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Information-Theoretic Implications of Classical and Quantum Causal Structures

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D.

18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression

Küffner, R., Zach, N., Norel, R., Hawe, J., Schoenfeld, D., Wang, L., Li, G., Fang, L., Mackey, L., Hardiman, O., Cudkowicz, M., Sherman, A., Ertaylan, G., Grosse-Wentrup, M., Hothorn, T., van Ligtenberg, J., Macke, J., Meyer, T., Schölkopf, B., Tran, L., Vaughan, R., Stolovitzky, G., Leitner, M.

Nature Biotechnology, 33, pages: 51-57, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Probabilistic Interpretation of Linear Solvers

Hennig, P.

SIAM Journal on Optimization, 25(1):234-260, 2015 (article)

Web PDF link (url) DOI [BibTex]

Web PDF link (url) DOI [BibTex]


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Developing biorobotics for veterinary research into cat movements

Mariti, C., Muscolo, G., Peters, J., Puig, D., Recchiuto, C., Sighieri, C., Solanas, A., von Stryk, O.

Journal of Veterinary Behavior: Clinical Applications and Research, 10(3):248-254, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Spatial statistics and attentional dynamics in scene viewing

Engbert, R., Trukenbrod, H., Barthelmé, S., Wichmann, F.

Journal of Vision, 15(1):1-17, 2015 (article)

Web PDF link (url) DOI [BibTex]

Web PDF link (url) DOI [BibTex]


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The Randomized Causation Coefficient

Lopez-Paz, D., Muandet, K., Recht, B.

Journal of Machine Learning, 16, pages: 2901-2907, 2015 (article)

link (url) [BibTex]

link (url) [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, 2015 (article)

Abstract
The Kalman filter is a well-established approach to get information on the time-dependent state of a system from noisy observations. It was developed in the context of the Apollo project to see the deviation of the true trajectory of a rocket from the desired trajectory. Afterwards it was applied to many different systems with small numbers of components of the respective state vector (typically about 10). In all cases the equation of motion for the state vector was known exactly. The fast dissipative magnetization dynamics is often investigated by x-ray magnetic circular dichroism movies (XMCD movies), which are often very noisy. In this situation the number of components of the state vector is extremely large (about 105), and the equation of motion for the dissipative magnetization dynamics (especially the values of the material parameters of this equation) is not well known. In the present paper it is shown by theoretical considerations that – nevertheless – there is no principle problem for the use of the Kalman filter to denoise XMCD movies of fast dissipative magnetization dynamics.

Web DOI [BibTex]

Web DOI [BibTex]


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Artificial intelligence: Learning to see and act

Schölkopf, B.

Nature, News & Views, 518(7540):486-487, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Context affects lightness at the level of surfaces

Maertens, M., Wichmann, F., Shapley, R.

Journal of Vision, 15(1):1-15, 2015 (article)

Web PDF link (url) DOI [BibTex]

Web PDF link (url) DOI [BibTex]


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Genome-wide analysis of local chromatin packing in Arabidopsis thaliana

Wang, C., Liu, C., Roqueiro, D., Grimm, D., Schwab, R., Becker, C., Lanz, C., Weigel, D.

Genome Research, 25(2):246-256, 2015 (article)

PDF DOI [BibTex]

PDF DOI [BibTex]


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Assessment of brain tissue damage in the Sub-Acute Stroke Region by Multiparametric Imaging using [89-Zr]-Desferal-EPO-PET/MRI

Castaneda, S. G., Katiyar, P., Russo, F., Disselhorst, J. A., Calaminus, C., Poli, S., Maurer, A., Ziemann, U., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

[BibTex]

[BibTex]


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Segmentation-based attenuation correction in positron emission tomography/magnetic resonance: erroneous tissue identification and its impact on positron emission tomography interpretation

Brendle, C., Schmidt, H., Oergel, A., Bezrukov, I., Mueller, M., Schraml, C., Pfannenberg, C., la Fougère, C., Nikolaou, K., Schwenzer, N.

Investigative Radiology, 50(5):339-346, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Active Reward Learning with a Novel Acquisition Function

Daniel, C., Kroemer, O., Viering, M., Metz, J., Peters, J.

Autonomous Robots, 39(3):389-405, 2015 (article)

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Early time point in vivo PET/MR is a promising biomarker for determining efficacy of a novel Db(\alphaEGFR)-scTRAIL fusion protein therapy in a colon cancer model

Divine, M. R., Harant, M., Katiyar, P., Disselhorst, J. A., Bukala, D., Aidone, S., Siegemund, M., Pfizenmaier, K., Kontermann, R., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

[BibTex]

[BibTex]


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A systematic search for transiting planets in the K2 data

Foreman-Mackey, D., Montet, B., Hogg, D., Morton, T., Wang, D., Schölkopf, B.

The Astrophysical Journal, 806(2), 2015 (article)

Abstract
Photometry of stars from the K2 extension of NASA’s Kepler mission is afflicted by systematic effects caused by small (few-pixel) drifts in the telescope pointing and other spacecraft issues. We present a method for searching K2 light curves for evidence of exoplanets by simultaneously fitting for these systematics and the transit signals of interest. This method is more computationally expensive than standard search algorithms but we demonstrate that it can be efficiently implemented and used to discover transit signals. We apply this method to the full Campaign 1 data set and report a list of 36 planet candidates transiting 31 stars, along with an analysis of the pipeline performance and detection efficiency based on artificial signal injections and recoveries. For all planet candidates, we present posterior distributions on the properties of each system based strictly on the transit observables.

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Learning Movement Primitive Attractor Goals and Sequential Skills from Kinesthetic Demonstrations

Manschitz, S., Kober, J., Gienger, M., Peters, J.

Robotics and Autonomous Systems, 74, Part A, pages: 97-107, 2015 (article)

link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Bayesian Optimization for Learning Gaits under Uncertainty

Calandra, R., Seyfarth, A., Peters, J., Deisenroth, M.

Annals of Mathematics and Artificial Intelligence, pages: 1-19, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Assessment of murine brain tissue shrinkage caused by different histological fixatives using magnetic resonance and computed tomography imaging

Wehrl, H. F., Bezrukov, I., Wiehr, S., Lehnhoff, M., Fuchs, K., Mannheim, J. G., Quintanilla-Martinez, L., Kneilling, M., Pichler, B. J., Sauter, A. W.

Histology and Histopathology, 30(5):601-613, 2015 (article)

[BibTex]

[BibTex]


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Improved Bayesian Information Criterion for Mixture Model Selection

Mehrjou, A., Hosseini, R., Araabi, B.

Pattern Recognition Letters, 69, pages: 22-27, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Correlation matrix nearness and completion under observation uncertainty

Alaíz, C. M., Dinuzzo, F., Sra, S.

IMA Journal of Numerical Analysis, 35(1):325-340, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Quantitative evaluation of segmentation- and atlas- based attenuation correction for PET/MR on pediatric patients

Bezrukov, I., Schmidt, H., Gatidis, S., Mantlik, F., Schäfer, J. F., Schwenzer, N., Pichler, B. J.

Journal of Nuclear Medicine, 56(7):1067-1074, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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Probabilistic numerics and uncertainty in computations

Hennig, P., Osborne, M. A., Girolami, M.

Proceedings of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 471(2179), 2015 (article)

Abstract
We deliver a call to arms for probabilistic numerical methods: algorithms for numerical tasks, including linear algebra, integration, optimization and solving differential equations, that return uncertainties in their calculations. Such uncertainties, arising from the loss of precision induced by numerical calculation with limited time or hardware, are important for much contemporary science and industry. Within applications such as climate science and astrophysics, the need to make decisions on the basis of computations with large and complex data have led to a renewed focus on the management of numerical uncertainty. We describe how several seminal classic numerical methods can be interpreted naturally as probabilistic inference. We then show that the probabilistic view suggests new algorithms that can flexibly be adapted to suit application specifics, while delivering improved empirical performance. We provide concrete illustrations of the benefits of probabilistic numeric algorithms on real scientific problems from astrometry and astronomical imaging, while highlighting open problems with these new algorithms. Finally, we describe how probabilistic numerical methods provide a coherent framework for identifying the uncertainty in calculations performed with a combination of numerical algorithms (e.g. both numerical optimizers and differential equation solvers), potentially allowing the diagnosis (and control) of error sources in computations.

PDF DOI [BibTex]

PDF DOI [BibTex]


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Mass and galaxy distributions of four massive galaxy clusters from Dark Energy Survey Science Verification data

Melchior, P., Suchyta, E., Huff, E., Hirsch, M., Kacprzak, T., Rykoff, E., Gruen, D., Armstrong, R., Bacon, D., Bechtol, K., others,

Monthly Notices of the Royal Astronomical Society, 449(3):2219-2238, Oxford University Press, 2015 (article)

DOI [BibTex]

DOI [BibTex]


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The search for single exoplanet transits in the Kepler light curves

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B.

IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

link (url) [BibTex]


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Entropic Movement Complexity Reflects Subjective Creativity Rankings of Visualized Hand Motion Trajectories

Peng, Z, Braun, DA

Frontiers in Psychology, 6(1879):1-13, December 2015 (article)

Abstract
In a previous study we have shown that human motion trajectories can be characterized by translating continuous trajectories into symbol sequences with well-defined complexity measures. Here we test the hypothesis that the motion complexity individuals generate in their movements might be correlated to the degree of creativity assigned by a human observer to the visualized motion trajectories. We asked participants to generate 55 novel hand movement patterns in virtual reality, where each pattern had to be repeated 10 times in a row to ensure reproducibility. This allowed us to estimate a probability distribution over trajectories for each pattern. We assessed motion complexity not only by the previously proposed complexity measures on symbolic sequences, but we also propose two novel complexity measures that can be directly applied to the distributions over trajectories based on the frameworks of Gaussian Processes and Probabilistic Movement Primitives. In contrast to previous studies, these new methods allow computing complexities of individual motion patterns from very few sample trajectories. We compared the different complexity measures to how a group of independent jurors rank ordered the recorded motion trajectories according to their personal creativity judgment. We found three entropic complexity measures that correlate significantly with human creativity judgment and discuss differences between the measures. We also test whether these complexity measures correlate with individual creativity in divergent thinking tasks, but do not find any consistent correlation. Our results suggest that entropic complexity measures of hand motion may reveal domain-specific individual differences in kinesthetic creativity.

DOI [BibTex]

DOI [BibTex]


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Bounded rationality, abstraction and hierarchical decision-making: an information-theoretic optimality principle

Genewein, T, Leibfried, F, Grau-Moya, J, Braun, DA

Frontiers in Robotics and AI, 2(27):1-24, October 2015 (article)

Abstract
Abstraction and hierarchical information-processing are hallmarks of human and animal intelligence underlying the unrivaled flexibility of behavior in biological systems. Achieving such a flexibility in artificial systems is challenging, even with more and more computational power. Here we investigate the hypothesis that abstraction and hierarchical information-processing might in fact be the consequence of limitations in information-processing power. In particular, we study an information-theoretic framework of bounded rational decision-making that trades off utility maximization against information-processing costs. We apply the basic principle of this framework to perception-action systems with multiple information-processing nodes and derive bounded optimal solutions. We show how the formation of abstractions and decision-making hierarchies depends on information-processing costs. We illustrate the theoretical ideas with example simulations and conclude by formalizing a mathematically unifying optimization principle that could potentially be extended to more complex systems.

DOI [BibTex]

DOI [BibTex]


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Signaling equilibria in sensorimotor interactions

Leibfried, F, Grau-Moya, J, Braun, DA

Cognition, 141, pages: 73-86, August 2015 (article)

Abstract
Although complex forms of communication like human language are often assumed to have evolved out of more simple forms of sensorimotor signaling, less attention has been devoted to investigate the latter. Here, we study communicative sensorimotor behavior of humans in a two-person joint motor task where each player controls one dimension of a planar motion. We designed this joint task as a game where one player (the sender) possesses private information about a hidden target the other player (the receiver) wants to know about, and where the sender's actions are costly signals that influence the receiver's control strategy. We developed a game-theoretic model within the framework of signaling games to investigate whether subjects' behavior could be adequately described by the corresponding equilibrium solutions. The model predicts both separating and pooling equilibria, in which signaling does and does not occur respectively. We observed both kinds of equilibria in subjects and found that, in line with model predictions, the propensity of signaling decreased with increasing signaling costs and decreasing uncertainty on the part of the receiver. Our study demonstrates that signaling games, which have previously been applied to economic decision-making and animal communication, provide a framework for human signaling behavior arising during sensorimotor interactions in continuous and dynamic environments.

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.

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.

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.

DOI [BibTex]

DOI [BibTex]

2011


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Combined whole-body PET/MR imaging: MR contrast agents do not affect the quantitative accuracy of PET following attenuation correction

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(SST15-05 ), 97th Scientific Assemble and Annual Meeting of the Radiological Society of North America (RSNA), December 2011 (talk)

Abstract
PURPOSE Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. We assess additional attenuation of the PET emission signals in the presence of oral and intraveneous (iv) MRCA made up of iron oxide and Gd-chelates, respectively. METHOD AND MATERIALS Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and integrated whole-body PET/MR (Biograph mMR, Siemens) using oral (Lumirem) and intraveneous (Gadovist) MRCA. Reference PET attenuation values were determined on a small-animal PET (Inveon, Siemens) using standard PET transmission imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% conc.), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs. The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1. PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction. RESULTS Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347. Lumirem had little effect on PET attenuation with (C3) being 13% and 10% higher than (C2) on PET/CT and PET/MR, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower than (Sy2) on PET/CT and 1.2% higher than (Sy2) on PET/MR. CONCLUSION MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

Web [BibTex]

2011

Web [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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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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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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Cooperative Cuts: a new use of submodularity in image segmentation

Jegelka, S.

Second I.S.T. Austria Symposium on Computer Vision and Machine Learning, October 2011 (talk)

Web [BibTex]

Web [BibTex]


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Effect of MR Contrast Agents on Quantitative Accuracy of PET in Combined Whole-Body PET/MR Imaging

Lois, C., Bezrukov, I., Schmidt, H., Schwenzer, N., Werner, M., Pichler, B., Kupferschläger, J., Beyer, T.

2011(MIC3-3), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
Combined whole-body PET/MR systems are being tested in clinical practice today. Integrated imaging protocols entail the use of MR contrast agents (MRCA) that could bias PET attenuation correction. In this work, we assess the effect of MRCA in PET/MR imaging. We analyze the effect of oral and intravenous MRCA on PET activity after attenuation correction. We conclude that in clinical scenarios, MRCA are not expected to lead to significant attenuation of PET signals, and that attenuation maps are not biased after the ingestion of adequate oral contrasts.

Web [BibTex]

Web [BibTex]


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First Results on Patients and Phantoms of a Fully Integrated Clinical Whole-Body PET/MRI

Schmidt, H., Schwenzer, N., Bezrukov, I., Kolb, A., Mantlik, F., Kupferschläger, J., Lois, C., Sauter, A., Brendle, C., Pfannenberg, C., Pichler, B.

2011(J2-8), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (talk)

Abstract
First clinical fully integrated whole-body PET/MR scanners are just entering the field. Here, we present studies toward quantification accuracy and variation within the PET field of view of small lesions from our BrainPET/MRI, a dedicated clinical brain scanner which was installed three years ago in Tbingen. Also, we present first results for patient and phantom scans of a fully integral whole-body PET/MRI, which was installed two months ago at our department. The quantification accuracy and homogeneity of the BrainPET-Insert (Siemens Medical Solutions, Germany) installed inside the magnet bore of a clinical 3T MRI scanner (Magnetom TIM Trio, Siemens Medical Solutions, Germany) was evaluated by using eight hollow spheres with inner diameters from 3.95 to 7.86 mm placed at different positions inside a homogeneous cylinder phantom with an 9:1 and 6:1 sphere to background ratio. The quantification accuracy for small lesions at different positions in the PET FoV shows a standard deviation of up to 11% and is acceptable for quantitative brain studies where the homogeneity of quantification on the entire FoV is essental. Image quality and resolution of the new Siemens whole-body PET/MR system (Biograph mMR, Siemens Medical Solutions, Germany) was evaluated according to the NEMA NU2 2007 protocol using a body phantom containing six spheres with inner diameter from 10 to 37 mm at sphere to background ratios of 8:1 and 4:1 and the F-18 point sources located at different positions inside the PET FoV, respectively. The evaluation of the whole-body PET/MR system reveals a good PET image quality and resolution comparable to state-of-the-art clinical PET/CT scanners. First images of patient studies carried out at the whole-body PET/MR are presented highlighting the potency of combined PET/MR imaging.

Web [BibTex]

Web [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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Effect of MR contrast agents on quantitative accuracy of PET in combined whole-body PET/MR imaging

Lois, C., Kupferschläger, J., Bezrukov, I., Schmidt, H., Werner, M., Mannheim, J., Pichler, B., Schwenzer, N., Beyer, T.

(OP314), Annual Congress of the European Association of Nuclear Medicine (EANM), October 2011 (talk)

Abstract
PURPOSE:Combined PET/MR imaging entails the use of MR contrast agents (MRCA) as part of integrated protocols. MRCA are made up of iron oxide and Gd-chelates for oral and intravenous (iv) application, respectively. We assess additional attenuation of the PET emission signals in the presence of oral and iv MRCA.MATERIALS AND METHODS:Phantom scans were performed on a clinical PET/CT (Biograph HiRez16, Siemens) and an integrated whole-body PET/MR (Biograph mMR, Siemens). Two common MRCA were evaluated: Lumirem (oral) and Gadovist (iv).Reference PET attenuation values were determined on a dedicated small-animal PET (Inveon, Siemens) using equivalent standard PET transmission source imaging (TX). Seven syringes of 5mL were filled with (a) Water, (b) Lumirem_100 (100% concentration), (c) Gadovist_100 (100%), (d) Gadovist_18 (18%), (e) Gadovist_02 (0.2%), (f) Imeron-400 CT iv-contrast (100%) and (g) Imeron-400 (2.4%). The same set of syringes was scanned on CT (Sensation16, Siemens) at 120kVp and 160mAs.The effect of MRCA on the attenuation of PET emission data was evaluated using a 20cm cylinder filled uniformly with [18F]-FDG (FDG) in water (BGD). Three 4.5cm diameter cylinders were inserted into the phantom: (C1) Teflon, (C2) Water+FDG (2:1) and (C3) Lumirem_100+FDG (2:1). Two 50mL syringes filled with Gadovist_02+FDG (Sy1) and water+FDG (Sy2) were attached to the sides of (C1) to mimick the effects of iv-contrast in vessels near bone. Syringe-to-background activity ratio was 4-to-1.PET emission data were acquired for 10min each using the PET/CT and the PET/MR. Images were reconstructed using CT- and MR-based attenuation correction (AC). Since Teflon is not correctly identified on MR, PET(/MR) data were reconstructed using MR-AC and CT-AC.RESULTS:Mean linear PET attenuation (cm-1) on TX was (a) 0.098, (b) 0.098, (c) 0.300, (d) 0.134, (e) 0.095, (f) 0.397 and (g) 0.105. Corresponding CT attenuation (HU) was: (a) 5, (b) 14, (c) 3070, (d) 1040, (e) 13, (f) 3070 and (g) 347.Lumirem had little effect on PET attenuation with (C3) being 13%, 10% and 11% higher than (C2) on PET/CT, PET/MR with MR-AC, and PET/MR with CT-AC, respectively. Gadovist_02 had even smaller effects with (Sy1) being 2.5% lower, 1.2% higher, and 3.5% lower than (Sy2) on PET/CT, PET/MR with MR-AC and PET/MR with CT-AC, respectively.CONCLUSION:MRCA in high and clinically relevant concentrations have attenuation values similar to that of CT contrast and water, respectively. In clinical PET/MR scenarios MRCA are not expected to lead to significant attenuation of the PET emission signals.

Web [BibTex]

Web [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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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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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]