of modeling errors, which are inevitable in com- plex robots, e.g., humanoid robots. In this paper, we suggest a learning approach for opertional space control as a direct inverse model learning problem. A first important insight for this paper is that a physically cor- rect solution to the inverse problem with redundant degrees-of-freedom does exist when learning of the inverse map is performed in a suitable piecewise linear way. The second crucial component for our work is based on the insight that many operational space controllers can be understood in terms of a constrained optimal control problem. The cost function as- sociated with this optimal control problem allows us to formulate a learn- ing algorithm that automatically synthesizes a globally consistent desired resolution of redundancy while learning the operational space controller. From the machine learning point of view, this learning problem corre- sponds to a reinforcement learning problem that maximizes an immediate reward. We employ an expectation-maximization policy search algorithm in order to solve this problem. Evaluations on a three degrees of freedom robot arm are used to illustrate the suggested approach. The applica- tion to a physically realistic simulator of the anthropomorphic SARCOS Master arm demonstrates feasibility for complex high degree-of-freedom robots. We also show that the proposed method works in the setting of learning resolved motion rate control on real, physical Mitsubishi PA-10 medical robotics arm.

link (url) DOI [BibTex]

link (url) DOI [BibTex]

2007


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HPLC analysis and pharmacokinetic study of quercitrin and isoquercitrin in rat plasma after administration of Hypericum japonicum thunb. extract.

Li, J., Wang, W., Zhang, L., Chen, H., Bi, S.

Biomedical Chromatography, 22(4):374-378, December 2007 (article)

Abstract
A simple HPLC method was developed for determination of quercitrin and isoquercitrin in rat plasma. Reversed-phase HPLC was employed for the quantitative analysis using kaempferol-3-O--d-glucopyranoside-7-O--l-rhamnoside as an internal standard. Following extraction from the plasma samples with ethyl acetate-isopropanol (95:5, v/v), these two compounds were successfully separated on a Luna C18 column (250 × 4.6 mm, 5 µm) with isocratic elution of acetonitrile-0.5% aqueous acetic acid (17:83, v/v) as the mobile phase. The flow-rate was set at 1 mL/min and the eluent was detected at 350 nm for both quercitrin and isoquercitrin. The method was linear over the studied ranges of 50-6000 and 50-5000 ng/mL for quercitrin and isoquercitrin, respectively. The intra- and inter-day precisions of the analysis were better than 13.1 and 13.2%, respectively. The lower limits of quantitation for quercitrin and isoquercitrin in plasma were both of 50 ng/mL. The mean extraction recoveries were 73 and 61% for quercitrin and i soquercitrin, respectively. The validated method was successfully applied to pharmacokinetic studies of the two analytes in rat plasma after the oral administration of Hypericum japonicum thunb. ethanol extract.

Web DOI [BibTex]


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Positional Oligomer Importance Matrices

Sonnenburg, S., Zien, A., Philips, P., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences, above all of DNA and proteins. In many cases, the most accurate classifiers are obtained by training SVMs with complex sequence kernels, for instance for transcription starts or splice sites. However, an often criticized downside of SVMs with complex kernels is that it is very hard for humans to understand the learned decision rules and to derive biological insights from them. To close this gap, we introduce the concept of positional oligomer importance matrices (POIMs) and develop an efficient algorithm for their computation. We demonstrate how they overcome the limitations of sequence logos, and how they can be used to find relevant motifs for different biological phenomena in a straight-forward way. Note that the concept of POIMs is not limited to interpreting SVMs, but is applicable to general k−mer based scoring systems.

Web [BibTex]

Web [BibTex]


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Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism

Saigo, H., Hattori, M., Tsuda, K.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
Secondary metabolic pathway in plant is important for finding druggable candidate enzymes. However, there are many enzymes whose functions are still undiscovered especially in organism-specific metabolic pathways. We propose reaction graph kernels for automatically assigning the EC numbers to unknown enzymatic reactions in a metabolic network. Experiments are carried out on KEGG/REACTION database and our method successfully predicted the first three digits of the EC number with 83% accuracy.We also exhaustively predicted missing enzymatic functions in the plant secondary metabolism pathways, and evaluated our results in biochemical validity.

Web [BibTex]

Web [BibTex]


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Machine Learning Algorithms for Polymorphism Detection

Schweikert, G., Zeller, G., Weigel, D., Schölkopf, B., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Web [BibTex]

Web [BibTex]


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A Tutorial on Spectral Clustering

von Luxburg, U.

Statistics and Computing, 17(4):395-416, December 2007 (article)

Abstract
In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. On the first glance spectral clustering appears slightly mysterious, and it is not obvious to see why it works at all and what it really does. The goal of this tutorial is to give some intuition on those questions. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Graph sharpening plus graph integration: a synergy that improves protein functional classification

Shin, HH., Lisewski, AM., Lichtarge, O.

Bioinformatics, 23(23):3217-3224, December 2007 (article)

Web DOI [BibTex]

Web DOI [BibTex]


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An Automated Combination of Kernels for Predicting Protein Subcellular Localization

Zien, A., Ong, C.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions.We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We utilize an extension of the multiclass support vector machine (SVM)method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets, and show that we perform better than the current state of the art. Furthermore, our method provides some insights as to which features are most useful for determining subcellular localization, which are in agreement with biological reasoning.

Web [BibTex]

Web [BibTex]


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A Tutorial on Kernel Methods for Categorization

Jäkel, F., Schölkopf, B., Wichmann, F.

Journal of Mathematical Psychology, 51(6):343-358, December 2007 (article)

Abstract
The abilities to learn and to categorize are fundamental for cognitive systems, be it animals or machines, and therefore have attracted attention from engineers and psychologists alike. Modern machine learning methods and psychological models of categorization are remarkably similar, partly because these two fields share a common history in artificial neural networks and reinforcement learning. However, machine learning is now an independent and mature field that has moved beyond psychologically or neurally inspired algorithms towards providing foundations for a theory of learning that is rooted in statistics and functional analysis. Much of this research is potentially interesting for psychological theories of learning and categorization but also hardly accessible for psychologists. Here, we provide a tutorial introduction to a popular class of machine learning tools, called kernel methods. These methods are closely related to perceptrons, radial-basis-function neural networks and exemplar theories of catego rization. Recent theoretical advances in machine learning are closely tied to the idea that the similarity of patterns can be encapsulated in a positive definite kernel. Such a positive definite kernel can define a reproducing kernel Hilbert space which allows one to use powerful tools from functional analysis for the analysis of learning algorithms. We give basic explanations of some key concepts—the so-called kernel trick, the representer theorem and regularization—which may open up the possibility that insights from machine learning can feed back into psychology.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Accurate Splice site Prediction Using Support Vector Machines

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., Rätsch, G.

BMC Bioinformatics, 8(Supplement 10):1-16, December 2007 (article)

Abstract
Background: For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks. Results: In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder. Availability: Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http:// www.fml.mpg.de/raetsch/projects/splice.

PDF DOI [BibTex]

PDF DOI [BibTex]


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A semigroup approach to queueing systems

Haji, A., Radl, A.

Semigroup Forum, 75(3):610-624, December 2007 (article)

Abstract
We prove asymptotic stability of the solutions of equations describing a simple queueing system consisting of two machines separated by a finite storage buffer. Following an approach by G. Gupur, we apply the theory of C0-semigroups and spectral theory of positive operators.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Point-spread functions for backscattered imaging in the scanning electron microscope

Hennig, P., Denk, W.

Journal of Applied Physics , 102(12):1-8, December 2007 (article)

Abstract
One knows the imaging system's properties are central to the correct interpretation of any image. In a scanning electron microscope regions of different composition generally interact in a highly nonlinear way during signal generation. Using Monte Carlo simulations we found that in resin-embedded, heavy metal-stained biological specimens staining is sufficiently dilute to allow an approximately linear treatment. We then mapped point-spread functions for backscattered-electron contrast, for primary energies of 3 and 7 keV and for different detector specifications. The point-spread functions are surprisingly well confined (both laterally and in depth) compared even to the distribution of only those scattered electrons that leave the sample again.

Web DOI [BibTex]

Web DOI [BibTex]


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Challenges in Brain-Computer Interface Development: Induction, Measurement, Decoding, Integration

Hill, NJ.

Invited keynote talk at the launch of BrainGain, the Dutch BCI research consortium, November 2007 (talk)

Abstract
I‘ll present a perspective on Brain-Computer Interface development from T{\"u}bingen. Some of the benefits promised by BCI technology lie in the near foreseeable future, and some further away. Our motivation is to make BCI technology feasible for the people who could benefit from what it has to offer soon: namely, people in the "completely locked-in" state. I‘ll mention some of the challenges of working with this user group, and explain the specific directions they have motivated us to take in developing experimental methods, algorithms, and software.

[BibTex]

[BibTex]


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Policy Learning for Robotics

Peters, J.

14th International Conference on Neural Information Processing (ICONIP), November 2007 (talk)

Web [BibTex]

Web [BibTex]


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A unifying framework for robot control with redundant DOFs

Peters, J., Mistry, M., Udwadia, F., Nakanishi, J., Schaal, S.

Autonomous Robots, 24(1):1-12, October 2007 (article)

Abstract
Recently, Udwadia (Proc. R. Soc. Lond. A 2003:1783–1800, 2003) suggested to derive tracking controllers for mechanical systems with redundant degrees-of-freedom (DOFs) using a generalization of Gauss’ principle of least constraint. This method allows reformulating control problems as a special class of optimal controllers. In this paper, we take this line of reasoning one step further and demonstrate that several well-known and also novel nonlinear robot control laws can be derived from this generic methodology. We show experimental verifications on a Sarcos Master Arm robot for some of the derived controllers. The suggested approach offers a promising unification and simplification of nonlinear control law design for robots obeying rigid body dynamics equations, both with or without external constraints, with over-actuation or underactuation, as well as open-chain and closed-chain kinematics.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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The Need for Open Source Software in Machine Learning

Sonnenburg, S., Braun, M., Ong, C., Bengio, S., Bottou, L., Holmes, G., LeCun, Y., Müller, K., Pereira, F., Rasmussen, C., Rätsch, G., Schölkopf, B., Smola, A., Vincent, P., Weston, J., Williamson, R.

Journal of Machine Learning Research, 8, pages: 2443-2466, October 2007 (article)

Abstract
Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a large body of powerful learning algorithms for diverse applications. However, the true potential of these methods is not realized, since existing implementations are not openly shared, resulting in software with low usability, and weak interoperability. We argue that this situation can be significantly improved by increasing incentives for researchers to publish their software under an open source model. Additionally, we outline the problems authors are faced with when trying to publish algorithmic implementations of machine learning methods. We believe that a resource of peer reviewed software accompanied by short articles would be highly valuable to both the machine learning and the general scientific community.

PDF Web [BibTex]

PDF Web [BibTex]


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Hilbert Space Representations of Probability Distributions

Gretton, A.

2nd Workshop on Machine Learning and Optimization at the ISM, October 2007 (talk)

Abstract
Many problems in unsupervised learning require the analysis of features of probability distributions. At the most fundamental level, we might wish to determine whether two distributions are the same, based on samples from each - this is known as the two-sample or homogeneity problem. We use kernel methods to address this problem, by mapping probability distributions to elements in a reproducing kernel Hilbert space (RKHS). Given a sufficiently rich RKHS, these representations are unique: thus comparing feature space representations allows us to compare distributions without ambiguity. Applications include testing whether cancer subtypes are distinguishable on the basis of DNA microarray data, and whether low frequency oscillations measured at an electrode in the cortex have a different distribution during a neural spike. A more difficult problem is to discover whether two random variables drawn from a joint distribution are independent. It turns out that any dependence between pairs of random variables can be encoded in a cross-covariance operator between appropriate RKHS representations of the variables, and we may test independence by looking at a norm of the operator. We demonstrate this independence test by establishing dependence between an English text and its French translation, as opposed to French text on the same topic but otherwise unrelated. Finally, we show that this operator norm is itself a difference in feature means.

PDF Web [BibTex]

PDF Web [BibTex]


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Regression with Intervals

Kashima, H., Yamazaki, K., Saigo, H., Inokuchi, A.

International Workshop on Data-Mining and Statistical Science (DMSS2007), October 2007, JSAI Incentive Award. Talk was given by Hisashi Kashima. (talk)

Web [BibTex]

Web [BibTex]


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On the Representer Theorem and Equivalent Degrees of Freedom of SVR

Dinuzzo, F., Neve, M., De Nicolao, G., Gianazza, U.

Journal of Machine Learning Research, 8, pages: 2467-2495, October 2007 (article)

Abstract
Support Vector Regression (SVR) for discrete data is considered. An alternative formulation of the representer theorem is derived. This result is based on the newly introduced notion of pseudoresidual and the use of subdifferential calculus. The representer theorem is exploited to analyze the sensitivity properties of ε-insensitive SVR and introduce the notion of approximate degrees of freedom. The degrees of freedom are shown to play a key role in the evaluation of the optimism, that is the difference between the expected in-sample error and the expected empirical risk. In this way, it is possible to define a Cp-like statistic that can be used for tuning the parameters of SVR. The proposed tuning procedure is tested on a simulated benchmark problem and on a real world problem (Boston Housing data set).

Web [BibTex]

Web [BibTex]


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Some observations on the masking effects of Mach bands

Curnow, T., Cowie, DA., Henning, GB., Hill, NJ.

Journal of the Optical Society of America A, 24(10):3233-3241, October 2007 (article)

Abstract
There are 8 cycle / deg ripples or oscillations in performance as a function of location near Mach bands in experiments measuring Mach bands’ masking effects on random polarity signal bars. The oscillations with increments are 180 degrees out of phase with those for decrements. The oscillations, much larger than the measurement error, appear to relate to the weighting function of the spatial-frequency-tuned channel detecting the broad- band signals. The ripples disappear with step maskers and become much smaller at durations below 25 ms, implying either that the site of masking has changed or that the weighting function and hence spatial-frequency tuning is slow to develop.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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MR-Based PET Attenuation Correction: Method and Validation

Hofmann, M., Steinke, F., Scheel, V., Brady, M., Schölkopf, B., Pichler, B.

Joint Molecular Imaging Conference, September 2007 (talk)

Abstract
PET/MR combines the high soft tissue contrast of Magnetic Resonance Imaging (MRI) and the functional information of Positron Emission Tomography (PET). For quantitative PET information, correction of tissue photon attenuation is mandatory. Usually in conventional PET, the attenuation map is obtained from a transmission scan, which uses a rotating source, or from the CT scan in case of combined PET/CT. In the case of a PET/MR scanner, there is insufficient space for the rotating source and ideally one would want to calculate the attenuation map from the MR image instead. Since MR images provide information about proton density of the different tissue types, it is not trivial to use this data for PET attenuation correction. We present a method for predicting the PET attenuation map from a given the MR image, using a combination of atlas-registration and recognition of local patterns. Using "leave one out cross validation" we show on a database of 16 MR-CT image pairs that our method reliably allows estimating the CT image from the MR image. Subsequently, as in PET/CT, the PET attenuation map can be predicted from the CT image. On an additional dataset of MR/CT/PET triplets we quantitatively validate that our approach allows PET quantification with an error that is smaller than what would be clinically significant. We demonstrate our approach on T1-weighted human brain scans. However, the presented methods are more general and current research focuses on applying the established methods to human whole body PET/MRI applications.

PDF Web [BibTex]

PDF Web [BibTex]


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Mining complex genotypic features for predicting HIV-1 drug resistance

Saigo, H., Uno, T., Tsuda, K.

Bioinformatics, 23(18):2455-2462, September 2007 (article)

Abstract
Human immunodeficiency virus type 1 (HIV-1) evolves in human body, and its exposure to a drug often causes mutations that enhance the resistance against the drug. To design an effective pharmacotherapy for an individual patient, it is important to accurately predict the drug resistance based on genotype data. Notably, the resistance is not just the simple sum of the effects of all mutations. Structural biological studies suggest that the association of mutations is crucial: Even if mutations A or B alone do not affect the resistance, a significant change might happen when the two mutations occur together. Linear regression methods cannot take the associations into account, while decision tree methods can reveal only limited associations. Kernel methods and neural networks implicitly use all possible associations for prediction, but cannot select salient associations explicitly. Our method, itemset boosting, performs linear regression in the complete space of power sets of mutations. It implements a forward feature selection procedure where, in each iteration, one mutation combination is found by an efficient branch-and-bound search. This method uses all possible combinations, and salient associations are explicitly shown. In experiments, our method worked particularly well for predicting the resistance of nucleotide reverse transcriptase inhibitors (NRTIs). Furthermore, it successfully recovered many mutation associations known in biological literature.

Web DOI [BibTex]

Web DOI [BibTex]


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Bayesian methods for NMR structure determination

Habeck, M.

29th Annual Discussion Meeting: Magnetic Resonance in Biophysical Chemistry, September 2007 (talk)

Web [BibTex]

Web [BibTex]


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Real-Time Fetal Heart Monitoring in Biomagnetic Measurements Using Adaptive Real-Time ICA

Waldert, S., Bensch, M., Bogdan, M., Rosenstiel, W., Schölkopf, B., Lowery, C., Eswaran, H., Preissl, H.

IEEE Transactions on Biomedical Engineering, 54(10):1867-1874, September 2007 (article)

Abstract
Electrophysiological signals of the developing fetal brain and heart can be investigated by fetal magnetoencephalography (fMEG). During such investigations, the fetal heart activity and that of the mother should be monitored continuously to provide an important indication of current well-being. Due to physical constraints of an fMEG system, it is not possible to use clinically established heart monitors for this purpose. Considering this constraint, we developed a real-time heart monitoring system for biomagnetic measurements and showed its reliability and applicability in research and for clinical examinations. The developed system consists of real-time access to fMEG data, an algorithm based on Independent Component Analysis (ICA), and a graphical user interface (GUI). The algorithm extracts the current fetal and maternal heart signal from a noisy and artifact-contaminated data stream in real-time and is able to adapt automatically to continuously varying environmental parameters. This algorithm has been na med Adaptive Real-time ICA (ARICA) and is applicable to real-time artifact removal as well as to related blind signal separation problems.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Overcomplete Independent Component Analysis via Linearly Constrained Minimum Variance Spatial Filtering

Grosse-Wentrup, M., Buss, M.

Journal of VLSI Signal Processing, 48(1-2):161-171, August 2007 (article)

Abstract
Independent Component Analysis (ICA) designed for complete bases is used in a variety of applications with great success, despite the often questionable assumption of having N sensors and M sources with N&#8805;M. In this article, we assume a source model with more sources than sensors (M>N), only L<N of which are assumed to have a non-Gaussian distribution. We argue that this is a realistic source model for a variety of applications, and prove that for ICA algorithms designed for complete bases (i.e., algorithms assuming N=M) based on mutual information the mixture coefficients of the L non-Gaussian sources can be reconstructed in spite of the overcomplete mixture model. Further, it is shown that the reconstructed temporal activity of non-Gaussian sources is arbitrarily mixed with Gaussian sources. To obtain estimates of the temporal activity of the non-Gaussian sources, we use the correctly reconstructed mixture coefficients in conjunction with linearly constrained minimum variance spatial filtering. This results in estimates of the non-Gaussian sources minimizing the variance of the interference of other sources. The approach is applied to the denoising of Event Related Fields recorded by MEG, and it is shown that it performs superiorly to ordinary ICA.

PDF PDF DOI [BibTex]