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2015


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Multilayer Fresnel zone plates for X-ray microscopy

Sanli, U. T., Keskinbora, K., Grévent, C., Szeghalmi, A., Knez, M., Schütz, G.

{Microscopy and Microanalysis}, 21(Suppl 3):1987-1988, Springer-Verlag New York, New York, NY, 2015 (article)

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DOI [BibTex]

2015


DOI [BibTex]


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Interfacial dominated ferromagnetism in nanograined ZnO: a \muSR and DFT study

Tietze, T., Audehm, P., Chen, Y., Schütz, G., Straumal, B. B., Protasova, S. G., Mazilkin, A. A., Straumal, P. B., Prokscha, T., Luetkens, H., Salman, Z., Suter, A., Baretzky, B., Fink, K., Wenzel, W., Danilov, D., Goering, E.

{Scientific Reports}, 5, pages: 8871-8876, Nature Publishing Group, London, UK, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Preparation of a ferromagnetic barrier in YBa2Cu3O7-delta thinner than the coherence length

Soltan, S., Albrecht, J., Goering, E., Schütz, G., Mustafa, L., Keimer, B., Habermeier, H.

{Journal of Applied Physics}, 118(22), AIP Publishing, New York, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Microanalytical methods for in-situ high-resolution analysis of rock varnish at the micrometer to nanometer scale

Macholdt, D. S., Jochum, K. P., Pöhlker, C., Stoll, B., Weis, U., Weber, B., Müller, M., Kapl, M., Buhre, S., Kilcoyne, A. L. D., Weigand, M., Scholz, D., Al-Amri, A. M., Andreae, M. O.

{Chemical Geology}, 411, pages: 57-68, Elsevier, Amsterdam, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Chemical composition, microstructure, and hygroscopic properties of aerosol particles at the Zotino Tall Tower Observatory (ZOTTO), Siberia, during a summer campaign

Mikhailov, E. F., Mironov, G. N., Pöhlker, C., Chi, X., Krüger, M., Shiraiwa, M., Förster, J., Pöschl, U., Vlasenko, S. S., Ryshkevich, T. I., Weigand, M., Kilcoyne, A. L. D., Andreae, M.

{Atmospheric Chemistry and Physics}, 15(15):8847-8869, European Geosciences Union, Katlenburg-Lindau, Germany, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Orbital reflectometry of PrNiO3/PrAlO3 superlattices

Wu, M., Benckiser, E., Audehm, P., Goering, E., Wochner, P., Christiani, G., Logvenov, G., Habermeier, H., Keimer, B.

{Physical Review B}, 91(19), American Physical Society, Woodbury, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Dynamic domain wall chirality rectification by rotating magnetic fields

Bisig, A., Mawass, M., Stärk, M., Moutafis, C., Rhensius, J., Heidler, J., Gliga, S., Weigand, M., Tyliszczak, T., Van Waeyenberge, B., Stoll, H., Schütz, G., Kläui, M.

{Applied Physics Letters}, 106(12), American Institute of Physics, Melville, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Imaging spin dynamics on the nanoscale using X-ray microscopy

Stoll, H., Noske, M., Weigand, M., Richter, K., Krüger, B., Reeve, R. M., Hänze, M., Adolff, C. F., Stein, F., Meier, G., Kläui, M., Schütz, G.

{Frontiers in Physics}, 3, Frontiers Media, Lausanne, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Structure Learning in Bayesian Sensorimotor Integration

Genewein, T, Hez, E, Razzaghpanah, Z, Braun, DA

PLoS Computational Biology, 11(8):1-27, August 2015 (article)

Abstract
Previous studies have shown that sensorimotor processing can often be described by Bayesian learning, in particular the integration of prior and feedback information depending on its degree of reliability. Here we test the hypothesis that the integration process itself can be tuned to the statistical structure of the environment. We exposed human participants to a reaching task in a three-dimensional virtual reality environment where we could displace the visual feedback of their hand position in a two dimensional plane. When introducing statistical structure between the two dimensions of the displacement, we found that over the course of several days participants adapted their feedback integration process in order to exploit this structure for performance improvement. In control experiments we found that this adaptation process critically depended on performance feedback and could not be induced by verbal instructions. Our results suggest that structural learning is an important meta-learning component of Bayesian sensorimotor integration.

ei

DOI [BibTex]

DOI [BibTex]


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Unique high-temperature performance of highly consensed MnBi permanent magnets

Chen, Y., Gregori, G., Leineweber, A., Qu, F., Chen, C., Tietze, T., Kronmüller, H., Schütz, G., Goering, E.

{Scripta Materialia}, 107, pages: 131-135, Pergamon, Tarrytown, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Quantifying Emergent Behavior of Autonomous Robots

Martius, G., Olbrich, E.

Entropy, 17(10):7266, 2015 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Electrical determination of vortex state in submicron magnetic elements

Gangwar, A., Bauer, H. G., Chauleau, J., Noske, M., Weigand, M., Stoll, H., Schütz, G., Back, C. H.

{Physical Review B}, 91(9), American Physical Society, Woodbury, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Mechanisms for the symmetric and antisymmetric switching of a magnetic vortex core: Differences and common aspects

Noske, M., Stoll, H., Fähnle, M., Hertel, R., Schütz, G.

{Physical Review B}, 91(1), American Physical Society, Woodbury, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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High resolution, high efficiency mulitlayer Fresnel zone plates for soft and hard X-rays

Sanli, U., Keskinbora, K., Gregorczyk, K., Leister, J., Teeny, N., Grévent, C., Knez, M., Schütz, G.

{Proceedings of SPIE}, 9592, SPIE, Bellingham, Washington, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Macroscopic drift current in the inverse Faraday effect

Hertel, R., Fähnle, M.

{Physical Review B}, 91(2), American Physical Society, Woodbury, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Single-step 3D nanofabrication of kinoform optics via gray-scale focused ion beam lithography for efficient X-ray focusing

Keskinbora, K., Grévent, C., Hirscher, M., Weigand, M., Schütz, G.

{Advanced Optical Materials}, 3, pages: 792-800, WILEY-VCH Verlag GmbH Co. KGaA, Weinheim, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Band structure engineering of two-dimensional magnonic vortex crystals

Behncke, C., Hänze, M., Adolff, C. F., Weigand, M., Meier, G.

{Physical Review B}, 91(22), American Physical Society, Woodbury, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Towards denoising XMCD movies of fast magnetization dynamics using extended Kalman filter

Kopp, M., Harmeling, S., Schütz, G., Schölkopf, B., Fähnle, M.

{Ultramicroscopy}, 148, pages: 115-122, North-Holland, Amsterdam, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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A Reward-Maximizing Spiking Neuron as a Bounded Rational Decision Maker

Leibfried, F, Braun, DA

Neural Computation, 27(8):1686-1720, July 2015 (article)

Abstract
Rate distortion theory describes how to communicate relevant information most efficiently over a channel with limited capacity. One of the many applications of rate distortion theory is bounded rational decision making, where decision makers are modeled as information channels that transform sensory input into motor output under the constraint that their channel capacity is limited. Such a bounded rational decision maker can be thought to optimize an objective function that trades off the decision maker's utility or cumulative reward against the information processing cost measured by the mutual information between sensory input and motor output. In this study, we interpret a spiking neuron as a bounded rational decision maker that aims to maximize its expected reward under the computational constraint that the mutual information between the neuron's input and output is upper bounded. This abstract computational constraint translates into a penalization of the deviation between the neuron's instantaneous and average firing behavior. We derive a synaptic weight update rule for such a rate distortion optimizing neuron and show in simulations that the neuron efficiently extracts reward-relevant information from the input by trading off its synaptic strengths against the collected reward.

ei

DOI [BibTex]

DOI [BibTex]


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Magnetic moments induce strong phonon renormalization in FeSi

Krannich, S., Sidis, Y., Lamago, D., Heid, R., Mignot, J., von Löhneysen, H., Ivanov, A., Steffens, P., Keller, T., Wang, L., Goering, E., Weber, F.

{Nature Communications}, 6, Nature Publishing Group, London, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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What is epistemic value in free energy models of learning and acting? A bounded rationality perspective

Ortega, PA, Braun, DA

Cognitive Neuroscience, 6(4):215-216, December 2015 (article)

Abstract
Free energy models of learning and acting do not only care about utility or extrinsic value, but also about intrinsic value, that is, the information value stemming from probability distributions that represent beliefs or strategies. While these intrinsic values can be interpreted as epistemic values or exploration bonuses under certain conditions, the framework of bounded rationality offers a complementary interpretation in terms of information-processing costs that we discuss here.

ei

DOI [BibTex]

DOI [BibTex]


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Perpendicular magnetisation from in-plane fields in nano-scaled antidot lattices

Gräfe, J., Haering, F., Tietze, T., Audehm, P., Weigand, M., Wiedwald, U., Ziemann, P., Gawronski, P., Schütz, G., Goering, E. J.

{Nanotechnology}, 26(22), IOP Pub., Bristol, UK, 2015 (article)

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DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Theory of ultrafast demagnetization after femtosecond laser pulses

Fähnle, M., Illg, C., Haag, M., Teeny, N.

{Acta Physica Polonica A}, 127(2):170-175, Państwowe Wydawnictwo Naukowe, Warszawa, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Non-linear radial spinwave modes in thin magnetic disks

Helsen, M., Gangwar, Ajay, De Clercq, J., Vansteenkiste, A., Weigand, M., Back, C. H., Van Waeyenberge, B.

{Applied Physics Letters}, 106(3), American Institute of Physics, Melville, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Hydrogen isotope separation in metal-organic frameworks: Kinetic or chemical affinity quantum-sieving?

Savchenko, I., Mavrandonakis, A., Heine, T., Oh, H., Teufel, J., Hirscher, M.

{Microporous and Mesoporous Materials}, 216, pages: 133-137, Elsevier, Amsterdam, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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High-resolution dichroic imaging of magnetic flux distributions in superconductors with scanning x-ray microscopy

Ruoß, S., Stahl, C., Weigand, M., Schütz, G., Albrecht, J.

{Applied Physics Letters}, 106, American Institute of Physics, Melville, NY, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Preparation and characterisation of epitaxial Pt/Cu/FeMn/Co thin films on (100)-oriented MgO single crystals

Schmidt, M., Gräfe, J., Audehm, P., Phillipp, F., Schütz, G., Goering, E.

{Physica Status Solidi A}, 212(10):2114-2123, Wiley-VCH, Weinheim, 2015 (article)

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DOI [BibTex]

DOI [BibTex]


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Probing the magnetic moments of [MnIII6CrIII]3+ single-molecule magnets - A cross comparison of XMCD and spin-resolved electron spectroscopy

Helmstedt, A., Dohmeier, N., Müller, N., Gryzia, A., Brechling, A., Heinzmann, U., Hoeke, V., Krickemeyer, E., Glaser, T., Leicht, P., Fonin, M., Tietze, T., Joly, L., Kuepper, K.

{Journal of Electron Spectroscopy and Related Phenomena}, 198, pages: 12-19, Elsevier B.V., Amsterdam, 2015 (article)

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DOI [BibTex]

DOI [BibTex]

2011


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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.

ei

PDF Web DOI [BibTex]

2011


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.

ei

Web DOI [BibTex]

Web DOI [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.

ei

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.

ei

Web DOI [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.

ei

PDF [BibTex]

PDF [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/).

ei

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.

ei

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.

ei

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.

ei

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.

ei

Web DOI [BibTex]

Web 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.

ei

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.

ei

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.

ei

PDF Web [BibTex]

PDF Web [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.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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MRI-Based Attenuation Correction for Whole-Body PET/MRI: Quantitative Evaluation of Segmentation- and Atlas-Based Methods

Hofmann, M., Bezrukov, I., Mantlik, F., Aschoff, P., Steinke, F., Beyer, T., Pichler, B., Schölkopf, B.

Journal of Nuclear Medicine, 52(9):1392-1399, September 2011 (article)

Abstract
PET/MRI is an emerging dual-modality imaging technology that requires new approaches to PET attenuation correction (AC). We assessed 2 algorithms for whole-body MRI-based AC (MRAC): a basic MR image segmentation algorithm and a method based on atlas registration and pattern recognition (AT&PR). METHODS: Eleven patients each underwent a whole-body PET/CT study and a separate multibed whole-body MRI study. The MR image segmentation algorithm uses a combination of image thresholds, Dixon fat-water segmentation, and component analysis to detect the lungs. MR images are segmented into 5 tissue classes (not including bone), and each class is assigned a default linear attenuation value. The AT&PR algorithm uses a database of previously aligned pairs of MRI/CT image volumes. For each patient, these pairs are registered to the patient MRI volume, and machine-learning techniques are used to predict attenuation values on a continuous scale. MRAC methods are compared via the quantitative analysis of AC PET images using volumes of interest in normal organs and on lesions. We assume the PET/CT values after CT-based AC to be the reference standard. RESULTS: In regions of normal physiologic uptake, the average error of the mean standardized uptake value was 14.1% ± 10.2% and 7.7% ± 8.4% for the segmentation and the AT&PR methods, respectively. Lesion-based errors were 7.5% ± 7.9% for the segmentation method and 5.7% ± 4.7% for the AT&PR method. CONCLUSION: The MRAC method using AT&PR provided better overall PET quantification accuracy than the basic MR image segmentation approach. This better quantification was due to the significantly reduced volume of errors made regarding volumes of interest within or near bones and the slightly reduced volume of errors made regarding areas outside the lungs.

ei

Web DOI [BibTex]


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Semi-supervised kernel canonical correlation analysis with application to human fMRI

Blaschko, M., Shelton, J., Bartels, A., Lampert, C., Gretton, A.

Pattern Recognition Letters, 32(11):1572-1583 , August 2011 (article)

Abstract
Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.

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PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Multi-subject learning for common spatial patterns in motor-imagery BCI

Devlaminck, D., Wyns, B., Grosse-Wentrup, M., Otte, G., Santens, P.

Computational Intelligence and Neuroscience, 2011(217987):1-9, August 2011 (article)

Abstract
Motor-imagery-based brain-computer interfaces (BCIs) commonly use the common spatial pattern filter (CSP) as preprocessing step before feature extraction and classification. The CSP method is a supervised algorithm and therefore needs subject-specific training data for calibration, which is very time consuming to collect. In order to reduce the amount of calibration data that is needed for a new subject, one can apply multitask (from now on called multisubject) machine learning techniques to the preprocessing phase. Here, the goal of multisubject learning is to learn a spatial filter for a new subject based on its own data and that of other subjects. This paper outlines the details of the multitask CSP algorithm and shows results on two data sets. In certain subjects a clear improvement can be seen, especially when the number of training trials is relatively low.

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PDF DOI [BibTex]

PDF DOI [BibTex]


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ccSVM: correcting Support Vector Machines for confounding factors in biological data classification

Li, L., Rakitsch, B., Borgwardt, K.

Bioinformatics, 27(13: ISMB/ECCB 2011):i342-i348, July 2011 (article)

Abstract
Motivation: Classifying biological data into different groups is a central task of bioinformatics: for instance, to predict the function of a gene or protein, the disease state of a patient or the phenotype of an individual based on its genotype. Support Vector Machines are a wide spread approach for classifying biological data, due to their high accuracy, their ability to deal with structured data such as strings, and the ease to integrate various types of data. However, it is unclear how to correct for confounding factors such as population structure, age or gender or experimental conditions in Support Vector Machine classification. Results: In this article, we present a Support Vector Machine classifier that can correct the prediction for observed confounding factors. This is achieved by minimizing the statistical dependence between the classifier and the confounding factors. We prove that this formulation can be transformed into a standard Support Vector Machine with rescaled input data. In our experiments, our confounder correcting SVM (ccSVM) improves tumor diagnosis based on samples from different labs, tuberculosis diagnosis in patients of varying age, ethnicity and gender, and phenotype prediction in the presence of population structure and outperforms state-of-the-art methods in terms of prediction accuracy.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Policy Search for Motor Primitives in Robotics

Kober, J., Peters, J.

Machine Learning, 84(1-2):171-203, July 2011 (article)

Abstract
Many motor skills in humanoid robotics can be learned using parametrized motor primitives. While successful applications to date have been achieved with imitation learning, most of the interesting motor learning problems are high-dimensional reinforcement learning problems. These problems are often beyond the reach of current reinforcement learning methods. In this paper, we study parametrized policy search methods and apply these to benchmark problems of motor primitive learning in robotics. We show that many well-known parametrized policy search methods can be derived from a general, common framework. This framework yields both policy gradient methods and expectation-maximization (EM) inspired algorithms. We introduce a novel EM-inspired algorithm for policy learning that is particularly well-suited for dynamical system motor primitives. We compare this algorithm, both in simulation and on a real robot, to several well-known parametrized policy search methods such as episodic REINFORCE, ‘Vanilla’ Policy Gradients with optimal baselines, episodic Natural Actor Critic, and episodic Reward-Weighted Regression. We show that the proposed method out-performs them on an empirical benchmark of learning dynamical system motor primitives both in simulation and on a real robot. We apply it in the context of motor learning and show that it can learn a complex Ball-in-a-Cup task on a real Barrett WAM™ robot arm.

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PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Epistasis detection on quantitative phenotypes by exhaustive enumeration using GPUs

Kam-Thong, T., Pütz, B., Karbalai, N., Müller-Myhsok, B., Borgwardt, K.

Bioinformatics, 27(13: ISMB/ECCB 2011):i214-i221, July 2011 (article)

Abstract
Motivation: In recent years, numerous genome-wide association studies have been conducted to identify genetic makeup that explains phenotypic differences observed in human population. Analytical tests on single loci are readily available and embedded in common genome analysis software toolset. The search for significant epistasis (gene–gene interactions) still poses as a computational challenge for modern day computing systems, due to the large number of hypotheses that have to be tested. Results: In this article, we present an approach to epistasis detection by exhaustive testing of all possible SNP pairs. The search strategy based on the Hilbert–Schmidt Independence Criterion can help delineate various forms of statistical dependence between the genetic markers and the phenotype. The actual implementation of this search is done on the highly parallelized architecture available on graphics processing units rendering the completion of the full search feasible within a day.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Empirical Inference

Schölkopf, B.

International Journal of Materials Research, 2011(7):809-814, July 2011 (article)

Abstract
Empirical Inference is the process of drawing conclusions from observational data. For instance, the data can be measurements from an experiment, which are used by a researcher to infer a scientific law. Another kind of empirical inference is performed by living beings, continuously recording data from their environment and carrying out appropriate actions. Do these problems have anything in common, and are there underlying principles governing the extraction of regularities from data? What characterizes hard inference problems, and how can we solve them? Such questions are studied by a community of scientists from various fields, engaged in machine learning research. This short paper, which is based on the author’s lecture to the scientific council of the Max Planck Society in February 2010, will attempt to describe some of the main ideas and problems of machine learning. It will provide illustrative examples of real world machine learning applications, including the use of machine learning towards the design of intelligent systems.

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Web DOI [BibTex]

Web DOI [BibTex]


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Online Multi-frame Blind Deconvolution with Super-resolution and Saturation Correction

Hirsch, M., Harmeling, S., Sra, S., Schölkopf, B.

Astronomy & Astrophysics, 531(A9):11, July 2011 (article)

Abstract
Astronomical images taken by ground-based telescopes suffer degradation due to atmospheric turbulence. This degradation can be tackled by costly hardware-based approaches such as adaptive optics, or by sophisticated software-based methods such as lucky imaging, speckle imaging, or multi-frame deconvolution. Software-based methods process a sequence of images to reconstruct a deblurred high-quality image. However, existing approaches are limited in one or several aspects: (i) they process all images in batch mode, which for thousands of images is prohibitive; (ii) they do not reconstruct a super-resolved image, even though an image sequence often contains enough information; (iii) they are unable to deal with saturated pixels; and (iv) they are usually non-blind, i.e., they assume the blur kernels to be known. In this paper we present a new method for multi-frame deconvolution called online blind deconvolution (OBD) that overcomes all these limitations simultaneously. Encouraging results on simulated and real astronomical images demonstrate that OBD yields deblurred images of comparable and often better quality than existing approaches.

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PDF DOI [BibTex]