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2010


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Estimating predictive stimulus features from psychophysical data: The decision image technique applied to human faces

Macke, J., Wichmann, F.

Journal of Vision, 10(5:22):1-24, May 2010 (article)

Abstract
One major challenge in the sensory sciences is to identify the stimulus features on which sensory systems base their computations, and which are predictive of a behavioral decision: they are a prerequisite for computational models of perception. We describe a technique (decision images) for extracting predictive stimulus features using logistic regression. A decision image not only defines a region of interest within a stimulus but is a quantitative template which defines a direction in stimulus space. Decision images thus enable the development of predictive models, as well as the generation of optimized stimuli for subsequent psychophysical investigations. Here we describe our method and apply it to data from a human face classification experiment. We show that decision images are able to predict human responses not only in terms of overall percent correct but also in terms of the probabilities with which individual faces are (mis-) classified by individual observers. We show that the most predictive dimension for gender categorization is neither aligned with the axis defined by the two class-means, nor with the first principal component of all faces-two hypotheses frequently entertained in the literature. Our method can be applied to a wide range of binary classification tasks in vision or other psychophysical contexts.

ei

Web DOI [BibTex]


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Animal detection in natural scenes: Critical features revisited

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

Journal of Vision, 10(4):1-27, April 2010 (article)

Abstract
S. J. Thorpe, D. Fize, and C. Marlot (1996) showed how rapidly observers can detect animals in images of natural scenes, but it is still unclear which image features support this rapid detection. A. B. Torralba and A. Oliva (2003) suggested that a simple image statistic based on the power spectrum allows the absence or presence of objects in natural scenes to be predicted. We tested whether human observers make use of power spectral differences between image categories when detecting animals in natural scenes. In Experiments 1 and 2 we found performance to be essentially independent of the power spectrum. Computational analysis revealed that the ease of classification correlates with the proposed spectral cue without being caused by it. This result is consistent with the hypothesis that in commercial stock photo databases a majority of animal images are pre-segmented from the background by the photographers and this pre-segmentation causes the power spectral differences between image categories and may, furthermore, help rapid animal detection. Data from a third experiment are consistent with this hypothesis. Together, our results make it exceedingly unlikely that human observers make use of power spectral differences between animal- and no-animal images during rapid animal detection. In addition, our results point to potential confounds in the commercially available “natural image” databases whose statistics may be less natural than commonly presumed.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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A generative model approach for decoding in the visual event-related potential-based brain-computer interface speller

Martens, SMM., Leiva, JM.

Journal of Neural Engineering, 7(2):1-10, April 2010 (article)

Abstract
There is a strong tendency towards discriminative approaches in brain-computer interface (BCI) research. We argue that generative model-based approaches are worth pursuing and propose a simple generative model for the visual ERP-based BCI speller which incorporates prior knowledge about the brain signals. We show that the proposed generative method needs less training data to reach a given letter prediction performance than the state of the art discriminative approaches.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Hilbert Space Embeddings and Metrics on Probability Measures

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

Journal of Machine Learning Research, 11, pages: 1517-1561, April 2010 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Graph Kernels

Vishwanathan, SVN., Schraudolph, NN., Kondor, R., Borgwardt, KM.

Journal of Machine Learning Research, 11, pages: 1201-1242, April 2010 (article)

Abstract
We present a unified framework to study graph kernels, special cases of which include the random walk (G{\"a}rtner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004; Mahét al., 2004) graph kernels. Through reduction to a Sylvester equation we improve the time complexity of kernel computation between unlabeled graphs with n vertices from O(n6) to O(n3). We find a spectral decomposition approach even more efficient when computing entire kernel matrices. For labeled graphs we develop conjugate gradient and fixed-point methods that take O(dn3) time per iteration, where d is the size of the label set. By extending the necessary linear algebra to Reproducing Kernel Hilbert Spaces (RKHS) we obtain the same result for d-dimensional edge kernels, and O(n4) in the infinite-dimensional case; on sparse graphs these algorithms only take O(n2) time per iteration in all cases. Experiments on graphs from bioinformatics and other application domains show that these techniques can speed up computation of the kernel by an order of magnitude or more. We also show that certain rational kernels (Cortes et al., 2002, 2003, 2004) when specialized to graphs reduce to our random walk graph kernel. Finally, we relate our framework to R-convolution kernels (Haussler, 1999) and provide a kernel that is close to the optimal assignment kernel of kernel of Fr{\"o}hlich et al. (2006) yet provably positive semi-definite.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Gene function prediction from synthetic lethality networks via ranking on demand

Lippert, C., Ghahramani, Z., Borgwardt, KM.

Bioinformatics, 26(7):912-918, April 2010 (article)

Abstract
Motivation: Synthetic lethal interactions represent pairs of genes whose individual mutations are not lethal, while the double mutation of both genes does incur lethality. Several studies have shown a correlation between functional similarity of genes and their distances in networks based on synthetic lethal interactions. However, there is a lack of algorithms for predicting gene function from synthetic lethality interaction networks. Results: In this article, we present a novel technique called kernelROD for gene function prediction from synthetic lethal interaction networks based on kernel machines. We apply our novel algorithm to Gene Ontology functional annotation prediction in yeast. Our experiments show that our method leads to improved gene function prediction compared with state-of-the-art competitors and that combining genetic and congruence networks leads to a further improvement in prediction accuracy.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Cooperative Cuts: Graph Cuts with Submodular Edge Weights

Jegelka, S., Bilmes, J.

(189), Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, March 2010 (techreport)

Abstract
We introduce a problem we call Cooperative cut, where the goal is to find a minimum-cost graph cut but where a submodular function is used to define the cost of a subsets of edges. That means, the cost of an edge that is added to the current cut set C depends on the edges in C. This generalization of the cost in the standard min-cut problem to a submodular cost function immediately makes the problem harder. Not only do we prove NP hardness even for nonnegative submodular costs, but also show a lower bound of Omega(|V|^(1/3)) on the approximation factor for the problem. On the positive side, we propose and compare four approximation algorithms with an overall approximation factor of min { |V|/2, |C*|, O( sqrt(|E|) log |V|), |P_max|}, where C* is the optimal solution, and P_max is the longest s, t path across the cut between given s, t. We also introduce additional heuristics for the problem which have attractive properties from the perspective of practical applications and implementations in that existing fast min-cut libraries may be used as subroutines. Both our approximation algorithms, and our heuristics, appear to do well in practice.

ei

PDF [BibTex]

PDF [BibTex]


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A toolbox for predicting G-quadruplex formation and stability

Wong, HM., Stegle, O., Rodgers, S., Huppert, J.

Journal of Nucleic Acids, 2010(564946):1-6, March 2010 (article)

Abstract
G-quadruplexes are four stranded nucleic acid structures formed around a core of guanines, arranged in squares with mutual hydrogen bonding. Many of these structures are highly thermally stable, especially in the presence of monovalent cations, such as those found under physiological conditions. Understanding of their physiological roles is expanding rapidly, and they have been implicated in regulating gene transcription and translation among other functions. We have built a community-focused website to act as a repository for the information that is now being developed. At its core, this site has a detailed database (QuadDB) of predicted G-quadruplexes in the human and other genomes, together with the predictive algorithm used to identify them. We also provide a QuadPredict server, which predicts thermal stability and acts as a repository for experimental data from all researchers. There are also a number of other data sources with computational predictions. We anticipate that the wide availability of this information will be of use both to researchers already active in this exciting field and to those who wish to investigate a particular gene hypothesis.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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

Persello, C., Bruzzone, L.

IEEE Transactions on Geoscience and Remote Sensing, 48(3):1232-1244, March 2010 (article)

Abstract
This paper presents a novel protocol for the accuracy assessment of the 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 high-resolution classification maps, we propose a protocol that is based on the analysis of two families of indices: 1) the traditional thematic accuracy indices and 2) a set of novel geometric indices that model different geometric properties of the objects recognized in the map. In this context, we present a set of indices that characterize five different types of geometric errors in the classification map: 1) oversegmentation; 2) undersegmentation; 3) edge location; 4) shape distortion; and 5) fragmentation. Moreover, we propose a new approach for tuning the free parameters of supervised classifiers on the basis of a multiobjective criterion function that aims at selecting the parameter values that result in the classification map that jointly optimize thematic and geometric error indices. Experimental results obtained on QuickBird images show the effectiveness of the proposed protocol in selecting classification maps characterized by a better tradeoff between thematic and geometric accuracies than standard procedures based only on thematic accuracy measures. In addition, results obtained with support vector machine classifiers confirm the effectiveness of the proposed multiobjective technique for the selection of free-parameter values for the classification algorithm.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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On the Entropy Production of Time Series with Unidirectional Linearity

Janzing, D.

Journal of Statistical Physics, 138(4-5):767-779, March 2010 (article)

Abstract
There are non-Gaussian time series that admit a causal linear autoregressive moving average (ARMA) model when regressing the future on the past, but not when regressing the past on the future. The reason is that, in the latter case, the regression residuals are not statistically independent of the regressor. In previous work, we have experimentally verified that many empirical time series indeed show such a time inversion asymmetry. For various physical systems, it is known that time-inversion asymmetries are linked to the thermodynamic entropy production in non-equilibrium states. Here we argue that unidirectional linearity is also accompanied by entropy generation. To this end, we study the dynamical evolution of a physical toy system with linear coupling to an infinite environment and show that the linearity of the dynamics is inherited by the forward-time conditional probabilities, but not by the backward-time conditionals. The reason is that the environment permanently provides particles that are in a product state before they interact with the system, but show statistical dependence afterwards. From a coarse-grained perspective, the interaction thus generates entropy. We quantitatively relate the strength of the non-linearity of the backward process to the minimal amount of entropy generation. The paper thus shows that unidirectional linearity is an indirect implication of the thermodynamic arrow of time, given that the joint dynamics of the system and its environment is linear.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Derivatives of Logarithmic Stationary Distributions for Policy Gradient Reinforcement Learning

Morimura, T., Uchibe, E., Yoshimoto, J., Peters, J., Doya, K.

Neural Computation, 22(2):342-376, February 2010 (article)

Abstract
Most conventional policy gradient reinforcement learning (PGRL) algorithms neglect (or do not explicitly make use of) a term in the average reward gradient with respect to the policy parameter. That term involves the derivative of the stationary state distribution that corresponds to the sensitivity of its distribution to changes in the policy parameter. Although the bias introduced by this omission can be reduced by setting the forgetting rate γ for the value functions close to 1, these algorithms do not permit γ to be set exactly at γ = 1. In this article, we propose a method for estimating the log stationary state distribution derivative (LSD) as a useful form of the derivative of the stationary state distribution through backward Markov chain formulation and a temporal difference learning framework. A new policy gradient (PG) framework with an LSD is also proposed, in which the average reward gradient can be estimated by setting //!-- MFG_und--//amp;#947; = 0, so it becomes unnecessary to learn the value functions. We also test the performance of the proposed algorithms using simple benchmark tasks and show that these can improve the performances of existing PG methods.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Bayesian Online Multitask Learning of Gaussian Processes

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

IEEE Transactions on Pattern Analysis and Machine Intelligence, 32(2):193-205, February 2010 (article)

Abstract
Standard single-task kernel methods have recently been extended to the case of multitask learning in the context of regularization theory. There are experimental results, especially in biomedicine, showing the benefit of the multitask approach compared to the single-task one. However, a possible drawback is computational complexity. For instance, when regularization networks are used, complexity scales as the cube of the overall number of training data, which may be large when several tasks are involved. The aim of this paper is to derive an efficient computational scheme for an important class of multitask kernels. More precisely, a quadratic loss is assumed and each task consists of the sum of a common term and a task-specific one. Within a Bayesian setting, a recursive online algorithm is obtained, which updates both estimates and confidence intervals as new data become available. The algorithm is tested on two simulated problems and a real data set relative to xenobiotics administration in human patients.

ei

DOI [BibTex]

DOI [BibTex]


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The semigroup approach to transport processes in networks

Dorn, B., Fijavz, M., Nagel, R., Radl, A.

Physica D: Nonlinear Phenomena, 239(15):1416-1421, January 2010 (article)

Abstract
We explain how operator semigroups can be used to study transport processes in networks. This method is applied to a linear Boltzmann equation on a finite as well as on an infinite network and yields well-posedness and information on the long term behavior of the solutions to the presented problems.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Optimization of k-Space Trajectories for Compressed Sensing by Bayesian Experimental Design

Seeger, M., Nickisch, H., Pohmann, R., Schölkopf, B.

Magnetic Resonance in Medicine, 63(1):116-126, January 2010 (article)

Abstract
The optimization of k-space sampling for nonlinear sparse MRI reconstruction is phrased as a Bayesian experimental design problem. Bayesian inference is approximated by a novel relaxation to standard signal processing primitives, resulting in an efficient optimization algorithm for Cartesian and spiral trajectories. On clinical resolution brain image data from a Siemens 3T scanner, automatically optimized trajectories lead to significantly improved images, compared to standard low-pass, equispaced, or variable density randomized designs. Insights into the nonlinear design optimization problem for MRI are given.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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From Motor Learning to Interaction Learning in Robots

Sigaud, O., Peters, J.

pages: 538, Studies in Computational Intelligence ; 264, (Editors: O Sigaud, J Peters), Springer, Berlin, Germany, January 2010 (book)

Abstract
From an engineering standpoint, the increasing complexity of robotic systems and the increasing demand for more autonomously learning robots, has become essential. This book is largely based on the successful workshop "From motor to interaction learning in robots" held at the IEEE/RSJ International Conference on Intelligent Robot Systems. The major aim of the book is to give students interested the topics described above a chance to get started faster and researchers a helpful compandium.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Consistent Nonparametric Tests of Independence

Gretton, A., Györfi, L.

Journal of Machine Learning Research, 11, pages: 1391-1423, 2010 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Inferring latent task structure for Multitask Learning by Multiple Kernel Learning

Widmer, C., Toussaint, N., Altun, Y., Rätsch, G.

BMC Bioinformatics, 11 Suppl 8, pages: S5, 2010 (article)

Abstract
The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics, many problems can be cast into the Multitask Learning scenario by incorporating data from several organisms. However, combining information from several tasks requires careful consideration of the degree of similarity between tasks. Our proposed method simultaneously learns or refines the similarity between tasks along with the Multitask Learning classifier. This is done by formulating the Multitask Learning problem as Multiple Kernel Learning, using the recently published q-Norm MKL algorithm.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Information-theoretic inference of common ancestors

Steudel, B., Ay, N.

Computing Research Repository (CoRR), abs/1010.5720, pages: 18, 2010 (techreport)

ei

Web [BibTex]

Web [BibTex]