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83 results (View BibTeX file of all listed publications)

2009

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Efficient Subwindow Search: A Branch and Bound Framework for Object Localization

Lampert, C., Blaschko, M., Hofmann, T.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 31(12):2129-2142, December 2009 (article)

Abstract
Most successful object recognition systems rely on binary classification, deciding only if an object is present or not, but not providing information on the actual object location. To estimate the object‘s location, one can take a sliding window approach, but this strongly increases the computational cost because the classifier or similarity function has to be evaluated over a large set of candidate subwindows. In this paper, we propose a simple yet powerful branch and bound scheme that allows efficient maximization of a large class of quality functions over all possible subimages. It converges to a globally optimal solution typically in linear or even sublinear time, in contrast to the quadratic scaling of exhaustive or sliding window search. We show how our method is applicable to different object detection and image retrieval scenarios. The achieved speedup allows the use of classifiers for localization that formerly were considered too slow for this task, such as SVMs with a spatial pyramid kernel or nearest-neighbor classifiers based on the chi^2 distance. We demonstrate state-of-the-art localization performance of the resulting systems on the UIUC Cars data set, the PASCAL VOC 2006 data set, and in the PASCAL VOC 2007 competition.

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2009

Lampert, C., Blaschko, M., Hofmann, T. Efficient Subwindow Search: A Branch and Bound Framework for Object Localization IEEE Transactions on Pattern Analysis and Machine Intelligence, 31(12):2129-2142, December 2009 (article)

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Generation of three-dimensional random rotations in fitting and matching problems

Habeck, M.

Computational Statistics, 24(4):719-731, December 2009 (article)

Abstract
An algorithm is developed to generate random rotations in three-dimensional space that follow a probability distribution arising in fitting and matching problems. The rotation matrices are orthogonally transformed into an optimal basis and then parameterized using Euler angles. The conditional distributions of the three Euler angles have a very simple form: the two azimuthal angles can be decoupled by sampling their sum and difference from a von Mises distribution; the cosine of the polar angle is exponentially distributed and thus straighforward to generate. Simulation results are shown and demonstrate the effectiveness of the method. The algorithm is compared to other methods for generating random rotations such as a random walk Metropolis scheme and a Gibbs sampling algorithm recently introduced by Green and Mardia. Finally, the algorithm is applied to a probabilistic version of the Procrustes problem of fitting two point sets and applied in the context of protein structure superposition.

PDF DOI [BibTex]

Habeck, M. Generation of three-dimensional random rotations in fitting and matching problems Computational Statistics, 24(4):719-731, December 2009 (article)

PDF DOI [BibTex]

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Adaptive Importance Sampling for Value Function Approximation in Off-policy Reinforcement Learning

Hachiya, H., Akiyama, T., Sugiyama, M., Peters, J.

Neural Networks, 22(10):1399-1410, December 2009 (article)

Abstract
Off-policy reinforcement learning is aimed at efficiently using data samples gathered from a policy that is different from the currently optimized policy. A common approach is to use importance sampling techniques for compensating for the bias of value function estimators caused by the difference between the data-sampling policy and the target policy. However, existing off-policy methods often do not take the variance of the value function estimators explicitly into account and therefore their performance tends to be unstable. To cope with this problem, we propose using an adaptive importance sampling technique which allows us to actively control the trade-off between bias and variance. We further provide a method for optimally determining the trade-off parameter based on a variant of cross-validation. We demonstrate the usefulness of the proposed approach through simulations.

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Hachiya, H., Akiyama, T., Sugiyama, M., Peters, J. Adaptive Importance Sampling for Value Function Approximation in Off-policy Reinforcement Learning Neural Networks, 22(10):1399-1410, December 2009 (article)

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Guest editorial: special issue on structured prediction

Parker, C., Altun, Y., Tadepalli, P.

Machine Learning, 77(2-3):161-164, December 2009 (article)

PDF DOI [BibTex]

Parker, C., Altun, Y., Tadepalli, P. Guest editorial: special issue on structured prediction Machine Learning, 77(2-3):161-164, December 2009 (article)

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Structured prediction by joint kernel support estimation

Lampert, CH., Blaschko, MB.

Machine Learning, 77(2-3):249-269, December 2009 (article)

PDF DOI [BibTex]

Lampert, CH., Blaschko, MB. Structured prediction by joint kernel support estimation Machine Learning, 77(2-3):249-269, December 2009 (article)

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A note on ethical aspects of BCI

Haselager, P., Vlek, R., Hill, J., Nijboer, F.

Neural Networks, 22(9):1352-1357, November 2009 (article)

Abstract
This paper focuses on ethical aspects of BCI, as a research and a clinical tool, that are challenging for practitioners currently working in the field. Specifically, the difficulties involved in acquiring informed consent from locked-in patients are investigated, in combination with an analysis of the shared moral responsibility in BCI teams, and the complications encountered in establishing effective communication with media.

Web DOI [BibTex]

Haselager, P., Vlek, R., Hill, J., Nijboer, F. A note on ethical aspects of BCI Neural Networks, 22(9):1352-1357, November 2009 (article)

Web DOI [BibTex]

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Model Learning with Local Gaussian Process Regression

Nguyen-Tuong, D., Seeger, M., Peters, J.

Advanced Robotics, 23(15):2015-2034, November 2009 (article)

Abstract
Precise models of robot inverse dynamics allow the design of significantly more accurate, energy-efficient and compliant robot control. However, in some cases the accuracy of rigid-body models does not suffice for sound control performance due to unmodeled nonlinearities arising from hydraulic cable dynamics, complex friction or actuator dynamics. In such cases, estimating the inverse dynamics model from measured data poses an interesting alternative. Nonparametric regression methods, such as Gaussian process regression (GPR) or locally weighted projection regression (LWPR), are not as restrictive as parametric models and, thus, offer a more flexible framework for approximating unknown nonlinearities. In this paper, we propose a local approximation to the standard GPR, called local GPR (LGP), for real-time model online learning by combining the strengths of both regression methods, i.e., the high accuracy of GPR and the fast speed of LWPR. The approach is shown to have competitive learning performance for hig h-dimensional data while being sufficiently fast for real-time learning. The effectiveness of LGP is exhibited by a comparison with the state-of-the-art regression techniques, such as GPR, LWPR and ν-support vector regression. The applicability of the proposed LGP method is demonstrated by real-time online learning of the inverse dynamics model for robot model-based control on a Barrett WAM robot arm.

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Methods for feature selection in a learning machine

Weston, J., Elisseeff, A., Schölkopf, B., Pérez-Cruz, F.

United States Patent, No 7624074, November 2009 (patent)

[BibTex]

Weston, J., Elisseeff, A., Schölkopf, B., Pérez-Cruz, F. Methods for feature selection in a learning machine United States Patent, No 7624074, November 2009 (patent)

[BibTex]

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Toward a Theory of Consciousness

Tononi, G., Balduzzi, D.

In The Cognitive Neurosciences, pages: 1201-1220, (Editors: Gazzaniga, M.S.), MIT Press, Cambridge, MA, USA, October 2009 (inbook)

Web [BibTex]

Tononi, G., Balduzzi, D. Toward a Theory of Consciousness In The Cognitive Neurosciences, pages: 1201-1220, (Editors: Gazzaniga, M.S.), MIT Press, Cambridge, MA, USA, October 2009 (inbook)

Web [BibTex]

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Inferring textual entailment with a probabilistically sound calculus

Harmeling, S.

Natural Language Engineering, 15(4):459-477, October 2009 (article)

Abstract
We introduce a system for textual entailment that is based on a probabilistic model of entailment. The model is defined using a calculus of transformations on dependency trees, which is characterized by the fact that derivations in that calculus preserve the truth only with a certain probability. The calculus is successfully evaluated on the datasets of the PASCAL Challenge on Recognizing Textual Entailment.

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Harmeling, S. Inferring textual entailment with a probabilistically sound calculus Natural Language Engineering, 15(4):459-477, October 2009 (article)

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Modeling and Visualizing Uncertainty in Gene Expression Clusters using Dirichlet Process Mixtures

Rasmussen, CE., de la Cruz, BJ., Ghahramani, Z., Wild, DL.

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4):615-628, October 2009 (article)

Abstract
Although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data, little attention has been paid to uncertainty in the results obtained. Dirichlet process mixture models provide a non-parametric Bayesian alternative to the bootstrap approach to modeling uncertainty in gene expression clustering. Most previously published applications of Bayesian model based clustering methods have been to short time series data. In this paper we present a case study of the application of non-parametric Bayesian clustering methods to the clustering of high-dimensional non-time series gene expression data using full Gaussian covariances. We use the probability that two genes belong to the same cluster in a Dirichlet process mixture model as a measure of the similarity of these gene expression profiles. Conversely, this probability can be used to define a dissimilarity measure, which, for the purposes of visualization, can be input to one of the standard linkage algorithms used for hierarchical clustering. Biologically plausible results are obtained from the Rosetta compendium of expression profiles which extend previously published cluster analyses of this data.

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Rasmussen, CE., de la Cruz, BJ., Ghahramani, Z., Wild, DL. Modeling and Visualizing Uncertainty in Gene Expression Clusters using Dirichlet Process Mixtures IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6(4):615-628, October 2009 (article)

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Thermodynamic efficiency of information and heat flow

Allahverdyan, A., Janzing, D., Mahler, G.

Journal of Statistical Mechanics: Theory and Experiment, 2009(09):P09011, September 2009 (article)

Abstract
A basic task of information processing is information transfer (flow). P0 Here we study a pair of Brownian particles each coupled to a thermal bath at temperatures T1 and T2 . The information flow in such a system is defined via the time-shifted mutual information. The information flow nullifies at equilibrium, and its efficiency is defined as the ratio of the flow to the total entropy production in the system. For a stationary state the information flows from higher to lower temperatures, and its efficiency is bounded from above by (max[T1 , T2 ])/(|T1 − T2 |). This upper bound is imposed by the second law and it quantifies the thermodynamic cost for information flow in the present class of systems. It can be reached in the adiabatic situation, where the particles have widely different characteristic times. The efficiency of heat flow—defined as the heat flow over the total amount of dissipated heat—is limited from above by the same factor. There is a complementarity between heat and information flow: the set-up which is most efficient for the former is the least efficient for the latter and vice versa. The above bound for the efficiency can be (transiently) overcome in certain non-stationary situations, but the efficiency is still limited from above. We study yet another measure of information processing (transfer entropy) proposed in the literature. Though this measure does not require any thermodynamic cost, the information flow and transfer entropy are shown to be intimately related for stationary states.

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Allahverdyan, A., Janzing, D., Mahler, G. Thermodynamic efficiency of information and heat flow Journal of Statistical Mechanics: Theory and Experiment, 2009(09):P09011, September 2009 (article)

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Does Cognitive Science Need Kernels?

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

Trends in Cognitive Sciences, 13(9):381-388, September 2009 (article)

Abstract
Kernel methods are among the most successful tools in machine learning and are used in challenging data analysis problems in many disciplines. Here we provide examples where kernel methods have proven to be powerful tools for analyzing behavioral data, especially for identifying features in categorization experiments. We also demonstrate that kernel methods relate to perceptrons and exemplar models of categorization. Hence, we argue that kernel methods have neural and psychological plausibility, and theoretical results concerning their behavior are therefore potentially relevant for human category learning. In particular, we believe kernel methods have the potential to provide explanations ranging from the implementational via the algorithmic to the computational level.

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Jäkel, F., Schölkopf, B., Wichmann, F. Does Cognitive Science Need Kernels? Trends in Cognitive Sciences, 13(9):381-388, September 2009 (article)

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Inference algorithms and learning theory for Bayesian sparse factor analysis

Rattray, M., Stegle, O., Sharp, K., Winn, J.

Journal of Physics: Conference Series , IW-SMI 2009, 197(1: International Workshop on Statistical-Mechanical Informatics 2009):1-10, (Editors: Inoue, M. , S. Ishii, Y. Kabashima, M. Okada), Institute of Physics, Bristol, UK, International Workshop on Statistical-Mechanical Informatics (IW-SMI), September 2009 (article)

Abstract
Bayesian sparse factor analysis has many applications; for example, it has been applied to the problem of inferring a sparse regulatory network from gene expression data. We describe a number of inference algorithms for Bayesian sparse factor analysis using a slab and spike mixture prior. These include well-established Markov chain Monte Carlo (MCMC) and variational Bayes (VB) algorithms as well as a novel hybrid of VB and Expectation Propagation (EP). For the case of a single latent factor we derive a theory for learning performance using the replica method. We compare the MCMC and VB/EP algorithm results with simulated data to the theoretical prediction. The results for MCMC agree closely with the theory as expected. Results for VB/EP are slightly sub-optimal but show that the new algorithm is effective for sparse inference. In large-scale problems MCMC is infeasible due to computational limitations and the VB/EP algorithm then provides a very useful computationally efficient alternative.

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Rattray, M., Stegle, O., Sharp, K., Winn, J. Inference algorithms and learning theory for Bayesian sparse factor analysis Journal of Physics: Conference Series , IW-SMI 2009, 197(1: International Workshop on Statistical-Mechanical Informatics 2009):1-10, (Editors: Inoue, M. , S. Ishii, Y. Kabashima, M. Okada), Institute of Physics, Bristol, UK, International Workshop on Statistical-Mechanical Informatics (IW-SMI), September 2009 (article)

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Finite-time output stabilization with second order sliding modes

Dinuzzo, F., Ferrara, A.

Automatica, 45(9):2169-2171, September 2009 (article)

Abstract
In this note, a class of discontinuous feedback laws that switch over branches of parabolas in the auxiliary state plane is analyzed. Conditions are provided under which controllers belonging to this class are second order sliding-mode algorithms: they ensure uniform global finite-time output stability for uncertain systems of relative degree two.

Web DOI [BibTex]

Dinuzzo, F., Ferrara, A. Finite-time output stabilization with second order sliding modes Automatica, 45(9):2169-2171, September 2009 (article)

Web DOI [BibTex]

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Robot Learning

Peters, J., Morimoto, J., Tedrake, R., Roy, N.

IEEE Robotics and Automation Magazine, 16(3):19-20, September 2009 (article)

Abstract
Creating autonomous robots that can learn to act in unpredictable environments has been a long-standing goal of robotics, artificial intelligence, and the cognitive sciences. In contrast, current commercially available industrial and service robots mostly execute fixed tasks and exhibit little adaptability. To bridge this gap, machine learning offers a myriad set of methods, some of which have already been applied with great success to robotics problems. As a result, there is an increasing interest in machine learning and statistics within the robotics community. At the same time, there has been a growth in the learning community in using robots as motivating applications for new algorithms and formalisms. Considerable evidence of this exists in the use of learning in high-profile competitions such as RoboCup and the Defense Advanced Research Projects Agency (DARPA) challenges, and the growing number of research programs funded by governments around the world.

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Peters, J., Morimoto, J., Tedrake, R., Roy, N. Robot Learning IEEE Robotics and Automation Magazine, 16(3):19-20, September 2009 (article)

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Higher order sliding mode controllers with optimal reaching

Dinuzzo, F., Ferrara, A.

IEEE Transactions on Automatic Control, 54(9):2126-2136, September 2009 (article)

Abstract
Higher order sliding mode (HOSM) control design is considered for systems with a known permanent relative degree. In this paper, we introduce the robust Fuller's problem that is a robust generalization of the Fuller's problem, a standard optimal control problem for a chain of integrators with bounded control. By solving the robust Fuller's problem it is possible to obtain feedback laws that are HOSM algorithms of generic order and, in addition, provide optimal finite-time reaching of the sliding manifold. A common difficulty in the use of existing HOSM algorithms is the tuning of design parameters: our methodology proves useful for the tuning of HOSM controller parameters in order to assure desired performances and prevent instabilities. The convergence and stability properties of the proposed family of controllers are theoretically analyzed. Simulation evidence demonstrates their effectiveness.

DOI [BibTex]

Dinuzzo, F., Ferrara, A. Higher order sliding mode controllers with optimal reaching IEEE Transactions on Automatic Control, 54(9):2126-2136, September 2009 (article)

DOI [BibTex]

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Kernel Methods in Computer Vision

Lampert, CH.

Foundations and Trends in Computer Graphics and Vision, 4(3):193-285, September 2009 (article)

Abstract
Over the last years, kernel methods have established themselves as powerful tools for computer vision researchers as well as for practitioners. In this tutorial, we give an introduction to kernel methods in computer vision from a geometric perspective, introducing not only the ubiquitous support vector machines, but also less known techniques for regression, dimensionality reduction, outlier detection and clustering. Additionally, we give an outlook on very recent, non-classical techniques for the prediction of structure data, for the estimation of statistical dependency and for learning the kernel function itself. All methods are illustrated with examples of successful application from the recent computer vision research literature.

Web DOI [BibTex]

Lampert, CH. Kernel Methods in Computer Vision Foundations and Trends in Computer Graphics and Vision, 4(3):193-285, September 2009 (article)

Web DOI [BibTex]

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A Novel Approach to the Selection of Spatially Invariant Features for the Classification of Hyperspectral Images with Improved Generalization Capability

Bruzzone, L., Persello, C.

IEEE Transactions on Geoscience and Remote Sensing, 47(9):3180-3191, September 2009 (article)

Abstract
This paper presents a novel approach to feature selection for the classification of hyperspectral images. The proposed approach aims at selecting a subset of the original set of features that exhibits at the same time high capability to discriminate among the considered classes and high invariance in the spatial domain of the investigated scene. This approach results in a more robust classification system with improved generalization properties with respect to standard feature-selection methods. The feature selection is accomplished by defining a multiobjective criterion function made up of two terms: (1) a term that measures the class separability and (2) a term that evaluates the spatial invariance of the selected features. In order to assess the spatial invariance of the feature subset, we propose both a supervised method (which assumes that training samples acquired in two or more spatially disjoint areas are available) and a semisupervised method (which requires only a standard training set acquired in a single area of the scene and takes advantage of unlabeled samples selected in portions of the scene spatially disjoint from the training set). The choice for the supervised or semisupervised method depends on the available reference data. The multiobjective problem is solved by an evolutionary algorithm that estimates the set of Pareto-optimal solutions. Experiments carried out on a hyperspectral image acquired by the Hyperion sensor on a complex area confirmed the effectiveness of the proposed approach.

Web DOI [BibTex]

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Fast Kernel-Based Independent Component Analysis

Shen, H., Jegelka, S., Gretton, A.

IEEE Transactions on Signal Processing, 57(9):3498-3511, September 2009 (article)

Abstract
Recent approaches to independent component analysis (ICA) have used kernel independence measures to obtain highly accurate solutions, particularly where classical methods experience difficulty (for instance, sources with near-zero kurtosis). FastKICA (fast HSIC-based kernel ICA) is a new optimization method for one such kernel independence measure, the Hilbert-Schmidt Independence Criterion (HSIC). The high computational efficiency of this approach is achieved by combining geometric optimization techniques, specifically an approximate Newton-like method on the orthogonal group, with accurate estimates of the gradient and Hessian based on an incomplete Cholesky decomposition. In contrast to other efficient kernel-based ICA algorithms, FastKICA is applicable to any twice differentiable kernel function. Experimental results for problems with large numbers of sources and observations indicate that FastKICA provides more accurate solutions at a given cost than gradient descent on HSIC. Comparing with other recently published ICA methods, FastKICA is competitive in terms of accuracy, relatively insensitive to local minima when initialized far from independence, and more robust towards outliers. An analysis of the local convergence properties of FastKICA is provided.

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Shen, H., Jegelka, S., Gretton, A. Fast Kernel-Based Independent Component Analysis IEEE Transactions on Signal Processing, 57(9):3498-3511, September 2009 (article)

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Qualia: The Geometry of Integrated Information

Balduzzi, D., Tononi, G.

PLoS Computational Biology, 5(8):1-24, August 2009 (article)

Abstract
According to the integrated information theory, the quantity of consciousness is the amount of integrated information generated by a complex of elements, and the quality of experience is specified by the informational relationships it generates. This paper outlines a framework for characterizing the informational relationships generated by such systems. Qualia space (Q) is a space having an axis for each possible state (activity pattern) of a complex. Within Q, each submechanism specifies a point corresponding to a repertoire of system states. Arrows between repertoires in Q define informational relationships. Together, these arrows specify a quale—a shape that completely and univocally characterizes the quality of a conscious experience. Φ— the height of this shape—is the quantity of consciousness associated with the experience. Entanglement measures how irreducible informational relationships are to their component relationships, specifying concepts and modes. Several corollaries follow from these premises. The quale is determined by both the mechanism and state of the system. Thus, two different systems having identical activity patterns may generate different qualia. Conversely, the same quale may be generated by two systems that differ in both activity and connectivity. Both active and inactive elements specify a quale, but elements that are inactivated do not. Also, the activation of an element affects experience by changing the shape of the quale. The subdivision of experience into modalities and submodalities corresponds to subshapes in Q. In principle, different aspects of experience may be classified as different shapes in Q, and the similarity between experiences reduces to similarities between shapes. Finally, specific qualities, such as the “redness” of red, while generated by a local mechanism, cannot be reduced to it, but require considering the entire quale. Ultimately, the present framework may offer a principled way for translating qualitative properties of experience into mathematics.

Web DOI [BibTex]

Balduzzi, D., Tononi, G. Qualia: The Geometry of Integrated Information PLoS Computational Biology, 5(8):1-24, August 2009 (article)

Web DOI [BibTex]

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Guest editorial: Special issue on robot learning, Part B

Peters, J., Ng, A.

Autonomous Robots, 27(2):91-92, August 2009 (article)

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Peters, J., Ng, A. Guest editorial: Special issue on robot learning, Part B Autonomous Robots, 27(2):91-92, August 2009 (article)

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Policy Search for Motor Primitives

Peters, J., Kober, J.

KI - Zeitschrift K{\"u}nstliche Intelligenz, 23(3):38-40, August 2009 (article)

Abstract
Many motor skills in humanoid robotics can be learned using parametrized motor primitives from demonstrations. However, most interesting motor learning problems require self-improvement often beyond the reach of current reinforcement learning methods due to the high dimensionality of the state-space. We develop an EM-inspired algorithm applicable to complex motor learning tasks. We compare this algorithm to several well-known parametrized policy search methods and show that it outperforms them. We apply it to motor learning problems and show that it can learn the complex Ball-in-a-Cup task using a real Barrett WAM robot arm.

Web [BibTex]

Peters, J., Kober, J. Policy Search for Motor Primitives KI - Zeitschrift K{\"u}nstliche Intelligenz, 23(3):38-40, August 2009 (article)

Web [BibTex]

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A neurophysiologically plausible population code model for human contrast discrimination

Goris, R., Wichmann, F., Henning, G.

Journal of Vision, 9(7):1-22, July 2009 (article)

Abstract
The pedestal effect is the improvement in the detectability of a sinusoidal grating in the presence of another grating of the same orientation, spatial frequency, and phase—usually called the pedestal. Recent evidence has demonstrated that the pedestal effect is differently modified by spectrally flat and notch-filtered noise: The pedestal effect is reduced in flat noise but virtually disappears in the presence of notched noise (G. B. Henning & F. A. Wichmann, 2007). Here we consider a network consisting of units whose contrast response functions resemble those of the cortical cells believed to underlie human pattern vision and demonstrate that, when the outputs of multiple units are combined by simple weighted summation—a heuristic decision rule that resembles optimal information combination and produces a contrast-dependent weighting profile—the network produces contrast-discrimination data consistent with psychophysical observations: The pedestal effect is present without noise, reduced in broadband noise, but almost disappears in notched noise. These findings follow naturally from the normalization model of simple cells in primary visual cortex, followed by response-based pooling, and suggest that in processing even low-contrast sinusoidal gratings, the visual system may combine information across neurons tuned to different spatial frequencies and orientations.

Web DOI [BibTex]

Goris, R., Wichmann, F., Henning, G. A neurophysiologically plausible population code model for human contrast discrimination Journal of Vision, 9(7):1-22, July 2009 (article)

Web DOI [BibTex]

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A Novel Context-Sensitive Semisupervised SVM Classifier Robust to Mislabeled Training Samples

Bruzzone, L., Persello, C.

IEEE Transactions on Geoscience and Remote Sensing, 47(7):2142-2154, July 2009 (article)

Abstract
This paper presents a novel context-sensitive semisupervised support vector machine (CS4VM) classifier, which is aimed at addressing classification problems where the available training set is not fully reliable, i.e., some labeled samples may be associated to the wrong information class (mislabeled patterns). Unlike standard context-sensitive methods, the proposed CS4VM classifier exploits the contextual information of the pixels belonging to the neighborhood system of each training sample in the learning phase to improve the robustness to possible mislabeled training patterns. This is achieved according to both the design of a semisupervised procedure and the definition of a novel contextual term in the cost function associated with the learning of the classifier. In order to assess the effectiveness of the proposed CS4VM and to understand the impact of the addressed problem in real applications, we also present an extensive experimental analysis carried out on training sets that include different percentages of mislabeled patterns having different distributions on the classes. In the analysis, we also study the robustness to mislabeled training patterns of some widely used supervised and semisupervised classification algorithms (i.e., conventional support vector machine (SVM), progressive semisupervised SVM, maximum likelihood, and k-nearest neighbor). Results obtained on a very high resolution image and on a medium resolution image confirm both the robustness and the effectiveness of the proposed CS4VM with respect to standard classification algorithms and allow us to derive interesting conclusions on the effects of mislabeled patterns on different classifiers.

Web DOI [BibTex]

Bruzzone, L., Persello, C. A Novel Context-Sensitive Semisupervised SVM Classifier Robust to Mislabeled Training Samples IEEE Transactions on Geoscience and Remote Sensing, 47(7):2142-2154, July 2009 (article)

Web DOI [BibTex]

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Falsificationism and Statistical Learning Theory: Comparing the Popper and Vapnik-Chervonenkis Dimensions

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

Journal for General Philosophy of Science, 40(1):51-58, July 2009 (article)

Abstract
We compare Karl Popper’s ideas concerning the falsifiability of a theory with similar notions from the part of statistical learning theory known as VC-theory. Popper’s notion of the dimension of a theory is contrasted with the apparently very similar VC-dimension. Having located some divergences, we discuss how best to view Popper’s work from the perspective of statistical learning theory, either as a precursor or as aiming to capture a different learning activity.

PDF DOI [BibTex]

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Guest editorial: Special issue on robot learning, Part A

Peters, J., Ng, A.

Autonomous Robots, 27(1):1-2, July 2009 (article)

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Peters, J., Ng, A. Guest editorial: Special issue on robot learning, Part A Autonomous Robots, 27(1):1-2, July 2009 (article)

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A Geometric Approach to Confidence Sets for Ratios: Fieller’s Theorem, Generalizations, and Bootstrap

von Luxburg, U., Franz, V.

Statistica Sinica, 19(3):1095-1117, July 2009 (article)

Abstract
We present a geometric method to determine confidence sets for the ratio E(Y)/E(X) of the means of random variables X and Y. This method reduces the problem of constructing confidence sets for the ratio of two random variables to the problem of constructing confidence sets for the means of one-dimensional random variables. It is valid in a large variety of circumstances. In the case of normally distributed random variables, the so constructed confidence sets coincide with the standard Fieller confidence sets. Generalizations of our construction lead to definitions of exact and conservative confidence sets for very general classes of distributions, provided the joint expectation of (X,Y) exists and the linear combinations of the form aX + bY are well-behaved. Finally, our geometric method allows to derive a very simple bootstrap approach for constructing conservative confidence sets for ratios which perform favorably in certain situations, in particular in the asymmetric heavy-tailed regime.

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Acquiring web page information without commitment to downloading the web page

Heilbron, L., Platt, J. C., Simard, P. Y., Schölkopf, B.

United States Patent, No 7565409, July 2009 (patent)

[BibTex]

Heilbron, L., Platt, J. C., Simard, P. Y., Schölkopf, B. Acquiring web page information without commitment to downloading the web page United States Patent, No 7565409, July 2009 (patent)

[BibTex]

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Text Clustering with Mixture of von Mises-Fisher Distributions

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

In Text mining: classification, clustering, and applications, pages: 121-161, Chapman & Hall/CRC data mining and knowledge discovery series, (Editors: Srivastava, A. N. and Sahami, M.), CRC Press, Boca Raton, FL, USA, June 2009 (inbook)

Web DOI [BibTex]

Sra, S., Banerjee, A., Ghosh, J., Dhillon, I. Text Clustering with Mixture of von Mises-Fisher Distributions In Text mining: classification, clustering, and applications, pages: 121-161, Chapman & Hall/CRC data mining and knowledge discovery series, (Editors: Srivastava, A. N. and Sahami, M.), CRC Press, Boca Raton, FL, USA, June 2009 (inbook)

Web DOI [BibTex]

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Center-surround patterns emerge as optimal predictors for human saccade targets

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

Journal of Vision, 9(5:7):1-15, May 2009 (article)

Abstract
The human visual system is foveated, that is, outside the central visual field resolution and acuity drop rapidly. Nonetheless much of a visual scene is perceived after only a few saccadic eye movements, suggesting an effective strategy for selecting saccade targets. It has been known for some time that local image structure at saccade targets influences the selection process. However, the question of what the most relevant visual features are is still under debate. Here we show that center-surround patterns emerge as the optimal solution for predicting saccade targets from their local image structure. The resulting model, a one-layer feed-forward network, is surprisingly simple compared to previously suggested models which assume much more complex computations such as multi-scale processing and multiple feature channels. Nevertheless, our model is equally predictive. Furthermore, our findings are consistent with neurophysiological hardware in the superior colliculus. Bottom-up visual saliency may thus not be computed cortically as has been thought previously.

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Data Mining for Biologists

Tsuda, K.

In Biological Data Mining in Protein Interaction Networks, pages: 14-27, (Editors: Li, X. and Ng, S.-K.), Medical Information Science Reference, Hershey, PA, USA, May 2009 (inbook)

Abstract
In this tutorial chapter, we review basics about frequent pattern mining algorithms, including itemset mining, association rule mining and graph mining. These algorithms can find frequently appearing substructures in discrete data. They can discover structural motifs, for example, from mutation data, protein structures and chemical compounds. As they have been primarily used for business data, biological applications are not so common yet, but their potential impact would be large. Recent advances in computers including multicore machines and ever increasing memory capacity support the application of such methods to larger datasets. We explain technical aspects of the algorithms, but do not go into details. Current biological applications are summarized and possible future directions are given.

Web [BibTex]

Tsuda, K. Data Mining for Biologists In Biological Data Mining in Protein Interaction Networks, pages: 14-27, (Editors: Li, X. and Ng, S.-K.), Medical Information Science Reference, Hershey, PA, USA, May 2009 (inbook)

Web [BibTex]

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Influence of Different Assignment Conditions on the Determination of Symmetric Homo-dimeric Structures with ARIA

Bardiaux, B., Bernard, A., Rieping, W., Habeck, M., Malliavin, TE., Nilges, M.

Proteins, 75(3):569-585, May 2009 (article)

Abstract
The ambiguous restraint for iterative assignment (ARIA) approach for NMR structure calculation is evaluated for symmetric homodimeric proteins by assessing the effect of several data analysis and assignment methods on the structure quality. In particular, we study the effects of network anchoring and spin-diffusion correction. The spin-diffusion correction improves the protein structure quality systematically, whereas network anchoring enhances the assignment efficiency by speeding up the convergence and coping with highly ambiguous data. For some homodimeric folds, network anchoring has been proved essential for unraveling both chain and proton assignment ambiguities.

Web DOI [BibTex]

Bardiaux, B., Bernard, A., Rieping, W., Habeck, M., Malliavin, TE., Nilges, M. Influence of Different Assignment Conditions on the Determination of Symmetric Homo-dimeric Structures with ARIA Proteins, 75(3):569-585, May 2009 (article)

Web DOI [BibTex]

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Beamforming in Noninvasive Brain-Computer Interfaces

Grosse-Wentrup, M., Liefhold, C., Gramann, K., Buss, M.

IEEE Transactions on Biomedical Engineering, 56(4):1209-1219, April 2009 (article)

Abstract
Spatial filtering (SF) constitutes an integral part of building EEG-based brain–computer interfaces (BCIs). Algorithms frequently used for SF, such as common spatial patterns (CSPs) and independent component analysis, require labeled training data for identifying filters that provide information on a subject‘s intention, which renders these algorithms susceptible to overfitting on artifactual EEG components. In this study, beamforming is employed to construct spatial filters that extract EEG sources originating within predefined regions of interest within the brain. In this way, neurophysiological knowledge on which brain regions are relevant for a certain experimental paradigm can be utilized to construct unsupervised spatial filters that are robust against artifactual EEG components. Beamforming is experimentally compared with CSP and Laplacian spatial filtering (LP) in a two-class motor-imagery paradigm. It is demonstrated that beamforming outperforms CSP and LP on noisy datasets, while CSP and beamforming perform almost equally well on datasets with few artifactual trials. It is concluded that beamforming constitutes an alternative method for SF that might be particularly useful for BCIs used in clinical settings, i.e., in an environment where artifact-free datasets are difficult to obtain.

PDF Web DOI [BibTex]

Grosse-Wentrup, M., Liefhold, C., Gramann, K., Buss, M. Beamforming in Noninvasive Brain-Computer Interfaces IEEE Transactions on Biomedical Engineering, 56(4):1209-1219, April 2009 (article)

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Constructing Sparse Kernel Machines Using Attractors

Lee, D., Jung, K., Lee, J.

IEEE Transactions on Neural Networks, 20(4):721-729, April 2009 (article)

Abstract
In this brief, a novel method that constructs a sparse kernel machine is proposed. The proposed method generates attractors as sparse solutions from a built-in kernel machine via a dynamical system framework. By readjusting the corresponding coefficients and bias terms, a sparse kernel machine that approximates a conventional kernel machine is constructed. The simulation results show that the constructed sparse kernel machine improves the efficiency of testing phase while maintaining comparable test error.

Web DOI [BibTex]

Lee, D., Jung, K., Lee, J. Constructing Sparse Kernel Machines Using Attractors IEEE Transactions on Neural Networks, 20(4):721-729, April 2009 (article)

Web DOI [BibTex]

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Optimal construction of k-nearest-neighbor graphs for identifying noisy clusters

Maier, M., Hein, M., von Luxburg, U.

Theoretical Computer Science, 410(19):1749-1764, April 2009 (article)

Abstract
We study clustering algorithms based on neighborhood graphs on a random sample of data points. The question we ask is how such a graph should be constructed in order to obtain optimal clustering results. Which type of neighborhood graph should one choose, mutual k-nearest-neighbor or symmetric k-nearest-neighbor? What is the optimal parameter k? In our setting, clusters are defined as connected components of the t-level set of the underlying probability distribution. Clusters are said to be identified in the neighborhood graph if connected components in the graph correspond to the true underlying clusters. Using techniques from random geometric graph theory, we prove bounds on the probability that clusters are identified successfully, both in a noise-free and in a noisy setting. Those bounds lead to several conclusions. First, k has to be chosen surprisingly high (rather of the order n than of the order logn) to maximize the probability of cluster identification. Secondly, the major difference between the mutual and the symmetric k-nearest-neighbor graph occurs when one attempts to detect the most significant cluster only.

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Overlap and refractory effects in a Brain-Computer Interface speller based on the visual P300 Event-Related Potential

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

Journal of Neural Engineering, 6(2):1-9, April 2009 (article)

Abstract
We reveal the presence of refractory and overlap effects in the event-related potentials in visual P300 speller datasets, and we show their negative impact on the performance of the system. This finding has important implications for how to encode the letters that can be selected for communication. However, we show that such effects are dependent on stimulus parameters: an alternative stimulus type based on apparent motion suffers less from the refractory effects and leads to an improved letter prediction performance.

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Nearest Neighbor Clustering: A Baseline Method for Consistent Clustering with Arbitrary Objective Functions

Bubeck, S., von Luxburg, U.

Journal of Machine Learning Research, 10, pages: 657-698, March 2009 (article)

Abstract
Clustering is often formulated as a discrete optimization problem. The objective is to find, among all partitions of the data set, the best one according to some quality measure. However, in the statistical setting where we assume that the finite data set has been sampled from some underlying space, the goal is not to find the best partition of the given sample, but to approximate the true partition of the underlying space. We argue that the discrete optimization approach usually does not achieve this goal, and instead can lead to inconsistency. We construct examples which provably have this behavior. As in the case of supervised learning, the cure is to restrict the size of the function classes under consideration. For appropriate “small” function classes we can prove very general consistency theorems for clustering optimization schemes. As one particular algorithm for clustering with a restricted function space we introduce “nearest neighbor clustering”. Similar to the k-nearest neighbor classifier in supervised learning, this algorithm can be seen as a general baseline algorithm to minimize arbitrary clustering objective functions. We prove that it is statistically consistent for all commonly used clustering objective functions.

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Protein Functional Class Prediction With a Combined Graph

Shin, H., Tsuda, K., Schölkopf, B.

Expert Systems with Applications, 36(2):3284-3292, March 2009 (article)

Abstract
In bioinformatics, there exist multiple descriptions of graphs for the same set of genes or proteins. For instance, in yeast systems, graph edges can represent different relationships such as protein–protein interactions, genetic interactions, or co-participation in a protein complex, etc. Relying on similarities between nodes, each graph can be used independently for prediction of protein function. However, since different graphs contain partly independent and partly complementary information about the problem at hand, one can enhance the total information extracted by combining all graphs. In this paper, we propose a method for integrating multiple graphs within a framework of semi-supervised learning. The method alternates between minimizing the objective function with respect to network output and with respect to combining weights. We apply the method to the task of protein functional class prediction in yeast. The proposed method performs significantly better than the same algorithm trained on any singl e graph.

Web DOI [BibTex]

Shin, H., Tsuda, K., Schölkopf, B. Protein Functional Class Prediction With a Combined Graph Expert Systems with Applications, 36(2):3284-3292, March 2009 (article)

Web DOI [BibTex]

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Gaussian Process Dynamic Programming

Deisenroth, M., Rasmussen, C., Peters, J.

Neurocomputing, 72(7-9):1508-1524, March 2009 (article)

Abstract
Reinforcement learning (RL) and optimal control of systems with contin- uous states and actions require approximation techniques in most interesting cases. In this article, we introduce Gaussian process dynamic programming (GPDP), an approximate value-function based RL algorithm. We consider both a classic optimal control problem, where problem-specific prior knowl- edge is available, and a classic RL problem, where only very general priors can be used. For the classic optimal control problem, GPDP models the unknown value functions with Gaussian processes and generalizes dynamic programming to continuous-valued states and actions. For the RL problem, GPDP starts from a given initial state and explores the state space using Bayesian active learning. To design a fast learner, available data has to be used efficiently. Hence, we propose to learn probabilistic models of the a priori unknown transition dynamics and the value functions on the fly. In both cases, we successfully apply the resulting continuous-valued controllers to the under-actuated pendulum swing up and analyze the performances of the suggested algorithms. It turns out that GPDP uses data very efficiently and can be applied to problems, where classic dynamic programming would be cumbersome.

PDF PDF DOI [BibTex]

Deisenroth, M., Rasmussen, C., Peters, J. Gaussian Process Dynamic Programming Neurocomputing, 72(7-9):1508-1524, March 2009 (article)

PDF PDF DOI [BibTex]

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An algebraic characterization of the optimum of regularized kernel methods

Dinuzzo, F., De Nicolao, G.

Machine Learning, 74(3):315-345, March 2009 (article)

Abstract
The representer theorem for kernel methods states that the solution of the associated variational problem can be expressed as the linear combination of a finite number of kernel functions. However, for non-smooth loss functions, the analytic characterization of the coefficients poses nontrivial problems. Standard approaches resort to constrained optimization reformulations which, in general, lack a closed-form solution. Herein, by a proper change of variable, it is shown that, for any convex loss function, the coefficients satisfy a system of algebraic equations in a fixed-point form, which may be directly obtained from the primal formulation. The algebraic characterization is specialized to regression and classification methods and the fixed-point equations are explicitly characterized for many loss functions of practical interest. The consequences of the main result are then investigated along two directions. First, the existence of an unconstrained smooth reformulation of the original non-smooth problem is proven. Second, in the context of SURE (Stein’s Unbiased Risk Estimation), a general formula for the degrees of freedom of kernel regression methods is derived.

PDF DOI [BibTex]

Dinuzzo, F., De Nicolao, G. An algebraic characterization of the optimum of regularized kernel methods Machine Learning, 74(3):315-345, March 2009 (article)

PDF DOI [BibTex]

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Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques

Hofmann, M., Pichler, B., Schölkopf, B., Beyer, T.

European Journal of Nuclear Medicine and Molecular Imaging, 36(Supplement 1):93-104, March 2009 (article)

Abstract
Introduction Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Objective Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. Discussion MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data.

PDF DOI [BibTex]

Hofmann, M., Pichler, B., Schölkopf, B., Beyer, T. Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques European Journal of Nuclear Medicine and Molecular Imaging, 36(Supplement 1):93-104, March 2009 (article)

PDF DOI [BibTex]

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Generating Spike Trains with Specified Correlation Coefficients

Macke, J., Berens, P., Ecker, A., Tolias, A., Bethge, M.

Neural Computation, 21(2):397-423, February 2009 (article)

Abstract
Spike trains recorded from populations of neurons can exhibit substantial pairwise correlations between neurons and rich temporal structure. Thus, for the realistic simulation and analysis of neural systems, it is essential to have efficient methods for generating artificial spike trains with specified correlation structure. Here we show how correlated binary spike trains can be simulated by means of a latent multivariate gaussian model. Sampling from the model is computationally very efficient and, in particular, feasible even for large populations of neurons. The entropy of the model is close to the theoretical maximum for a wide range of parameters. In addition, this framework naturally extends to correlations over time and offers an elegant way to model correlated neural spike counts with arbitrary marginal distributions.

PDF Web DOI [BibTex]

Macke, J., Berens, P., Ecker, A., Tolias, A., Bethge, M. Generating Spike Trains with Specified Correlation Coefficients Neural Computation, 21(2):397-423, February 2009 (article)

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Automatic detection of preclinical neurodegeneration: Presymptomatic Huntington disease

Klöppel, S., Chu, C., Tan, G., Draganski, B., Johnson, H., Paulsen, J., Kienzle, W., Tabrizi, S., Ashburner, J., Frackowiak, R.

Neurology, 72(5):426-431, February 2009 (article)

Abstract
Background: Treatment of neurodegenerative diseases is likely to be most beneficial in the very early, possibly preclinical stages of degeneration. We explored the usefulness of fully automatic structural MRI classification methods for detecting subtle degenerative change. The availability of a definitive genetic test for Huntington disease (HD) provides an excellent metric for judging the performance of such methods in gene mutation carriers who are free of symptoms. Methods: Using the gray matter segment of MRI scans, this study explored the usefulness of a multivariate support vector machine to automatically identify presymptomatic HD gene mutation carriers (PSCs) in the absence of any a priori information. A multicenter data set of 96 PSCs and 95 age- and sex-matched controls was studied. The PSC group was subclassified into three groups based on time from predicted clinical onset, an estimate that is a function of DNA mutation size and age. Results: Subjects with at least a 33% chance of developing unequivocal signs of HD in 5 years were correctly assigned to the PSC group 69% of the time. Accuracy improved to 83% when regions affected by the disease were selected a priori for analysis. Performance was at chance when the probability of developing symptoms in 5 years was less than 10%. Conclusions: Presymptomatic Huntington disease gene mutation carriers close to estimated diagnostic onset were successfully separated from controls on the basis of single anatomic scans, without additional a priori information. Prior information is required to allow separation when degenerative changes are either subtle or variable.

Web [BibTex]

Klöppel, S., Chu, C., Tan, G., Draganski, B., Johnson, H., Paulsen, J., Kienzle, W., Tabrizi, S., Ashburner, J., Frackowiak, R. Automatic detection of preclinical neurodegeneration: Presymptomatic Huntington disease Neurology, 72(5):426-431, February 2009 (article)

Web [BibTex]

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Enumeration of condition-dependent dense modules in protein interaction networks

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

Bioinformatics, 25(7):933-940, February 2009 (article)

Abstract
Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.

Web DOI [BibTex]

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K. Enumeration of condition-dependent dense modules in protein interaction networks Bioinformatics, 25(7):933-940, February 2009 (article)

Web DOI [BibTex]

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Prototype Classification: Insights from Machine Learning

Graf, A., Bousquet, O., Rätsch, G., Schölkopf, B.

Neural Computation, 21(1):272-300, January 2009 (article)

Abstract
We shed light on the discrimination between patterns belonging to two different classes by casting this decoding problem into a generalized prototype framework. The discrimination process is then separated into two stages: a projection stage that reduces the dimensionality of the data by projecting it on a line and a threshold stage where the distributions of the projected patterns of both classes are separated. For this, we extend the popular mean-of-class prototype classification using algorithms from machine learning that satisfy a set of invariance properties. We report a simple yet general approach to express different types of linear classification algorithms in an identical and easy-to-visualize formal framework using generalized prototypes where these prototypes are used to express the normal vector and offset of the hyperplane. We investigate nonmargin classifiers such as the classical prototype classifier, the Fisher classifier, and the relevance vector machine. We then study hard and soft margin cl assifiers such as the support vector machine and a boosted version of the prototype classifier. Subsequently, we relate mean-of-class prototype classification to other classification algorithms by showing that the prototype classifier is a limit of any soft margin classifier and that boosting a prototype classifier yields the support vector machine. While giving novel insights into classification per se by presenting a common and unified formalism, our generalized prototype framework also provides an efficient visualization and a principled comparison of machine learning classification.

PDF Web DOI [BibTex]

Graf, A., Bousquet, O., Rätsch, G., Schölkopf, B. Prototype Classification: Insights from Machine Learning Neural Computation, 21(1):272-300, January 2009 (article)

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Automatic classification of brain resting states using fMRI temporal signals

Soldati, N., Robinson, S., Persello, C., Jovicich, J., Bruzzone, L.

Electronics Letters, 45(1):19-21, January 2009 (article)

Abstract
A novel technique is presented for the automatic discrimination between networks of dasiaresting statesdasia of the human brain and physiological fluctuations in functional magnetic resonance imaging (fMRI). The method is based on features identified via a statistical approach to group independent component analysis time courses, which may be extracted from fMRI data. This technique is entirely automatic and, unlike other approaches, uses temporal rather than spatial information. The method achieves 83% accuracy in the identification of resting state networks.

Web DOI [BibTex]

Soldati, N., Robinson, S., Persello, C., Jovicich, J., Bruzzone, L. Automatic classification of brain resting states using fMRI temporal signals Electronics Letters, 45(1):19-21, January 2009 (article)

Web DOI [BibTex]

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The DICS repository: module-assisted analysis of disease-related gene lists

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H.

Bioinformatics, 25(6):830-831, January 2009 (article)

Abstract
The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein–protein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context.

Web DOI [BibTex]

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H. The DICS repository: module-assisted analysis of disease-related gene lists Bioinformatics, 25(6):830-831, January 2009 (article)

Web DOI [BibTex]

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Large Margin Methods for Part of Speech Tagging

Altun, Y.

In Automatic Speech and Speaker Recognition: Large Margin and Kernel Methods, pages: 141-160, (Editors: Keshet, J. and Bengio, S.), Wiley, Hoboken, NJ, USA, January 2009 (inbook)

Web [BibTex]

Altun, Y. Large Margin Methods for Part of Speech Tagging In Automatic Speech and Speaker Recognition: Large Margin and Kernel Methods, pages: 141-160, (Editors: Keshet, J. and Bengio, S.), Wiley, Hoboken, NJ, USA, January 2009 (inbook)

Web [BibTex]

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Pre−processed feature ranking for a support vector machine

Weston, J., Elisseeff, A., Schölkopf, B., Pérez-Cruz, F., Guyon, I.

United States Patent, No. 7475048, January 2009 (patent)

[BibTex]

Weston, J., Elisseeff, A., Schölkopf, B., Pérez-Cruz, F., Guyon, I. Pre−processed feature ranking for a support vector machine United States Patent, No. 7475048, January 2009 (patent)

[BibTex]