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2008


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Predicting phenotypic effects of gene perturbations in C. elegans using an integrated network model

Borgwardt, K.

BioEssays, 30(8):707–710, August 2008 (article)

Abstract
Predicting the phenotype of an organism from its genotype is a central question in genetics. Most importantly, we would like to find out if the perturbation of a single gene may be the cause of a disease. However, our current ability to predict the phenotypic effects of perturbations of individual genes is limited. Network models of genes are one tool for tackling this problem. In a recent study, (Lee et al.) it has been shown that network models covering the majority of genes of an organism can be used for accurately predicting phenotypic effects of gene perturbations in multicellular organisms.

Web DOI [BibTex]


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Learning Robot Dynamics for Computed Torque Control Using Local Gaussian Processes Regression

Nguyen-Tuong, D., Peters, J.

In LAB-RS 2008, pages: 59-64, (Editors: Stoica, A. , E. Tunstel, T. Huntsberger, T. Arslan, S. Vijayakumar, A. O. El-Rayis), IEEE Computer Society, Los Alamitos, CA, USA, 2008 ECSIS Symposium on Learning and Adaptive Behaviors for Robotic Systems, August 2008 (inproceedings)

Abstract
Accurate models of the robot dynamics allow the design of significantly more precise, energy-efficient and more compliant computed torque control for robots. However, in some cases the accuracy of rigid-body models does not suffice for sound control performance due to unmodeled nonlinearities such as hydraulic cables, complex friction, or actuator dynamics. In such cases, learning the models from data poses an interesting alternative and estimating the dynamics model using regression techniques becomes an important problem. However, the most accurate regression methods, e.g. Gaussian processes regression (GPR) and support vector regression (SVR), suffer from exceptional high computational complexity which prevents their usage for large numbers of samples or online learning to date. We proposed an approximation to the standard GPR using local Gaussian processes models. Due to reduced computational cost, local Gaussian processes (LGP) is capable for an online learning. Comparisons with other nonparametric regre ssions, e.g. standard GPR, SVR and locally weighted projection regression (LWPR), show that LGP has higher accuracy than LWPR and close to the performance of standard GPR and SVR while being sufficiently fast for online learning.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Multi-class Common Spatial Pattern and Information Theoretic Feature Extraction

Grosse-Wentrup, M., Buss, M.

IEEE Transactions on Biomedical Engineering, 55(8):1991-2000, August 2008 (article)

Abstract
We address two shortcomings of the common spatial patterns (CSP) algorithm for spatial filtering in the context of brain--computer interfaces (BCIs) based on electroencephalography/magnetoencephalography (EEG/MEG): First, the question of optimality of CSP in terms of the minimal achievable classification error remains unsolved. Second, CSP has been initially proposed for two-class paradigms. Extensions to multiclass paradigms have been suggested, but are based on heuristics. We address these shortcomings in the framework of information theoretic feature extraction (ITFE). We show that for two-class paradigms, CSP maximizes an approximation of mutual information of extracted EEG/MEG components and class labels. This establishes a link between CSP and the minimal classification error. For multiclass paradigms, we point out that CSP by joint approximate diagonalization (JAD) is equivalent to independent component analysis (ICA), and provide a method to choose those independent components (ICs) that approximately maximize mutual information of ICs and class labels. This eliminates the need for heuristics in multiclass CSP, and allows incorporating prior class probabilities. The proposed method is applied to the dataset IIIa of the third BCI competition, and is shown to increase the mean classification accuracy by 23.4% in comparison to multiclass CSP.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Haptic Control with Environment Estimation for Telesurgery

Bhattacharjee, T., Son, HI., Lee, DY.

In International Conference of the IEEE Engineering in Medicine and Biology Society, pages: 3241-3244, IEEE, Piscataway, NJ, USA, 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS), August 2008 (inproceedings)

Abstract
Success of telesurgical operations depends on better position tracking ability of the slave device. Improved position tracking of the slave device can lead to safer and less strenuous telesurgical operations. The two-channel force-position control architecture is widely used for better position tracking ability. This architecture requires force sensors for direct force feedback. Force sensors may not be a good choice in the telesurgical environment because of the inherent noise, and limitation in the deployable place and space. Hence, environment force estimation is developed using the concept of the robot function parameter matrix and a recursive least squares method. Simulation results show efficacy of the proposed method. The slave device successfully tracks the position of the master device, and the estimation error quickly becomes negligible.

Web DOI [BibTex]

Web DOI [BibTex]


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Example-based Learning for Single-image Super-resolution and JPEG Artifact Removal

Kim, K., Kwon, Y.

(173), Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany, August 2008 (techreport)

Abstract
This paper proposes a framework for single-image super-resolution and JPEG artifact removal. The underlying idea is to learn a map from input low-quality images (suitably preprocessed low-resolution or JPEG encoded images) to target high-quality images based on example pairs of input and output images. To retain the complexity of the resulting learning problem at a moderate level, a patch-based approach is taken such that kernel ridge regression (KRR) scans the input image with a small window (patch) and produces a patchvalued output for each output pixel location. These constitute a set of candidate images each of which reflects different local information. An image output is then obtained as a convex combination of candidates for each pixel based on estimated confidences of candidates. To reduce the time complexity of training and testing for KRR, a sparse solution is found by combining the ideas of kernel matching pursuit and gradient descent. As a regularized solution, KRR leads to a better generalization than simply storing the examples as it has been done in existing example-based super-resolution algorithms and results in much less noisy images. However, this may introduce blurring and ringing artifacts around major edges as sharp changes are penalized severely. A prior model of a generic image class which takes into account the discontinuity property of images is adopted to resolve this problem. Comparison with existing super-resolution and JPEG artifact removal methods shows the effectiveness of the proposed method. Furthermore, the proposed method is generic in that it has the potential to be applied to many other image enhancement applications.

PDF [BibTex]

PDF [BibTex]


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mGene: A Novel Discriminative Gene Finder

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

Worm Genomics and Systems Biology meeting, July 2008 (talk)

[BibTex]

[BibTex]


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Learning an Interest Operator from Human Eye Movements

Kienzle, W.

Biologische Kybernetik, Eberhard-Karls-Universität Tübingen, Tübingen, Germany, July 2008 (phdthesis)

[BibTex]

[BibTex]


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A Novel Protocol for Accuracy Assessment in Classification of Very High Resolution Multispectral and SAR Images

Bruzzone, L., Persello, C.

In pages: II-265-II-268 , IEEE, Piscataway, NJ, USA, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), July 2008 (inproceedings)

Abstract
This paper presents a novel protocol for the accuracy assessment of thematic maps obtained by the classification of very high resolution images. As the thematic accuracy alone is not sufficient to adequately characterize the geometrical properties of classification maps, we propose a novel protocol that is based on the analysis of two families of indexes: (i) the traditional thematic accuracy indexes, and (ii) a set of geometric indexes that characterize different geometric properties of the objects recognized in the map. These indexes can be used in the training phase of a classifier for identifying the parameters values that optimize classification results on the basis of a multi-objective criterion. Experimental results obtained on Quickbird images show the effectiveness of the proposed protocol in selecting classification maps characterized by better tradeoff between thematic and geometric accuracy with respect to standard accuracy measures.

Web DOI [BibTex]

Web DOI [BibTex]


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A Decoupled Approach to Exemplar-based Unsupervised Learning

Nowozin, S., BakIr, G.

In ICML 2008, pages: 704-711, (Editors: Cohen, W. W., A. McCallum, S. Roweis), ACM Press, New York, NY, USA, 25th International Conference on Machine Learning, July 2008 (inproceedings)

Abstract
A recent trend in exemplar based unsupervised learning is to formulate the learning problem as a convex optimization problem. Convexity is achieved by restricting the set of possible prototypes to training exemplars. In particular, this has been done for clustering, vector quantization and mixture model density estimation. In this paper we propose a novel algorithm that is theoretically and practically superior to these convex formulations. This is possible by posing the unsupervised learning problem as a single convex master problem" with non-convex subproblems. We show that for the above learning tasks the subproblems are extremely wellbehaved and can be solved efficiently.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Policy Learning: A Unified Perspective With Applications In Robotics

Peters, J., Kober, J., Nguyen-Tuong, D.

8th European Workshop on Reinforcement Learning for Robotics (EWRL 2008), 8, pages: 10, July 2008 (poster)

Abstract
Policy Learning approaches are among the best suited methods for high-dimensional, continuous control systems such as anthropomorphic robot arms and humanoid robots. In this paper, we show two contributions: firstly, we show a unified perspective which allows us to derive several policy learning al- gorithms from a common point of view, i.e, policy gradient algorithms, natural- gradient algorithms and EM-like policy learning. Secondly, we present several applications to both robot motor primitive learning as well as to robot control in task space. Results both from simulation and several different real robots are shown.

PDF [BibTex]

PDF [BibTex]


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Discovering Common Sequence Variation in Arabidopsis thaliana

Rätsch, G., Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthman, N., Hu, T., Fu, G., Hinds, D., Cheng, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Ecker, J., Weigel, D., Schneeberger, K., Bohlen, A.

16th Annual International Conference Intelligent Systems for Molecular Biology (ISMB), July 2008 (talk)

Web [BibTex]

Web [BibTex]


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CogRob 2008: The 6th International Cognitive Robotics Workshop

Lespérance, Y., Lakemeyer, G., Peters, J., Pirri, F.

Proceedings of the 6th International Cognitive Robotics Workshop (CogRob 2008), pages: 35, Patras University Press, Patras, Greece, 6th International Cognitive Robotics Workshop (CogRob), July 2008 (proceedings)

Web [BibTex]

Web [BibTex]


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A Novel Approach to the Selection of Robust and Invariant Features for Classification of Hyperspectral Images

Bruzzone, L., Persello, C.

In pages: I-66-I-69 , IEEE, Piscataway, NJ, USA, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), July 2008 (inproceedings)

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 two main properties:( i) high capability to discriminate among the considered classes, (ii) high invariance (stationarity) in the spatial domain of the investigated scene. The feature selection is accomplished by defining a multi-objective criterion that considers two terms: (i) a term that assesses the class separability, (ii) a term that evaluates the spatial invariance of the selected features. The multi-objective problem is solved by an evolutionary algorithm that estimates the Pareto-optimal solutions. Experiments carried out on a hyperspectral image acquired by the Hyperion sensor confirmed the effectiveness of the proposed technique.

Web DOI [BibTex]

Web DOI [BibTex]


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The skew spectrum of graphs

Kondor, R., Borgwardt, K.

In pages: 496-503, (Editors: Cohen, W.W. , A. McCallum, S.T. Roweis), ACM Press, New York, NY, USA, Twenty-Fifth International Conference on Machine Learning (ICML), July 2008 (inproceedings)

Abstract
The central issue in representing graph-structured data instances in learning algorithms is designing features which are invariant to permuting the numbering of the vertices. We present a new system of invariant graph features which we call the skew spectrum of graphs. The skew spectrum is based on mapping the adjacency matrix of any (weigted, directed, unlabeled) graph to a function on the symmetric group and computing bispectral invariants. The reduced form of the skew spectrum is computable in O(n3) time, and experiments show that on several benchmark datasets it can outperform state of the art graph kernels.

Web DOI [BibTex]

Web DOI [BibTex]


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Relating clustering stability to properties of cluster boundaries

Ben-David, S., von Luxburg, U.

In COLT 2008, pages: 379-390, (Editors: Servedio, R. A., T. Zhang), Omnipress, Madison, WI, USA, 21st Annual Conference on Learning Theory, July 2008 (inproceedings)

Abstract
In this paper, we investigate stability-based methods for cluster model selection, in particular to select the number K of clusters. The scenario under consideration is that clustering is performed by minimizing a certain clustering quality function, and that a unique global minimizer exists. On the one hand we show that stability can be upper bounded by certain properties of the optimal clustering, namely by the mass in a small tube around the cluster boundaries. On the other hand, we provide counterexamples which show that a reverse statement is not true in general. Finally, we give some examples and arguments why, from a theoretic point of view, using clustering stability in a high sample setting can be problematic. It can be seen that distribution-free guarantees bounding the difference between the finite sample stability and the “true stability” cannot exist, unless one makes strong assumptions on the underlying distribution.

PDF Web [BibTex]

PDF Web [BibTex]


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Coding Theory in Brain-Computer Interfaces

Martens, SMM.

Soria Summerschool on Computational Mathematics "Algebraic Coding Theory" (S3CM), July 2008 (talk)

Web [BibTex]

Web [BibTex]


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At-TAX: A Whole Genome Tiling Array Resource for Developmental Expression Analysis and Transcript Identification in Arabidopsis thaliana

Laubinger, S., Zeller, G., Henz, S., Sachsenberg, T., Widmer, C., Naouar, N., Vuylsteke, M., Schölkopf, B., Rätsch, G., Weigel, D.

Genome Biology, 9(7: R112):1-16, July 2008 (article)

Abstract
Gene expression maps for model organisms, including Arabidopsis thaliana, have typically been created using gene-centric expression arrays. Here, we describe a comprehensive expression atlas, Arabidopsis thaliana Tiling Array Express (At-TAX), which is based on whole-genome tiling arrays. We demonstrate that tiling arrays are accurate tools for gene expression analysis and identified more than 1,000 unannotated transcribed regions. Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Compressed Sensing and Bayesian Experimental Design

Seeger, M., Nickisch, H.

In ICML 2008, pages: 912-919, (Editors: Cohen, W. W., A. McCallum, S. Roweis), ACM Press, New York, NY, USA, 25th International Conference on Machine Learning, July 2008 (inproceedings)

Abstract
We relate compressed sensing (CS) with Bayesian experimental design and provide a novel efficient approximate method for the latter, based on expectation propagation. In a large comparative study about linearly measuring natural images, we show that the simple standard heuristic of measuring wavelet coefficients top-down systematically outperforms CS methods using random measurements; the sequential projection optimisation approach of (Ji & Carin, 2007) performs even worse. We also show that our own approximate Bayesian method is able to learn measurement filters on full images efficiently which ouperform the wavelet heuristic. To our knowledge, ours is the first successful attempt at "learning compressed sensing" for images of realistic size. In contrast to common CS methods, our framework is not restricted to sparse signals, but can readily be applied to other notions of signal complexity or noise models. We give concrete ideas how our method can be scaled up to large signal representations.

PDF PDF Web DOI [BibTex]

PDF PDF Web DOI [BibTex]


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Tailoring density estimation via reproducing kernel moment matching

Song, L., Zhang, X., Smola, A., Gretton, A., Schölkopf, B.

In Proceedings of the 25th International Conference onMachine Learning, pages: 992-999, (Editors: WW Cohen and A McCallum and S Roweis), ACM Press, New York, NY, USA, ICML, July 2008 (inproceedings)

Abstract
Moment matching is a popular means of parametric density estimation. We extend this technique to nonparametric estimation of mixture models. Our approach works by embedding distributions into a reproducing kernel Hilbert space, and performing moment matching in that space. This allows us to tailor density estimators to a function class of interest (i.e., for which we would like to compute expectations). We show our density estimation approach is useful in applications such as message compression in graphical models, and image classification and retrieval.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Injective Hilbert Space Embeddings of Probability Measures

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

In Proceedings of the 21st Annual Conference on Learning Theory, pages: 111-122, (Editors: RA Servedio and T Zhang), Omnipress, Madison, WI, USA, 21st Annual Conference on Learning Theory (COLT), July 2008 (inproceedings)

Abstract
A Hilbert space embedding for probability measures has recently been proposed, with applications including dimensionality reduction, homogeneity testing and independence testing. This embedding represents any probability measure as a mean element in a reproducing kernel Hilbert space (RKHS). The embedding function has been proven to be injective when the reproducing kernel is universal. In this case, the embedding induces a metric on the space of probability distributions defined on compact metric spaces. In the present work, we consider more broadly the problem of specifying characteristic kernels, defined as kernels for which the RKHS embedding of probability measures is injective. In particular, characteristic kernels can include non-universal kernels. We restrict ourselves to translation-invariant kernels on Euclidean space, and define the associated metric on probability measures in terms of the Fourier spectrum of the kernel and characteristic functions of these measures. The support of the kernel spectrum is important in finding whether a kernel is characteristic: in particular, the embedding is injective if and only if the kernel spectrum has the entire domain as its support. Characteristic kernels may nonetheless have difficulty in distinguishing certain distributions on the basis of finite samples, again due to the interaction of the kernel spectrum and the characteristic functions of the measures.

PDF Web [BibTex]

PDF Web [BibTex]


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Motor Skill Learning for Cognitive Robotics

Peters, J.

6th International Cognitive Robotics Workshop (CogRob), July 2008 (talk)

Abstract
Autonomous robots that can assist humans in situations of daily life have been a long standing vision of robotics, artificial intelligence, and cognitive sciences. A first step towards this goal is to create robots that can learn tasks triggered by environmental context or higher level instruction. However, learning techniques have yet to live up to this promise as only few methods manage to scale to high-dimensional manipulator or humanoid robots. In this tutorial, we give a general overview on motor skill learning for cognitive robotics using research at ATR, USC, CMU and Max-Planck in order to illustrate the problems in motor skill learning. For doing so, we discuss task-appropriate representations and algorithms for learning robot motor skills. Among the topics are the learning basic movements or motor primitives by imitation and reinforcement learning, learning rhytmic and discrete movements, fast regression methods for learning inverse dynamics and setups for learning task-space policies. Examples on various robots, e.g., SARCOS DB, the SARCOS Master Arm, BDI Little Dog and a Barrett WAM, are shown and include Ball-in-a-Cup, T-Ball, Juggling, Devil-Sticking, Operational Space Control and many others.

Web [BibTex]

Web [BibTex]


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A Hilbert-Schmidt Dependence Maximization Approach to Unsupervised Structure Discovery

Blaschko, M., Gretton, A.

In MLG 2008, pages: 1-3, 6th International Workshop on Mining and Learning with Graphs, July 2008 (inproceedings)

Abstract
In recent work by (Song et al., 2007), it has been proposed to perform clustering by maximizing a Hilbert-Schmidt independence criterion with respect to a predefined cluster structure Y , by solving for the partition matrix, II. We extend this approach here to the case where the cluster structure Y is not fixed, but is a quantity to be optimized; and we use an independence criterion which has been shown to be more sensitive at small sample sizes (the Hilbert-Schmidt Normalized Information Criterion, or HSNIC, Fukumizu et al., 2008). We demonstrate the use of this framework in two scenarios. In the first, we adopt a cluster structure selection approach in which the HSNIC is used to select a structure from several candidates. In the second, we consider the case where we discover structure by directly optimizing Y.

PDF Web [BibTex]

PDF Web [BibTex]


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Reinforcement Learning of Perceptual Coupling for Motor Primitives

Kober, J., Peters, J.

8th European Workshop on Reinforcement Learning for Robotics (EWRL 2008), 8, pages: 16, July 2008 (poster)

Abstract
Reinforcement learning is a natural choice for the learning of complex motor tasks by reward-related self-improvement. As the space of movements is high-dimensional and continuous, a policy parametrization is needed which can be used in this context. Traditional motor primitive approaches deal largely with open-loop policies which can only deal with small perturbations. In this paper, we present a new type of motor primitive policies which serve as closed-loop policies together with an appropriate learning algorithm. Our new motor primitives are an augmented version version of the dynamic systems motor primitives that incorporates perceptual coupling to external variables. We show that these motor primitives can perform complex tasks such a Ball-in-a-Cup or Kendama task even with large variances in the initial conditions where a human would hardly be able to learn this task. We initialize the open-loop policies by imitation learning and the perceptual coupling with a handcrafted solution. We first improve the open-loop policies and subsequently the perceptual coupling using a novel reinforcement learning method which is particularly well-suited for motor primitives.

PDF [BibTex]

PDF [BibTex]


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Painless Embeddings of Distributions: the Function Space View (Part 1)

Fukumizu, K., Gretton, A., Smola, A.

25th International Conference on Machine Learning (ICML), July 2008 (talk)

Abstract
This tutorial will give an introduction to the recent understanding and methodology of the kernel method: dealing with higher order statistics by embedding painlessly random variables/probability distributions. In the early days of kernel machines research, the "kernel trick" was considered a useful way of constructing nonlinear algorithms from linear ones. More recently, however, it has become clear that a potentially more far reaching use of kernels is as a linear way of dealing with higher order statistics by embedding distributions in a suitable reproducing kernel Hilbert space (RKHS). Notably, unlike the straightforward expansion of higher order moments or conventional characteristic function approach, the use of kernels or RKHS provides a painless, tractable way of embedding distributions. This line of reasoning leads naturally to the questions: what does it mean to embed a distribution in an RKHS? when is this embedding injective (and thus, when do different distributions have unique mappings)? what implications are there for learning algorithms that make use of these embeddings? This tutorial aims at answering these questions. There are a great variety of applications in machine learning and computer science, which require distribution estimation and/or comparison.

PDF Web [BibTex]

PDF Web [BibTex]


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Reinforcement Learning for Robotics

Peters, J.

8th European Workshop on Reinforcement Learning for Robotics (EWRL), July 2008 (talk)

Web [BibTex]

Web [BibTex]


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Adaptive Importance Sampling with Automatic Model Selection in Value Function Approximation

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

In AAAI 2008, pages: 1351-1356, (Editors: Fox, D. , C. P. Gomes), AAAI Press, Menlo Park, CA, USA, Twenty-Third Conference on Artificial Intelligence, July 2008 (inproceedings)

Abstract
Off-policy reinforcement learning is aimed at efficiently reusing data samples gathered in the past, which is an essential problem for physically grounded AI as experiments are usually prohibitively expensive. A common approach is to use importance sampling techniques for compensating for the bias caused by the difference between data-sampling policies and the target policy. However, existing off-policy methods do not often take the variance of 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.

PDF Web [BibTex]

PDF Web [BibTex]


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Sparse Multiscale Gaussian Process Regression

Walder, C., Kim, K., Schölkopf, B.

In Proceedings of the 25th International Conference on Machine Learning, pages: 1112-1119, (Editors: WW Cohen and A McCallum and S Roweis), ACM Press, New York, NY, USA, ICML, July 2008 (inproceedings)

Abstract
Most existing sparse Gaussian process (g.p.) models seek computational advantages by basing their computations on a set of m basis functions that are the covariance function of the g.p. with one of its two inputs fixed. We generalise this for the case of Gaussian covariance function, by basing our computations on m Gaussian basis functions with arbitrary diagonal covariance matrices (or length scales). For a fixed number of basis functions and any given criteria, this additional flexibility permits approximations no worse and typically better than was previously possible. We perform gradient based optimisation of the marginal likelihood, which costs O(m2n) time where n is the number of data points, and compare the method to various other sparse g.p. methods. Although we focus on g.p. regression, the central idea is applicable to all kernel based algorithms, and we also provide some results for the support vector machine (s.v.m.) and kernel ridge regression (k.r.r.). Our approach outperforms the other methods, particularly for the case of very few basis functions, i.e. a very high sparsity ratio.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Unsupervised Bayesian Time-series Segmentation based on Linear Gaussian State-space Models

Chiappa, S.

(171), Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany, June 2008 (techreport)

Abstract
Unsupervised time-series segmentation in the general scenario in which the number of segment-types and segment boundaries are a priori unknown is a fundamental problem in many applications and requires an accurate segmentation model as well as a way of determining an appropriate number of segment-types. In most approaches, segmentation and determination of number of segment-types are addressed in two separate steps, since the segmentation model assumes a predefined number of segment-types. The determination of number of segment-types is thus achieved by training and comparing several separate models. In this paper, we take a Bayesian approach to a segmentation model based on linear Gaussian state-space models to achieve structure selection within the model. An appropriate prior distribution on the parameters is used to enforce a sparse parametrization, such that the model automatically selects the smallest number of underlying dynamical systems that explain the data well and a parsimonious structure for each dynamical system. As the resulting model is computationally intractable, we introduce a variational approximation, in which a reformulation of the problem enables to use an efficient inference algorithm.

[BibTex]

[BibTex]


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A New Non-monotonic Gradient Projection Method for the Non-negative Least Squares Problem

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

(TR-08-28), University of Texas, Austin, TX, USA, June 2008 (techreport)

Web [BibTex]

Web [BibTex]


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Flexible Models for Population Spike Trains

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

AREADNE 2008: Research in Encoding and Decoding of Neural Ensembles, 2, pages: 52, June 2008 (poster)

PDF [BibTex]

PDF [BibTex]


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Graphical Analysis of NMR Structural Quality and Interactive Contact Map of NOE Assignments in ARIA

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

BMC Structural Biology, 8(30):1-5, June 2008 (article)

Abstract
BACKGROUND: The Ambiguous Restraints for Iterative Assignment (ARIA) approach is widely used for NMR structure determination. It is based on simultaneously calculating structures and assigning NOE through an iterative protocol. The final solution consists of a set of conformers and a list of most probable assignments for the input NOE peak list. RESULTS: ARIA was extended with a series of graphical tools to facilitate a detailed analysis of the intermediate and final results of the ARIA protocol. These additional features provide (i) an interactive contact map, serving as a tool for the analysis of assignments, and (ii) graphical representations of structure quality scores and restraint statistics. The interactive contact map between residues can be clicked to obtain information about the restraints and their contributions. Profiles of quality scores are plotted along the protein sequence, and contact maps provide information of the agreement with the data on a residue pair level. CONCLUSIONS: The g raphical tools and outputs described here significantly extend the validation and analysis possibilities of NOE assignments given by ARIA as well as the analysis of the quality of the final structure ensemble. These tools are included in the latest version of ARIA, which is available at http://aria.pasteur.fr. The Web site also contains an installation guide, a user manual and example calculations.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Example-Based Learning for Single-Image Super-Resolution

Kim, K., Kwon, Y.

In DAGM 2008, pages: 456-463, (Editors: Rigoll, G. ), Springer, Berlin, Germany, 30th Annual Symposium of the German Association for Pattern Recognition, June 2008 (inproceedings)

Abstract
This paper proposes a regression-based method for single-image super-resolution. Kernel ridge regression (KRR) is used to estimate the high-frequency details of the underlying high-resolution image. A sparse solution of KRR is found by combining the ideas of kernel matching pursuit and gradient descent, which allows time-complexity to be kept to a moderate level. To resolve the problem of ringing artifacts occurring due to the regularization effect, the regression results are post-processed using a prior model of a generic image class. Experimental results demonstrate the effectiveness of the proposed method.

PDF DOI [BibTex]

PDF DOI [BibTex]


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A Multiple Kernel Learning Approach to Joint Multi-Class Object Detection

Lampert, C., Blaschko, M.

In DAGM 2008, pages: 31-40, (Editors: Rigoll, G. ), Springer, Berlin, Germany, 30th Annual Symposium of the German Association for Pattern Recognition, June 2008, Main Award DAGM 2008 (inproceedings)

Abstract
Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost. In this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection.

PDF ZIP Web DOI [BibTex]

PDF ZIP Web DOI [BibTex]


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Natural Evolution Strategies

Wierstra, D., Schaul, T., Peters, J., Schmidhuber, J.

In CEC 2008, pages: 3381-3387, IEEE, Piscataway, NJ, USA, IEEE Congress on Evolutionary Computation, June 2008 (inproceedings)

Abstract
This paper presents natural evolution strategies (NES), a novel algorithm for performing real-valued dasiablack boxpsila function optimization: optimizing an unknown objective function where algorithm-selected function measurements constitute the only information accessible to the method. Natural evolution strategies search the fitness landscape using a multivariate normal distribution with a self-adapting mutation matrix to generate correlated mutations in promising regions. NES shares this property with covariance matrix adaption (CMA), an evolution strategy (ES) which has been shown to perform well on a variety of high-precision optimization tasks. The natural evolution strategies algorithm, however, is simpler, less ad-hoc and more principled. Self-adaptation of the mutation matrix is derived using a Monte Carlo estimate of the natural gradient towards better expected fitness. By following the natural gradient instead of the dasiavanillapsila gradient, we can ensure efficient update steps while preventing early convergence due to overly greedy updates, resulting in reduced sensitivity to local suboptima. We show NES has competitive performance with CMA on unimodal tasks, while outperforming it on several multimodal tasks that are rich in deceptive local optima.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Pairwise Correlations and Multineuronal Firing Patterns in the Primary Visual Cortex of the Awake, Behaving Macaque

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

AREADNE 2008: Research in Encoding and Decoding of Neural Ensembles, 2, pages: 48, June 2008 (poster)

PDF [BibTex]

PDF [BibTex]


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Operational Space Control: A Theoretical and Empirical Comparison

Nakanishi, J., Cory, R., Mistry, M., Peters, J., Schaal, S.

International Journal of Robotics Research, 27(6):737-757, June 2008 (article)

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Visual saliency re-visited: Center-surround patterns emerge as optimal predictors for human fixation targets

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

Journal of Vision, 8(6):635, 8th Annual Meeting of the Vision Sciences Society (VSS), June 2008 (poster)

Abstract
Humans perceives the world by directing the center of gaze from one location to another via rapid eye movements, called saccades. In the period between saccades the direction of gaze is held fixed for a few hundred milliseconds (fixations). It is primarily during fixations that information enters the visual system. Remarkably, however, after only a few fixations we perceive a coherent, high-resolution scene despite the visual acuity of the eye quickly decreasing away from the center of gaze: This suggests an effective strategy for selecting saccade targets. Top-down effects, such as the observer's task, thoughts, or intentions have an effect on saccadic selection. Equally well known is that bottom-up effects-local image structure-influence saccade targeting regardless of top-down effects. However, the question of what the most salient visual features are is still under debate. Here we model the relationship between spatial intensity patterns in natural images and the response of the saccadic system using tools from machine learning. This allows us to identify the most salient image patterns that guide the bottom-up component of the saccadic selection system, which we refer to as perceptive fields. We show that center-surround patterns emerge as the optimal solution to the problem of predicting saccade targets. Using a novel nonlinear system identification technique we reduce our learned classifier to a one-layer feed-forward network which is surprisingly simple compared to previously suggested models assuming more complex computations such as multi-scale processing, oriented filters and lateral inhibition. Nevertheless, our model is equally predictive and generalizes better to novel image sets. 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.

Web DOI [BibTex]

Web DOI [BibTex]


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Multi-Classification by Categorical Features via Clustering

Seldin, Y.

25th International Conference on Machine Learning (ICML), June 2008 (talk)

Abstract
We derive a generalization bound for multi-classification schemes based on grid clustering in categorical parameter product spaces. Grid clustering partitions the parameter space in the form of a Cartesian product of partitions for each of the parameters. The derived bound provides a means to evaluate clustering solutions in terms of the generalization power of a built-on classifier. For classification based on a single feature the bound serves to find a globally optimal classification rule. Comparison of the generalization power of individual features can then be used for feature ranking. Our experiments show that in this role the bound is much more precise than mutual information or normalized correlation indices.

PDF Web [BibTex]

PDF Web [BibTex]


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Kernel Methods in Machine Learning

Hofmann, T., Schölkopf, B., Smola, A.

Annals of Statistics, 36(3):1171-1220, June 2008 (article)

Abstract
We review machine learning methods employing positive definite kernels. These methods formulate learning and estimation problems in a reproducing kernel Hilbert space (RKHS) of functions defined on the data domain, expanded in terms of a kernel. Working in linear spaces of function has the benefit of facilitating the construction and analysis of learning algorithms while at the same time allowing large classes of functions. The latter include nonlinear functions as well as functions defined on nonvectorial data.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Cross-validation Optimization for Large Scale Structured Classification Kernel Methods

Seeger, M.

Journal of Machine Learning Research, 9, pages: 1147-1178, June 2008 (article)

Abstract
We propose a highly efficient framework for penalized likelihood kernel methods applied to multi-class models with a large, structured set of classes. As opposed to many previous approaches which try to decompose the fitting problem into many smaller ones, we focus on a Newton optimization of the complete model, making use of model structure and linear conjugate gradients in order to approximate Newton search directions. Crucially, our learning method is based entirely on matrix-vector multiplication primitives with the kernel matrices and their derivatives, allowing straightforward specialization to new kernels, and focusing code optimization efforts to these primitives only. Kernel parameters are learned automatically, by maximizing the cross-validation log likelihood in a gradient-based way, and predictive probabilities are estimated. We demonstrate our approach on large scale text classification tasks with hierarchical structure on thousands of classes, achieving state-of-the-art results in an order of magnitude less time than previous work.

PDF PDF [BibTex]

PDF PDF [BibTex]


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Partitioning of Image Datasets using Discriminative Context Information

Lampert, CH.

In CVPR 2008, pages: 1-8, IEEE Computer Society, Los Alamitos, CA, USA, IEEE Computer Society Conference on Computer Vision and Pattern Recognition, June 2008 (inproceedings)

Abstract
We propose a new method to partition an unlabeled dataset, called Discriminative Context Partitioning (DCP). It is motivated by the idea of splitting the dataset based only on how well the resulting parts can be separated from a context class of disjoint data points. This is in contrast to typical clustering techniques like K-means that are based on a generative model by implicitly or explicitly searching for modes in the distribution of samples. The discriminative criterion in DCP avoids the problems that density based methods have when the a priori assumption of multimodality is violated, when the number of samples becomes small in relation to the dimensionality of the feature space, or if the cluster sizes are strongly unbalanced. We formulate DCP‘s separation property as a large-margin criterion, and show how the resulting optimization problem can be solved efficiently. Experiments on the MNIST and USPS datasets of handwritten digits and on a subset of the Caltech256 dataset show that, given a suitable context, DCP can achieve good results even in situation where density-based clustering techniques fail.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Non-monotonic Poisson Likelihood Maximization

Sra, S., Kim, D., Schölkopf, B.

(170), Max-Planck Institute for Biological Cybernetics, Tübingen, Germany, June 2008 (techreport)

Abstract
This report summarizes the theory and some main applications of a new non-monotonic algorithm for maximizing a Poisson Likelihood, which for Positron Emission Tomography (PET) is equivalent to minimizing the associated Kullback-Leibler Divergence, and for Transmission Tomography is similar to maximizing the dual of a maximum entropy problem. We call our method non-monotonic maximum likelihood (NMML) and show its application to different problems such as tomography and image restoration. We discuss some theoretical properties such as convergence for our algorithm. Our experimental results indicate that speedups obtained via our non-monotonic methods are substantial.

PDF [BibTex]

PDF [BibTex]


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Bayesian online multi-task learning using regularization networks

Pillonetto, G., Dinuzzo, F., De Nicolao, G.

In pages: 4517-4522, IEEE Service Center, Piscataway, NJ, USA, 2008 American Control Conference (ACC), June 2008 (inproceedings)

Abstract
Recently, standard single-task kernel methods have been extended to the case of multi-task learning under the framework of regularization. Experimental results have shown that such an approach can perform much better than single-task techniques, especially when few examples per task are available. However, a possible drawback may be computational complexity. For instance, when using regularization networks, complexity scales as the cube of the overall number of data associated with all the tasks. In this paper, an efficient computational scheme is derived for a widely applied class of multi-task kernels. More precisely, a quadratic loss is assumed and the multi-task kernel is the sum of a common term and a task-specific one. The proposed algorithm performs online learning recursively updating the estimates as new data become available. The learning problem is formulated in a Bayesian setting. The optimal estimates are obtained by solving a sequence of subproblems which involve projection of random variables onto suitable subspaces. The algorithm is tested on a simulated data set.

Web DOI [BibTex]

Web DOI [BibTex]


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Integrated Information in Discrete Dynamical Systems: Motivation and Theoretical Framework

Balduzzi, D., Tononi, G.

PLoS Computational Biology, 4(6):1-18, June 2008 (article)

Abstract
This paper introduces a time- and state-dependent measure of integrated information, φ, which captures the repertoire of causal states available to a system as a whole. Specifically, φ quantifies how much information is generated (uncertainty is reduced) when a system enters a particular state through causal interactions among its elements, above and beyond the information generated independently by its parts. Such mathematical characterization is motivated by the observation that integrated information captures two key phenomenological properties of consciousness: (i) there is a large repertoire of conscious experiences so that, when one particular experience occurs, it generates a large amount of information by ruling out all the others; and (ii) this information is integrated, in that each experience appears as a whole that cannot be decomposed into independent parts. This paper extends previous work on stationary systems and applies integrated information to discrete networks as a function of their dynamics and causal architecture. An analysis of basic examples indicates the following: (i) φ varies depending on the state entered by a network, being higher if active and inactive elements are balanced and lower if the network is inactive or hyperactive. (ii) φ varies for systems with identical or similar surface dynamics depending on the underlying causal architecture, being low for systems that merely copy or replay activity states. (iii) φ varies as a function of network architecture. High φ values can be obtained by architectures that conjoin functional specialization with functional integration. Strictly modular and homogeneous systems cannot generate high φ because the former lack integration, whereas the latter lack information. Feedforward and lattice architectures are capable of generating high φ but are inefficient. (iv) In Hopfield networks, φ is low for attractor states and neutral states, but increases if the networks are optimized to achieve tension between local and global interactions. These basic examples appear to match well against neurobiological evidence concerning the neural substrates of consciousness. More generally, φ appears to be a useful metric to characterize the capacity of any physical system to integrate information.

Web DOI [BibTex]


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Correlational Spectral Clustering

Blaschko, MB., Lampert, CH.

In CVPR 2008, pages: 1-8, IEEE Computer Society, Los Alamitos, CA, USA, IEEE Computer Society Conference on Computer Vision and Pattern Recognition, June 2008 (inproceedings)

Abstract
We present a new method for spectral clustering with paired data based on kernel canonical correlation analysis, called correlational spectral clustering. Paired data are common in real world data sources, such as images with text captions. Traditional spectral clustering algorithms either assume that data can be represented by a single similarity measure, or by co-occurrence matrices that are then used in biclustering. In contrast, the proposed method uses separate similarity measures for each data representation, and allows for projection of previously unseen data that are only observed in one representation (e.g. images but not text). We show that this algorithm generalizes traditional spectral clustering algorithms and show consistent empirical improvement over spectral clustering on a variety of datasets of images with associated text.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Approximate Dynamic Programming with Gaussian Processes

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

In ACC 2008, pages: 4480-4485, IEEE Service Center, Piscataway, NJ, USA, 2008 American Control Conference, June 2008 (inproceedings)

Abstract
In general, it is difficult to determine an optimal closed-loop policy in nonlinear control problems with continuous-valued state and control domains. Hence, approximations are often inevitable. The standard method of discretizing states and controls suffers from the curse of dimensionality and strongly depends on the chosen temporal sampling rate. In this paper, we introduce Gaussian process dynamic programming (GPDP) and determine an approximate globally optimal closed-loop policy. In GPDP, value functions in the Bellman recursion of the dynamic programming algorithm are modeled using Gaussian processes. GPDP returns an optimal statefeedback for a finite set of states. Based on these outcomes, we learn a possibly discontinuous closed-loop policy on the entire state space by switching between two independently trained Gaussian processes. A binary classifier selects one Gaussian process to predict the optimal control signal. We show that GPDP is able to yield an almost optimal solution to an LQ problem using few sample points. Moreover, we successfully apply GPDP to the underpowered pendulum swing up, a complex nonlinear control problem.

PDF Web [BibTex]

PDF Web [BibTex]


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Beyond Sliding Windows: Object Localization by Efficient Subwindow Search

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

In CVPR 2008, pages: 1-8, IEEE Computer Society, Los Alamitos, CA, USA, IEEE Computer Society Conference on Computer Vision and Pattern Recognition, June 2008, Best paper award (inproceedings)

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 perform localization, one can take a sliding window approach, but this strongly increases the computational cost, because the classifier function has to be evaluated over a large set of candidate subwindows. In this paper, we propose a simple yet powerful branchand- bound scheme that allows efficient maximization of a large class of classifier functions over all possible subimages. It converges to a globally optimal solution typically in sublinear time. We show how our method is applicable to different object detection and 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 2-distance. We demonstrate state-of-the-art performance of the resulting systems on the UIUC Cars dataset, the PASCAL VOC 2006 dataset and in the PASCAL VOC 2007 competition.

PDF PDF Web DOI [BibTex]

PDF PDF Web DOI [BibTex]


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Computed Torque Control with Nonparametric Regression Models

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

In ACC 2008, pages: 212-217, IEEE Service Center, Piscataway, NJ, USA, 2008 American Control Conference, June 2008 (inproceedings)

Abstract
Computed torque control allows the design of considerably more precise, energy-efficient and compliant controls for robots. However, the major obstacle is the requirement of an accurate model for torque generation, which cannot be obtained in some cases using rigid-body formulations due to unmodeled nonlinearities, such as complex friction or actuator dynamics. In such cases, models approximated from robot data present an appealing alternative. In this paper, we compare two nonparametric regression methods for model approximation, i.e., locally weighted projection regression (LWPR) and Gaussian process regression (GPR). While locally weighted regression was employed for real-time model estimation in learning adaptive control, Gaussian process regression has not been used in control to-date due to high computational requirements. The comparison includes the assessment of model approximation for both regression methods using data originated from SARCOS robot arm, as well as an evaluation of the robot tracking p erformance in computed torque control employing the approximated models. Our results show that GPR can be applied for real-time control achieving higher accuracy. However, for the online learning LWPR is superior by reason of lower computational requirements.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Multi-Classification by Categorical Features via Clustering

Seldin, Y., Tishby, N.

In In the proceedings of the 25th International Conference on Machine Learning (ICML 2008), pages: 920-927, 25th International Conference on Machine Learning (ICML), June 2008 (inproceedings)

Abstract
We derive a generalization bound for multi-classification schemes based on grid clustering in categorical parameter product spaces. Grid clustering partitions the parameter space in the form of a Cartesian product of partitions for each of the parameters. The derived bound provides a means to evaluate clustering solutions in terms of the generalization power of a built-on classifier. For classification based on a single feature the bound serves to find a globally optimal classification rule. Comparison of the generalization power of individual features can then be used for feature ranking. Our experiments show that in this role the bound is much more precise than mutual information or normalized correlation indices.

PDF Web [BibTex]

PDF Web [BibTex]


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A Kernel Test of Nonlinear Granger Causality

Sun, X.

In Proceedings of the Workshop on Inference and Estimation in Probabilistic Time-Series Models, pages: 79-89, (Editors: Barber, D. , A. T. Cemgil, S. Chiappa), Isaac Newton Institute for Mathematical Sciences, Cambridge, United Kingdom, Workshop on Inference and Estimation in Probabilistic Time-Series Models, June 2008 (inproceedings)

Abstract
We present a novel test of nonlinear Granger causality in bivariate time series. The trace norm of conditional covariance operators is used to capture the prediction errors. Based on this measure, a subsampling-based multiple testing procedure tests the prediction improvement of one time series by the other one. The distributional properties of the resulting p-values reveal the direction of Granger causality. Encouraging results of experiments with simulated and real-world data support our approach.

PDF [BibTex]

PDF [BibTex]