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2012


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Evaluation of marginal likelihoods via the density of states

Habeck, M.

In Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics (AISTATS 2012) , 22, pages: 486-494, (Editors: N Lawrence and M Girolami), JMLR: W&CP 22, AISTATS, 2012 (inproceedings)

Abstract
Bayesian model comparison involves the evaluation of the marginal likelihood, the expectation of the likelihood under the prior distribution. Typically, this high-dimensional integral over all model parameters is approximated using Markov chain Monte Carlo methods. Thermodynamic integration is a popular method to estimate the marginal likelihood by using samples from annealed posteriors. Here we show that there exists a robust and flexible alternative. The new method estimates the density of states, which counts the number of states associated with a particular value of the likelihood. If the density of states is known, computation of the marginal likelihood reduces to a one- dimensional integral. We outline a maximum likelihood procedure to estimate the density of states from annealed posterior samples. We apply our method to various likelihoods and show that it is superior to thermodynamic integration in that it is more flexible with regard to the annealing schedule and the family of bridging distributions. Finally, we discuss the relation of our method with Skilling's nested sampling.

PDF [BibTex]

2012

PDF [BibTex]


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Distributed multisensory signals acquisition and analysis in dyadic interactions

Tawari, A., Tran, C., Doshi, A., Zander, TO.

In Proceedings of the 2012 ACM Annual Conference on Human Factors in Computing Systems Extended Abstracts, pages: 2261-2266, (Editors: JA Konstan and EH Chi and K Höök), ACM, New York, NY, USA, CHI, 2012 (inproceedings)

DOI [BibTex]

DOI [BibTex]


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Measuring Cognitive Load by means of EEG-data - how detailed is the picture we can get?

Scharinger, C., Cierniak, G., Walter, C., Zander, TO., Gerjets, P.

In Meeting of the EARLI SIG 22 Neuroscience and Education, 2012 (inproceedings)

[BibTex]

[BibTex]


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Optimal kernel choice for large-scale two-sample tests

Gretton, A., Sriperumbudur, B., Sejdinovic, D., Strathmann, H., Balakrishnan, S., Pontil, M., Fukumizu, K.

In Advances in Neural Information Processing Systems 25, pages: 1214-1222, (Editors: P Bartlett and FCN Pereira and CJC. Burges and L Bottou and KQ Weinberger), Curran Associates Inc., 26th Annual Conference on Neural Information Processing Systems (NIPS), 2012 (inproceedings)

PDF [BibTex]

PDF [BibTex]


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Measurement and calibration of noise bias in weak lensing galaxy shape estimation

Kacprzak, T., Zuntz, J., Rowe, B., Bridle, S., Refregier, A., Amara, A., Voigt, L., Hirsch, M.

Monthly Notices of the Royal Astronomical Society, 427(4):2711-2722, Oxford University Press, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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Image analysis for cosmology: results from the GREAT10 Galaxy Challenge

Kitching, T. D., Balan, S. T., Bridle, S., Cantale, N., Courbin, F., Eifler, T., Gentile, M., Gill, M. S. S., Harmeling, S., Heymans, C., others,

Monthly Notices of the Royal Astronomical Society, 423(4):3163-3208, Oxford University Press, 2012 (article)

DOI [BibTex]

DOI [BibTex]


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On the Hardness of Domain Adaptation and the Utility of Unlabeled Target Samples

Ben-David, S., Urner, R.

In Algorithmic Learning Theory - 23rd International Conference, 7568, pages: 139-153, Lecture Notes in Computer Science, (Editors: Bshouty, NH. and Stoltz, G and Vayatis, N and Zeugmann, T), Springer Berlin Heidelberg, ALT, 2012 (inproceedings)

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Domain Adaptation–Can Quantity compensate for Quality?

Ben-David, S., Shalev-Shwartz, S., Urner, R.

In International Symposium on Artificial Intelligence and Mathematics, ISAIM, 2012 (inproceedings)

link (url) [BibTex]

link (url) [BibTex]


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Learning from Weak Teachers

Urner, R., Ben-David, S., Shamir, O.

In Proceedings of the 15th International Conference on Artificial Intelligence and Statistics, 22, pages: 1252-1260, (Editors: Lawrence, N. and Girolami, M.), JMLR, AISTATS, 2012 (inproceedings)

link (url) [BibTex]

link (url) [BibTex]


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First SN Discoveries from the Dark Energy Survey

Abbott, T., Abdalla, F., Achitouv, I., Ahn, E., Aldering, G., Allam, S., Alonso, D., Amara, A., Annis, J., Antonik, M., others,

The Astronomer's Telegram, 4668, pages: 1, 2012 (article)

[BibTex]

[BibTex]


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A sensorimotor paradigm for Bayesian model selection

Genewein, T, Braun, DA

Frontiers in Human Neuroscience, 6(291):1-16, October 2012 (article)

Abstract
Sensorimotor control is thought to rely on predictive internal models in order to cope efficiently with uncertain environments. Recently, it has been shown that humans not only learn different internal models for different tasks, but that they also extract common structure between tasks. This raises the question of how the motor system selects between different structures or models, when each model can be associated with a range of different task-specific parameters. Here we design a sensorimotor task that requires subjects to compensate visuomotor shifts in a three-dimensional virtual reality setup, where one of the dimensions can be mapped to a model variable and the other dimension to the parameter variable. By introducing probe trials that are neutral in the parameter dimension, we can directly test for model selection. We found that model selection procedures based on Bayesian statistics provided a better explanation for subjects’ choice behavior than simple non-probabilistic heuristics. Our experimental design lends itself to the general study of model selection in a sensorimotor context as it allows to separately query model and parameter variables from subjects.

DOI [BibTex]

DOI [BibTex]


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Adaptive Coding of Actions and Observations

Ortega, PA, Braun, DA

pages: 1-4, NIPS Workshop on Information in Perception and Action, December 2012 (conference)

Abstract
The application of expected utility theory to construct adaptive agents is both computationally intractable and statistically questionable. To overcome these difficulties, agents need the ability to delay the choice of the optimal policy to a later stage when they have learned more about the environment. How should agents do this optimally? An information-theoretic answer to this question is given by the Bayesian control rule—the solution to the adaptive coding problem when there are not only observations but also actions. This paper reviews the central ideas behind the Bayesian control rule.

link (url) [BibTex]

link (url) [BibTex]


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Risk-Sensitivity in Bayesian Sensorimotor Integration

Grau-Moya, J, Ortega, PA, Braun, DA

PLoS Computational Biology, 8(9):1-7, sep 2012 (article)

Abstract
Information processing in the nervous system during sensorimotor tasks with inherent uncertainty has been shown to be consistent with Bayesian integration. Bayes optimal decision-makers are, however, risk-neutral in the sense that they weigh all possibilities based on prior expectation and sensory evidence when they choose the action with highest expected value. In contrast, risk-sensitive decision-makers are sensitive to model uncertainty and bias their decision-making processes when they do inference over unobserved variables. In particular, they allow deviations from their probabilistic model in cases where this model makes imprecise predictions. Here we test for risk-sensitivity in a sensorimotor integration task where subjects exhibit Bayesian information integration when they infer the position of a target from noisy sensory feedback. When introducing a cost associated with subjects' response, we found that subjects exhibited a characteristic bias towards low cost responses when their uncertainty was high. This result is in accordance with risk-sensitive decision-making processes that allow for deviations from Bayes optimal decision-making in the face of uncertainty. Our results suggest that both Bayesian integration and risk-sensitivity are important factors to understand sensorimotor integration in a quantitative fashion.

DOI [BibTex]

DOI [BibTex]


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Free Energy and the Generalized Optimality Equations for Sequential Decision Making

Ortega, PA, Braun, DA

pages: 1-10, 10th European Workshop on Reinforcement Learning (EWRL), July 2012 (conference)

Abstract
The free energy functional has recently been proposed as a variational principle for bounded rational decision-making, since it instantiates a natural trade-off between utility gains and information processing costs that can be axiomatically derived. Here we apply the free energy principle to general decision trees that include both adversarial and stochastic environments. We derive generalized sequential optimality equations that not only include the Bellman optimality equations as a limit case, but also lead to well-known decision-rules such as Expectimax, Minimax and Expectiminimax. We show how these decision-rules can be derived from a single free energy principle that assigns a resource parameter to each node in the decision tree. These resource parameters express a concrete computational cost that can be measured as the amount of samples that are needed from the distribution that belongs to each node. The free energy principle therefore provides the normative basis for generalized optimality equations that account for both adversarial and stochastic environments.

link (url) [BibTex]

link (url) [BibTex]

2011


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Statistical estimation for optimization problems on graphs

Langovoy, M., Sra, S.

In pages: 1-6, NIPS Workshop on Discrete Optimization in Machine Learning (DISCML): Uncertainty, Generalization and Feedback , December 2011 (inproceedings)

Abstract
Large graphs abound in machine learning, data mining, and several related areas. A useful step towards analyzing such graphs is that of obtaining certain summary statistics — e.g., or the expected length of a shortest path between two nodes, or the expected weight of a minimum spanning tree of the graph, etc. These statistics provide insight into the structure of a graph, and they can help predict global properties of a graph. Motivated thus, we propose to study statistical properties of structured subgraphs (of a given graph), in particular, to estimate the expected objective function value of a combinatorial optimization problem over these subgraphs. The general task is very difficult, if not unsolvable; so for concreteness we describe a more specific statistical estimation problem based on spanning trees. We hope that our position paper encourages others to also study other types of graphical structures for which one can prove nontrivial statistical estimates.

PDF Web [BibTex]

2011

PDF Web [BibTex]


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On the discardability of data in Support Vector Classification problems

Del Favero, S., Varagnolo, D., Dinuzzo, F., Schenato, L., Pillonetto, G.

In pages: 3210-3215, IEEE, Piscataway, NJ, USA, 50th IEEE Conference on Decision and Control and European Control Conference (CDC - ECC), December 2011 (inproceedings)

Abstract
We analyze the problem of data sets reduction for support vector classification. The work is also motivated by distributed problems, where sensors collect binary measurements at different locations moving inside an environment that needs to be divided into a collection of regions labeled in two different ways. The scope is to let each agent retain and exchange only those measurements that are mostly informative for the collective reconstruction of the decision boundary. For the case of separable classes, we provide the exact conditions and an efficient algorithm to determine if an element in the training set can become a support vector when new data arrive. The analysis is then extended to the non-separable case deriving a sufficient discardability condition and a general data selection scheme for classification. Numerical experiments relative to the distributed problem show that the proposed procedure allows the agents to exchange a small amount of the collected data to obtain a highly predictive decision boundary.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Causal Inference on Discrete Data using Additive Noise Models

Peters, J., Janzing, D., Schölkopf, B.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 33(12):2436-2450, December 2011 (article)

Abstract
Inferring the causal structure of a set of random variables from a finite sample of the joint distribution is an important problem in science. The case of two random variables is particularly challenging since no (conditional) independences can be exploited. Recent methods that are based on additive noise models suggest the following principle: Whenever the joint distribution {\bf P}^{(X,Y)} admits such a model in one direction, e.g., Y=f(X)+N, N \perp\kern-6pt \perp X, but does not admit the reversed model X=g(Y)+\tilde{N}, \tilde{N} \perp\kern-6pt \perp Y, one infers the former direction to be causal (i.e., X\rightarrow Y). Up to now, these approaches only dealt with continuous variables. In many situations, however, the variables of interest are discrete or even have only finitely many states. In this work, we extend the notion of additive noise models to these cases. We prove that it almost never occurs that additive noise models can be fit in both directions. We further propose an efficient algorithm that is able to perform this way of causal inference on finite samples of discrete variables. We show that the algorithm works on both synthetic and real data sets.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

Becker, C., Hagmann, J., Müller, J., Koenig, D., Stegle, O., Borgwardt, K., Weigel, D.

Nature, 480(7376):245-249, December 2011 (article)

Abstract
Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation1, 2. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles3, 4, and these can influence the expression of nearby genes1, 2. However, to understand their role in evolution5, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor6. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations7. Like individual positions, the same regions were often affected by differential methylation in independent lines, with evidence for recurrent cycles of forward and reverse mutations. Transposable elements and short interfering RNAs have been causally linked to DNA methylation8. In agreement, differentially methylated sites were farther from transposable elements and showed less association with short interfering RNA expression than invariant positions. The biased distribution and frequent reversion of epimutations have important implications for the potential contribution of sequence-independent epialleles to plant evolution.

Web DOI [BibTex]

Web DOI [BibTex]


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Information, learning and falsification

Balduzzi, D.

In pages: 1-4, NIPS Philosophy and Machine Learning Workshop, December 2011 (inproceedings)

Abstract
There are (at least) three approaches to quantifying information. The first, algorithmic information or Kolmogorov complexity, takes events as strings and, given a universal Turing machine, quantifies the information content of a string as the length of the shortest program producing it [1]. The second, Shannon information, takes events as belonging to ensembles and quantifies the information resulting from observing the given event in terms of the number of alternate events that have been ruled out [2]. The third, statistical learning theory, has introduced measures of capacity that control (in part) the expected risk of classifiers [3]. These capacities quantify the expectations regarding future data that learning algorithms embed into classifiers. Solomonoff and Hutter have applied algorithmic information to prove remarkable results on universal induction. Shannon information provides the mathematical foundation for communication and coding theory. However, both approaches have shortcomings. Algorithmic information is not computable, severely limiting its practical usefulness. Shannon information refers to ensembles rather than actual events: it makes no sense to compute the Shannon information of a single string – or rather, there are many answers to this question depending on how a related ensemble is constructed. Although there are asymptotic results linking algorithmic and Shannon information, it is unsatisfying that there is such a large gap – a difference in kind – between the two measures. This note describes a new method of quantifying information, effective information, that links algorithmic information to Shannon information, and also links both to capacities arising in statistical learning theory [4, 5]. After introducing the measure, we show that it provides a non-universal analog of Kolmogorov complexity. We then apply it to derive basic capacities in statistical learning theory: empirical VC-entropy and empirical Rademacher complexity. A nice byproduct of our approach is an interpretation of the explanatory power of a learning algorithm in terms of the number of hypotheses it falsifies [6], counted in two different ways for the two capacities. We also discuss how effective information relates to information gain, Shannon and mutual information.

PDF Web [BibTex]

PDF Web [BibTex]


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A general linear non-Gaussian state-space model: Identifiability, identification, and applications

Zhang, K., Hyvärinen, A.

In JMLR Workshop and Conference Proceedings Volume 20, pages: 113-128, (Editors: Hsu, C.-N. , W.S. Lee ), MIT Press, Cambridge, MA, USA, 3rd Asian Conference on Machine Learning (ACML), November 2011 (inproceedings)

Abstract
State-space modeling provides a powerful tool for system identification and prediction. In linear state-space models the data are usually assumed to be Gaussian and the models have certain structural constraints such that they are identifiable. In this paper we propose a non-Gaussian state-space model which does not have such constraints. We prove that this model is fully identifiable. We then propose an efficient two-step method for parameter estimation: one first extracts the subspace of the latent processes based on the temporal information of the data, and then performs multichannel blind deconvolution, making use of both the temporal information and non-Gaussianity. We conduct a series of simulations to illustrate the performance of the proposed method. Finally, we apply the proposed model and parameter estimation method on real data, including major world stock indices and magnetoencephalography (MEG) recordings. Experimental results are encouraging and show the practical usefulness of the proposed model and method.

PDF Web [BibTex]

PDF Web [BibTex]


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Non-stationary correction of optical aberrations

Schuler, C., Hirsch, M., Harmeling, S., Schölkopf, B.

In pages: 659-666 , (Editors: DN Metaxas and L Quan and A Sanfeliu and LJ Van Gool), IEEE, Piscataway, NJ, USA, 13th IEEE International Conference on Computer Vision (ICCV), November 2011 (inproceedings)

Abstract
Taking a sharp photo at several megapixel resolution traditionally relies on high grade lenses. In this paper, we present an approach to alleviate image degradations caused by imperfect optics. We rely on a calibration step to encode the optical aberrations in a space-variant point spread function and obtain a corrected image by non-stationary deconvolution. By including the Bayer array in our image formation model, we can perform demosaicing as part of the deconvolution.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Learning low-rank output kernels

Dinuzzo, F., Fukumizu, K.

In JMLR Workshop and Conference Proceedings Volume 20, pages: 181-196, (Editors: Hsu, C.-N. , W.S. Lee), JMLR, Cambridge, MA, USA, 3rd Asian Conference on Machine Learning (ACML) , November 2011 (inproceedings)

Abstract
Output kernel learning techniques allow to simultaneously learn a vector-valued function and a positive semidefinite matrix which describes the relationships between the outputs. In this paper, we introduce a new formulation that imposes a low-rank constraint on the output kernel and operates directly on a factor of the kernel matrix. First, we investigate the connection between output kernel learning and a regularization problem for an architecture with two layers. Then, we show that a variety of methods such as nuclear norm regularized regression, reduced-rank regression, principal component analysis, and low rank matrix approximation can be seen as special cases of the output kernel learning framework. Finally, we introduce a block coordinate descent strategy for learning low-rank output kernels.

PDF Web [BibTex]

PDF Web [BibTex]


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HHfrag: HMM-based fragment detection using HHpred

Kalev, I., Habeck, M.

Bioinformatics, 27(22):3110-3116, November 2011 (article)

Abstract
Motivation: Over the last decade, both static and dynamic fragment libraries for protein structure prediction have been introduced. The former are built from clusters in either sequence or structure space and aim to extract a universal structural alphabet. The latter are tailored for a particular query protein sequence and aim to provide local structural templates that need to be assembled in order to build the full-length structure. Results: Here, we introduce HHfrag, a dynamic HMM-based fragment search method built on the profile–profile comparison tool HHpred. We show that HHfrag provides advantages over existing fragment assignment methods in that it: (i) improves the precision of the fragments at the expense of a minor loss in sequence coverage; (ii) detects fragments of variable length (6–21 amino acid residues); (iii) allows for gapped fragments and (iv) does not assign fragments to regions where there is no clear sequence conservation. We illustrate the usefulness of fragments detected by HHfrag on targets from most recent CASP.

Web DOI [BibTex]

Web DOI [BibTex]


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Reward-Weighted Regression with Sample Reuse for Direct Policy Search in Reinforcement Learning

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

Neural Computation, 23(11):2798-2832, November 2011 (article)

Abstract
Direct policy search is a promising reinforcement learning framework, in particular for controlling continuous, high-dimensional systems. Policy search often requires a large number of samples for obtaining a stable policy update estimator, and this is prohibitive when the sampling cost is expensive. In this letter, we extend an expectation-maximization-based policy search method so that previously collected samples can be efficiently reused. The usefulness of the proposed method, reward-weighted regression with sample reuse (R), is demonstrated through robot learning experiments.

Web DOI [BibTex]


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Stability Condition for Teleoperation System with Packet Loss

Hong, A., Cho, JH., Lee, DY.

In pages: 760-761, 2011 KSME Annual Fall Conference, November 2011 (inproceedings)

Abstract
This paper focuses on the stability condition of teleoperation system where there is a packet loss in communication channel. Communication channel between master and slave cause packet loss and it obviously leads to a performance degradation and instability of teleoperation system. We consider two-channel control architecture for teleoperation system, and control inputs to remote site are produced by position of master and slave. In this paper, teleoperation system is modeled in discrete domain to include packet loss process. Also, the stability condition for teleoperation system with packet loss is discussed with input-to-state stability. Finally, the stability condition is presented in LMI approach.

[BibTex]

[BibTex]


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Model Learning in Robotics: a Survey

Nguyen-Tuong, D., Peters, J.

Cognitive Processing, 12(4):319-340, November 2011 (article)

Abstract
Models are among the most essential tools in robotics, such as kinematics and dynamics models of the robot's own body and controllable external objects. It is widely believed that intelligent mammals also rely on internal models in order to generate their actions. However, while classical robotics relies on manually generated models that are based on human insights into physics, future autonomous, cognitive robots need to be able to automatically generate models that are based on information which is extracted from the data streams accessible to the robot. In this paper, we survey the progress in model learning with a strong focus on robot control on a kinematic as well as dynamical level. Here, a model describes essential information about the behavior of the environment and the in uence of an agent on this environment. In the context of model based learning control, we view the model from three di fferent perspectives. First, we need to study the di erent possible model learning architectures for robotics. Second, we discuss what kind of problems these architecture and the domain of robotics imply for the applicable learning methods. From this discussion, we deduce future directions of real-time learning algorithms. Third, we show where these scenarios have been used successfully in several case studies.

PDF [BibTex]

PDF [BibTex]


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Fast removal of non-uniform camera shake

Hirsch, M., Schuler, C., Harmeling, S., Schölkopf, B.

In pages: 463-470 , (Editors: DN Metaxas and L Quan and A Sanfeliu and LJ Van Gool), IEEE, Piscataway, NJ, USA, 13th IEEE International Conference on Computer Vision (ICCV), November 2011 (inproceedings)

Abstract
Camera shake leads to non-uniform image blurs. State-of-the-art methods for removing camera shake model the blur as a linear combination of homographically transformed versions of the true image. While this is conceptually interesting, the resulting algorithms are computationally demanding. In this paper we develop a forward model based on the efficient filter flow framework, incorporating the particularities of camera shake, and show how an efficient algorithm for blur removal can be obtained. Comprehensive comparisons on a number of real-world blurry images show that our approach is not only substantially faster, but it also leads to better deblurring results.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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FaST linear mixed models for genome-wide association studies

Lippert, C., Listgarten, J., Liu, Y., Kadie, CM., Davidson, RI., Heckerman, D.

Nature Methods, 8(10):833–835, October 2011 (article)

Abstract
We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data for 120,000 individuals in just a few hours, whereas current algorithms fail on data for even 20,000 individuals (http://mscompbio.codeplex.com/).

PDF DOI [BibTex]

PDF DOI [BibTex]


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The effect of noise correlations in populations of diversely tuned neurons

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

Journal of Neuroscience, 31(40):14272-14283, October 2011 (article)

Abstract
The amount of information encoded by networks of neurons critically depends on the correlation structure of their activity. Neurons with similar stimulus preferences tend to have higher noise correlations than others. In homogeneous populations of neurons, this limited range correlation structure is highly detrimental to the accuracy of a population code. Therefore, reduced spike count correlations under attention, after adaptation, or after learning have been interpreted as evidence for a more efficient population code. Here, we analyze the role of limited range correlations in more realistic, heterogeneous population models. We use Fisher information and maximum-likelihood decoding to show that reduced correlations do not necessarily improve encoding accuracy. In fact, in populations with more than a few hundred neurons, increasing the level of limited range correlations can substantially improve encoding accuracy. We found that this improvement results from a decrease in noise entropy that is associated with increasing correlations if the marginal distributions are unchanged. Surprisingly, for constant noise entropy and in the limit of large populations, the encoding accuracy is independent of both structure and magnitude of noise correlations.

Web DOI [BibTex]

Web DOI [BibTex]


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Attenuation correction in MR-BrainPET with segmented T1-weighted MR images of the patient’s head: A comparative study with CT

Wagenknecht, G., Rota Kops, E., Mantlik, F., Fried, E., Pilz, T., Hautzel, H., Tellmann, L., Pichler, B., Herzog, H.

In pages: 2261-2266 , IEEE, Piscataway, NJ, USA, IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC), October 2011 (inproceedings)

Abstract
Our method for attenuation correction (AC) in MR-BrainPET with segmented T1-weighted MR images of the pa-tient's head was applied to data from different MR-BrainPET scanners (Jülich, Tübingen) and compared to CT-based results. The study objectives presented in this paper are twofold. The first objective is to examine if the segmentation method developed for and successfully applied to 3D MP-RAGE data can also be used to segment other T1-weighted MR data such as 3D FLASH data. The second aim is to show if the similarity of segmented MR-based (SBA) and CT-based AC (CBA) obtained at HR+ PET can also be confirmed for BrainPET for which the new AC method is intended for. In order to reach the first objective, 14 segmented MR data sets (three 3D MP-RAGE data sets from Jülich and eleven 3D FLASH data sets from Tubingen) were compared to the resp. CT data based on the Dice coefficient and scatter plots. For bone, a CT threshold HU>;500 was applied. Dice coefficients (mean±std) for the upper cranial part of the skull, the skull above cavities, and in the caudal part including the cerebellum are 0.73±0.1, 0.79±0.04, and 0.49±0.02 for the Jülich data and 0.7U0.1, 0.72±0.1, and 0.60±0.05 for the Tubingen data. To reach the second aim, SBA and CBA were compared for six subjects based on VOI (AAL atlas) analysis. Mean absolute relative difference (maRD) values are maRD(JUFVBWl-FDG): 0.99%±0.83%, maRD(JüFVBW2-FDG): 0.90%±0.89%, and maRD(JUEP-Fluma- zenil): 1.85%±1.25% for the Jülich data and maRD(TuTP02- FDG): 2.99%±1.65%, maRD(TuNP01-FDG): 5.37%±2.29%, and maRD(TuNP02-FDG): 6.52%±1.69% for the three best-segmented Tübingen data sets. The results show similar segmentation quality for both Tl- weighted MR sequence types. The application to AC in BrainPET - hows a high similarity to CT-based AC if the standardized ACF value for bone used in SBA is in good accordance to the bone density of the patient in question.

Web DOI [BibTex]

Web DOI [BibTex]


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Analysis of Fixed-Point and Coordinate Descent Algorithms for Regularized Kernel Methods

Dinuzzo, F.

IEEE Transactions on Neural Networks, 22(10):1576-1587, October 2011 (article)

Abstract
In this paper, we analyze the convergence of two general classes of optimization algorithms for regularized kernel methods with convex loss function and quadratic norm regularization. The first methodology is a new class of algorithms based on fixed-point iterations that are well-suited for a parallel implementation and can be used with any convex loss function. The second methodology is based on coordinate descent, and generalizes some techniques previously proposed for linear support vector machines. It exploits the structure of additively separable loss functions to compute solutions of line searches in closed form. The two methodologies are both very easy to implement. In this paper, we also show how to remove non-differentiability of the objective functional by exactly reformulating a convex regularization problem as an unconstrained differentiable stabilization problem.

Web DOI [BibTex]

Web DOI [BibTex]


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A biomimetic approach to robot table tennis

Mülling, K., Kober, J., Peters, J.

Adaptive Behavior , 19(5):359-376 , October 2011 (article)

Abstract
Playing table tennis is a difficult motor task that requires fast movements, accurate control and adaptation to task parameters. Although human beings see and move slower than most robot systems, they significantly outperform all table tennis robots. One important reason for this higher performance is the human movement generation. In this paper, we study human movements during table tennis and present a robot system that mimics human striking behavior. Our focus lies on generating hitting motions capable of adapting to variations in environmental conditions, such as changes in ball speed and position. Therefore, we model the human movements involved in hitting a table tennis ball using discrete movement stages and the virtual hitting point hypothesis. The resulting model was evaluated both in a physically realistic simulation and on a real anthropomorphic seven degrees of freedom Barrett WAM™ robot arm.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Whole-genome sequencing of multiple Arabidopsis thaliana populations

Cao, J., Schneeberger, K., Ossowski, S., Günther, T., Bender, S., Fitz, J., Koenig, D., Lanz, C., Stegle, O., Lippert, C., Wang, X., Ott, F., Müller, J., Alonso-Blanco, C., Borgwardt, K., Schmid, K., Weigel, D.

Nature Genetics, 43(10):956–963, October 2011 (article)

Abstract
The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.

Web DOI [BibTex]

Web DOI [BibTex]


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Learning anticipation policies for robot table tennis

Wang, Z., Lampert, C., Mülling, K., Schölkopf, B., Peters, J.

In pages: 332-337 , (Editors: NM Amato), IEEE, Piscataway, NJ, USA, IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), September 2011 (inproceedings)

Abstract
Playing table tennis is a difficult task for robots, especially due to their limitations of acceleration. A key bottleneck is the amount of time needed to reach the desired hitting position and velocity of the racket for returning the incoming ball. Here, it often does not suffice to simply extrapolate the ball's trajectory after the opponent returns it but more information is needed. Humans are able to predict the ball's trajectory based on the opponent's moves and, thus, have a considerable advantage. Hence, we propose to incorporate an anticipation system into robot table tennis players, which enables the robot to react earlier while the opponent is performing the striking movement. Based on visual observation of the opponent's racket movement, the robot can predict the aim of the opponent and adjust its movement generation accordingly. The policies for deciding how and when to react are obtained by reinforcement learning. We conduct experiments with an existing robot player to show that the learned reaction policy can significantly improve the performance of the overall system.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Estimating integrated information with TMS pulses during wakefulness, sleep and under anesthesia

Balduzzi, D.

In pages: 4717-4720 , IEEE, Piscataway, NJ, USA, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE EMBC), September 2011 (inproceedings)

Abstract
This paper relates a recently proposed measure of information integration to experiments investigating the evoked high-density electroencephalography (EEG) response to transcranial magnetic stimulation (TMS) during wakefulness, early non-rapid eye movement (NREM) sleep and under anesthesia. We show that bistability, arising at the cellular and population level during NREM sleep and under anesthesia, dramatically reduces the brain’s ability to integrate information.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Improving Denoising Algorithms via a Multi-scale Meta-procedure

Burger, H., Harmeling, S.

In Pattern Recognition, pages: 206-215, (Editors: Mester, R. , M. Felsberg), Springer, Berlin, Germany, 33rd DAGM Symposium, September 2011 (inproceedings)

Abstract
Many state-of-the-art denoising algorithms focus on recovering high-frequency details in noisy images. However, images corrupted by large amounts of noise are also degraded in the lower frequencies. Thus properly handling all frequency bands allows us to better denoise in such regimes. To improve existing denoising algorithms we propose a meta-procedure that applies existing denoising algorithms across different scales and combines the resulting images into a single denoised image. With a comprehensive evaluation we show that the performance of many state-of-the-art denoising algorithms can be improved.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Gan, X., Stegle, O., Behr, J., Steffen, J., Drewe, P., Hildebrand, K., Lyngsoe, R., Schultheiss, S., Osborne, E., Sreedharan, V., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E., Harberd, N., Kemen, E., Toomajian, C., Kover, P., Clark, R., Rätsch, G., Mott, R.

Nature, 477(7365):419–423, September 2011 (article)

Abstract
Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions.

Web DOI [BibTex]

Web DOI [BibTex]


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Weisfeiler-Lehman Graph Kernels

Shervashidze, N., Schweitzer, P., van Leeuwen, E., Mehlhorn, K., Borgwardt, M.

Journal of Machine Learning Research, 12, pages: 2539-2561, September 2011 (article)

Abstract
In this article, we propose a family of efficient kernels for large graphs with discrete node labels. Key to our method is a rapid feature extraction scheme based on the Weisfeiler-Lehman test of isomorphism on graphs. It maps the original graph to a sequence of graphs, whose node attributes capture topological and label information. A family of kernels can be defined based on this Weisfeiler-Lehman sequence of graphs, including a highly efficient kernel comparing subtree-like patterns. Its runtime scales only linearly in the number of edges of the graphs and the length of the Weisfeiler-Lehman graph sequence. In our experimental evaluation, our kernels outperform state-of-the-art graph kernels on several graph classification benchmark data sets in terms of accuracy and runtime. Our kernels open the door to large-scale applications of graph kernels in various disciplines such as computational biology and social network analysis.

PDF Web [BibTex]

PDF Web [BibTex]


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What are the Causes of Performance Variation in Brain-Computer Interfacing?

Grosse-Wentrup, M.

International Journal of Bioelectromagnetism, 13(3):115-116, September 2011 (article)

Abstract
While research on brain-computer interfacing (BCI) has seen tremendous progress in recent years, performance still varies substantially between as well as within subjects, with roughly 10 - 20% of subjects being incapable of successfully operating a BCI system. In this short report, I argue that this variation in performance constitutes one of the major obstacles that impedes a successful commercialization of BCI systems. I review the current state of research on the neuro-physiological causes of performance variation in BCI, discuss recent progress and open problems, and delineate potential research programs for addressing this issue.

PDF Web [BibTex]

PDF Web [BibTex]


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Learning robot grasping from 3-D images with Markov Random Fields

Boularias, A., Kroemer, O., Peters, J.

In pages: 1548-1553 , (Editors: Amato, N.M.), IEEE, Piscataway, NJ, USA, IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), September 2011 (inproceedings)

Abstract
Learning to grasp novel objects is an essential skill for robots operating in unstructured environments. We therefore propose a probabilistic approach for learning to grasp. In particular, we learn a function that predicts the success probability of grasps performed on surface points of a given object. Our approach is based on Markov Random Fields (MRF), and motivated by the fact that points that are geometrically close to each other tend to have similar grasp success probabilities. The MRF approach is successfully tested in simulation, and on a real robot using 3-D scans of various types of objects. The empirical results show a significant improvement over methods that do not utilize the smoothness assumption and classify each point separately from the others.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Neurofeedback of Fronto-Parietal Gamma-Oscillations

Grosse-Wentrup, M.

In pages: 172-175, (Editors: Müller-Putz, G.R. , R. Scherer, M. Billinger, A. Kreilinger, V. Kaiser, C. Neuper), Verlag der Technischen Universität Graz, Graz, Austria, 5th International Brain-Computer Interface Conference (BCI), September 2011 (inproceedings)

Abstract
In recent work, we have provided evidence that fronto-parietal γ-range oscillations are a cause of within-subject performance variations in brain-computer interfaces (BCIs) based on motor-imagery. Here, we explore the feasibility of using neurofeedback of fronto-parietal γ-power to induce a mental state that is beneficial for BCI-performance. We provide empirical evidence based on two healthy subjects that intentional attenuation of fronto-parietal γ-power results in an enhanced resting-state sensorimotor-rhythm (SMR). As a large resting-state amplitude of the SMR has been shown to correlate with good BCI-performance, our approach may provide a means to reduce performance variations in BCIs.

PDF Web [BibTex]

PDF Web [BibTex]


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Learning inverse kinematics with structured prediction

Bocsi, B., Nguyen-Tuong, D., Csato, L., Schölkopf, B., Peters, J.

In pages: 698-703 , (Editors: NM Amato), IEEE, Piscataway, NJ, USA, IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), September 2011 (inproceedings)

Abstract
Learning inverse kinematics of robots with redundant degrees of freedom (DoF) is a difficult problem in robot learning. The difficulty lies in the non-uniqueness of the inverse kinematics function. Existing methods tackle non-uniqueness by segmenting the configuration space and building a global solution from local experts. The usage of local experts implies the definition of an oracle, which governs the global consistency of the local models; the definition of this oracle is difficult. We propose an algorithm suitable to learn the inverse kinematics function in a single global model despite its multivalued nature. Inverse kinematics is approximated from examples using structured output learning methods. Unlike most of the existing methods, which estimate inverse kinematics on velocity level, we address the learning of the direct function on position level. This problem is a significantly harder. To support the proposed method, we conducted real world experiments on a tracking control task and tested our algorithms on these models.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Automatic foreground-background refocusing

Loktyushin, A., Harmeling, S.

In pages: 3445-3448, (Editors: Macq, B. , P. Schelkens), IEEE, Piscataway, NJ, USA, 18th IEEE International Conference on Image Processing (ICIP), September 2011 (inproceedings)

Abstract
A challenging problem in image restoration is to recover an image with a blurry foreground. Such images can easily occur with modern cameras, when the auto-focus aims mistakenly at the background (which will appear sharp) instead of the foreground, where usually the object of interest is. In this paper we propose an automatic procedure that (i) estimates the amount of out-of-focus blur, (ii) segments the image into foreground and background incorporating clues from the blurriness, (iii) recovers the sharp foreground, and finally (iv) blurs the background to refocus the scene. On several real photographs with blurry foreground and sharp background, we demonstrate the effectiveness and limitations of our method.

Web DOI [BibTex]

Web DOI [BibTex]


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Gravitational Lensing Accuracy Testing 2010 (GREAT10) Challenge Handbook

Kitching, T., Amara, A., Gill, M., Harmeling, S., Heymans, C., Massey, R., Rowe, B., Schrabback, T., Voigt, L., Balan, S., Bernstein, G., Bethge, M., Bridle, S., Courbin, F., Gentile, M., Heavens, A., Hirsch, M., Hosseini, R., Kiessling, A., Kirk, D., Kuijken, K., Mandelbaum, R., Moghaddam, B., Nurbaeva, G., Paulin-Henriksson, S., Rassat, A., Rhodes, J., Schölkopf, B., Shawe-Taylor, J., Shmakova, M., Taylor, A., Velander, M., van Waerbeke, L., Witherick, D., Wittman, D.

Annals of Applied Statistics, 5(3):2231-2263, September 2011 (article)

Abstract
GRavitational lEnsing Accuracy Testing 2010 (GREAT10) is a public image analysis challenge aimed at the development of algorithms to analyze astronomical images. Specifically, the challenge is to measure varying image distortions in the presence of a variable convolution kernel, pixelization and noise. This is the second in a series of challenges set to the astronomy, computer science and statistics communities, providing a structured environment in which methods can be improved and tested in preparation for planned astronomical surveys. GREAT10 extends upon previous work by introducing variable fields into the challenge. The “Galaxy Challenge” involves the precise measurement of galaxy shape distortions, quantified locally by two parameters called shear, in the presence of a known convolution kernel. Crucially, the convolution kernel and the simulated gravitational lensing shape distortion both now vary as a function of position within the images, as is the case for real data. In addition, we introduce the “Star Challenge” that concerns the reconstruction of a variable convolution kernel, similar to that in a typical astronomical observation. This document details the GREAT10 Challenge for potential participants. Continually updated information is also available from www.greatchallenges.info.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Reinforcement Learning to adjust Robot Movements to New Situations

Kober, J., Oztop, E., Peters, J.

In Robotics: Science and Systems VI, pages: 33-40, (Editors: Matsuoka, Y. , H. F. Durrant-Whyte, J. Neira), MIT Press, Cambridge, MA, USA, 2010 Robotics: Science and Systems Conference (RSS), September 2011 (inproceedings)

Abstract
Many complex robot motor skills can be represented using elementary movements, and there exist efficient techniques for learning parametrized motor plans using demonstrations and self-improvement. However, in many cases, the robot currently needs to learn a new elementary movement even if a parametrized motor plan exists that covers a similar, related situation. Clearly, a method is needed that modulates the elementary movement through the meta-parameters of its representation. In this paper, we show how to learn such mappings from circumstances to meta-parameters using reinforcement learning.We introduce an appropriate reinforcement learning algorithm based on a kernelized version of the reward-weighted regression. We compare this algorithm to several previous methods on a toy example and show that it performs well in comparison to standard algorithms. Subsequently, we show two robot applications of the presented setup; i.e., the generalization of throwing movements in darts, and of hitting movements in table tennis. We show that both tasks can be learned successfully using simulated and real robots.

PDF Web [BibTex]

PDF Web [BibTex]


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Simultaneous EEG Recordings with Dry and Wet Electrodes in Motor-Imagery

Saab, J., Battes, B., Grosse-Wentrup, M.

In pages: 312-315, (Editors: Müller-Putz, G.R. , R. Scherer, M. Billinger, A. Kreilinger, V. Kaiser, C. Neuper), Verlag der Technischen Universität Graz, Graz, Austria, 5th International Brain-Computer Interface Conference (BCI), September 2011 (inproceedings)

Abstract
Robust dry EEG electrodes are arguably the key to making EEG Brain-Computer Interfaces (BCIs) a practical technology. Existing studies on dry EEG electrodes can be characterized by the recording method (stand-alone dry electrodes or simultaneous recording with wet electrodes), the dry electrode technology (e.g. active or passive), the paradigm used for testing (e.g. event-related potentials), and the measure of performance (e.g. comparing dry and wet electrode frequency spectra). In this study, an active-dry electrode prototype is tested, during a motor-imagery task, with EEG-BCI in mind. It is used simultaneously with wet electrodes and assessed using classification accuracy. Our results indicate that the two types of electrodes are comparable in their performance but there are improvements to be made, particularly in finding ways to reduce motion-related artifacts.

PDF Web [BibTex]

PDF Web [BibTex]


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Learning task-space tracking control with kernels

Nguyen-Tuong, D., Peters, J.

In pages: 704-709 , (Editors: Amato, N.M.), IEEE, Piscataway, NJ, USA, IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), September 2011 (inproceedings)

Abstract
Task-space tracking control is essential for robot manipulation. In practice, task-space control of redundant robot systems is known to be susceptive to modeling errors. Here, data driven learning methods may present an interesting alternative approach. However, learning models for task-space tracking control from sampled data is an ill-posed problem. In particular, the same input data point can yield many different output values which can form a non-convex solution space. Because the problem is ill-posed, models cannot be learned from such data using common regression methods. While learning of task-space control mappings is globally ill-posed, it has been shown in recent work that it is locally a well-defined problem. In this paper, we use this insight to formulate a local kernel-based learning approach for online model learning for taskspace tracking control. For evaluations, we show in simulation the ability of the method for online model learning for task-space tracking control of redundant robots.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Automatic particle picking using diffusion filtering and random forest classification

Joubert, P., Nickell, S., Beck, F., Habeck, M., Hirsch, M., Schölkopf, B.

In pages: 6, International Workshop on Microscopic Image Analysis with Application in Biology (MIAAB), September 2011 (inproceedings)

Abstract
An automatic particle picking algorithm for processing electron micrographs of a large molecular complex, the 26S proteasome, is described. The algorithm makes use of a coherence enhancing diffusion filter to denoise the data, and a random forest classifier for removing false positives. It does not make use of a 3D reference model, but uses a training set of manually picked particles instead. False positive and false negative rates of around 25% to 30% are achieved on a testing set. The algorithm was developed for a specific particle, but contains steps that should be useful for developing automatic picking algorithms for other particles.

PDF Web [BibTex]

PDF Web [BibTex]


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Active Versus Semi-supervised Learning Paradigm for the Classification of Remote Sensing Images

Persello, C., Bruzzone, L.

In pages: 1-15, (Editors: Bruzzone, L.), SPIE, Bellingham, WA, USA, Image and Signal Processing for Remote Sensing XVII, September 2011 (inproceedings)

Abstract
This paper presents a comparative study in order to analyze active learning (AL) and semi-supervised learning (SSL) for the classification of remote sensing (RS) images. The two learning paradigms are analyzed both from the theoretical and experimental point of view. The aim of this work is to identify the advantages and disadvantages of AL and SSL methods, and to point out the boundary conditions on the applicability of these methods with respect to both the number of available labeled samples and the reliability of classification results. In our experimental analysis, AL and SSL techniques have been applied to the classification of both synthetic and real RS data, defining different classification problems starting from different initial training sets and considering different distributions of the classes. This analysis allowed us to derive important conclusion about the use of these classification approaches and to obtain insight about which one of the two approaches is more appropriate according to the specific classification problem, the available initial training set and the available budget for the acquisition of new labeled samples.

Web DOI [BibTex]

Web DOI [BibTex]