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2012


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CSB: A Python framework for computational structural biology

Kalev, I., Mechelke, M., Kopec, K., Holder, T., Carstens, S., Habeck, M.

Bioinformatics, 28(22):2996-2997, 2012 (article)

Abstract
Summary: Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. Availability: Stable release packages are available for download from the Python Package Index (PyPI), as well as from the project’s web site http://csb.codeplex.com.

ei

Web DOI [BibTex]

2012


Web DOI [BibTex]


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Design of a Haptic Interface for a Gastrointestinal Endoscopy Simulation

Yu, S., Woo, H. S., Son, H. I., Ahn, W., Jung, H., Lee, D. Y., Yi, S. Y.

Advanced Robotics, 26(18):2115-2143, 2012 (article)

ei

DOI [BibTex]

DOI [BibTex]


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Significant global reduction of carbon uptake by water-cycle driven extreme vegetation anomalies

Zscheischler, J., Mahecha, M., von Buttlar, J., Harmeling, S., Jung, M., Randerson, J., Reichstein, M.

Nature Geoscience, 2012 (article) In revision

ei

[BibTex]

[BibTex]


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Emotionally Assisted Human-Robot Interaction Using a Wearable Device for Reading Facial Expressions

Gruebler, A., Berenz, V., Suzuki, K.

Advanced Robotics, 26(10):1143-1159, 2012 (article)

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link (url) DOI [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)

ei

DOI [BibTex]

DOI [BibTex]


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From Dynamic Movement Primitives to Associative Skill Memories

Pastor, P., Kalakrishnan, M., Meier, F., Stulp, F., Buchli, J., Theodorou, E., Schaal, S.

Robotics and Autonomous Systems, 2012 (article)

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Project Page [BibTex]

Project Page [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)

ei

DOI [BibTex]

DOI [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)

ei

[BibTex]

[BibTex]


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Autonomous battery management for mobile robots based on risk and gain assessment

Berenz, V., Tanaka, F., Suzuki, K.

Artif. Intell. Rev., 37(3):217-237, 2012 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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A metric for comparing the anthropomorphic motion capability of artificial hands

Feix, T., Romero, J., Ek, C. H., Schmiedmayer, H., Kragic, D.

IEEE RAS Transactions on Robotics, TRO, pages: 974-980, 2012 (article)

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Publisher site Human Grasping Database Project [BibTex]

Publisher site Human Grasping Database Project [BibTex]


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The Ankyrin 3 (ANK3) Bipolar Disorder Gene Regulates Psychiatric-related Behaviors that are Modulated by Lithium and Stress

Leussis, M., Berry-Scott, E., Saito, M., Jhuang, H., Haan, G., Alkan, O., Luce, C., Madison, J., Sklar, P., Serre, T., Root, D., Petryshen, T.

Biological Psychiatry , 2012 (article)

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Prepublication Article Abstract [BibTex]

Prepublication Article Abstract [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.

ei

DOI [BibTex]

DOI [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.

ei

DOI [BibTex]

DOI [BibTex]


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Model-free reinforcement learning of impedance control in stochastic environments

Stulp, Freek, Buchli, Jonas, Ellmer, Alice, Mistry, Michael, Theodorou, Evangelos A., Schaal, S.

Autonomous Mental Development, IEEE Transactions on, 4(4):330-341, 2012 (article)

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[BibTex]

[BibTex]


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Natural Metrics and Least-Committed Priors for Articulated Tracking

Soren Hauberg, Stefan Sommer, Kim S. Pedersen

Image and Vision Computing, 30(6-7):453-461, Elsevier, 2012 (article)

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Publishers site Code PDF [BibTex]

Publishers site Code PDF [BibTex]


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Reinforcement Learning with Sequences of Motion Primitives for Robust Manipulation

Stulp, F., Theodorou, E., Schaal, S.

IEEE Transactions on Robotics, 2012 (article)

am

[BibTex]

[BibTex]

1999


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Lernen mit Kernen: Support-Vektor-Methoden zur Analyse hochdimensionaler Daten

Schölkopf, B., Müller, K., Smola, A.

Informatik - Forschung und Entwicklung, 14(3):154-163, September 1999 (article)

Abstract
We describe recent developments and results of statistical learning theory. In the framework of learning from examples, two factors control generalization ability: explaining the training data by a learning machine of a suitable complexity. We describe kernel algorithms in feature spaces as elegant and efficient methods of realizing such machines. Examples thereof are Support Vector Machines (SVM) and Kernel PCA (Principal Component Analysis). More important than any individual example of a kernel algorithm, however, is the insight that any algorithm that can be cast in terms of dot products can be generalized to a nonlinear setting using kernels. Finally, we illustrate the significance of kernel algorithms by briefly describing industrial and academic applications, including ones where we obtained benchmark record results.

ei

PDF PDF DOI [BibTex]

1999


PDF PDF DOI [BibTex]


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Input space versus feature space in kernel-based methods

Schölkopf, B., Mika, S., Burges, C., Knirsch, P., Müller, K., Rätsch, G., Smola, A.

IEEE Transactions On Neural Networks, 10(5):1000-1017, September 1999 (article)

Abstract
This paper collects some ideas targeted at advancing our understanding of the feature spaces associated with support vector (SV) kernel functions. We first discuss the geometry of feature space. In particular, we review what is known about the shape of the image of input space under the feature space map, and how this influences the capacity of SV methods. Following this, we describe how the metric governing the intrinsic geometry of the mapped surface can be computed in terms of the kernel, using the example of the class of inhomogeneous polynomial kernels, which are often used in SV pattern recognition. We then discuss the connection between feature space and input space by dealing with the question of how one can, given some vector in feature space, find a preimage (exact or approximate) in input space. We describe algorithms to tackle this issue, and show their utility in two applications of kernel methods. First, we use it to reduce the computational complexity of SV decision functions; second, we combine it with the kernel PCA algorithm, thereby constructing a nonlinear statistical denoising technique which is shown to perform well on real-world data.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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p73 and p63 are homotetramers capable of weak heterotypic interactions with each other but not with p53.

Davison, T., Vagner, C., Kaghad, M., Ayed, A., Caput, D., CH, ..

Journal of Biological Chemistry, 274(26):18709-18714, June 1999 (article)

Abstract
Mutations in the p53 tumor suppressor gene are the most frequent genetic alterations found in human cancers. Recent identification of two human homologues of p53 has raised the prospect of functional interactions between family members via a conserved oligomerization domain. Here we report in vitro and in vivo analysis of homo- and hetero-oligomerization of p53 and its homologues, p63 and p73. The oligomerization domains of p63 and p73 can independently fold into stable homotetramers, as previously observed for p53. However, the oligomerization domain of p53 does not associate with that of either p73 or p63, even when p53 is in 15-fold excess. On the other hand, the oligomerization domains of p63 and p73 are able to weakly associate with one another in vitro. In vivo co-transfection assays of the ability of p53 and its homologues to activate reporter genes showed that a DNA-binding mutant of p53 was not able to act in a dominant negative manner over wild-type p73 or p63 but that a p73 mutant could inhibit the activity of wild-type p63. These data suggest that mutant p53 in cancer cells will not interact with endogenous or exogenous p63 or p73 via their respective oligomerization domains. It also establishes that the multiple isoforms of p63 as well as those of p73 are capable of interacting via their common oligomerization domain.

ei

Web [BibTex]

Web [BibTex]


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Spatial Learning and Localization in Animals: A Computational Model and Its Implications for Mobile Robots

Balakrishnan, K., Bousquet, O., Honavar, V.

Adaptive Behavior, 7(2):173-216, 1999 (article)

ei

[BibTex]

[BibTex]


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SVMs for Histogram Based Image Classification

Chapelle, O., Haffner, P., Vapnik, V.

IEEE Transactions on Neural Networks, (9), 1999 (article)

Abstract
Traditional classification approaches generalize poorly on image classification tasks, because of the high dimensionality of the feature space. This paper shows that Support Vector Machines (SVM) can generalize well on difficult image classification problems where the only features are high dimensional histograms. Heavy-tailed RBF kernels of the form $K(mathbf{x},mathbf{y})=e^{-rhosum_i |x_i^a-y_i^a|^{b}}$ with $aleq 1$ and $b leq 2$ are evaluated on the classification of images extracted from the Corel Stock Photo Collection and shown to far outperform traditional polynomial or Gaussian RBF kernels. Moreover, we observed that a simple remapping of the input $x_i rightarrow x_i^a$ improves the performance of linear SVMs to such an extend that it makes them, for this problem, a valid alternative to RBF kernels.

ei

GZIP [BibTex]

GZIP [BibTex]


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Parameterized modeling and recognition of activities

Yacoob, Y., Black, M. J.

Computer Vision and Image Understanding, 73(2):232-247, 1999 (article)

Abstract
In this paper we consider a class of human activities—atomic activities—which can be represented as a set of measurements over a finite temporal window (e.g., the motion of human body parts during a walking cycle) and which has a relatively small space of variations in performance. A new approach for modeling and recognition of atomic activities that employs principal component analysis and analytical global transformations is proposed. The modeling of sets of exemplar instances of activities that are similar in duration and involve similar body part motions is achieved by parameterizing their representation using principal component analysis. The recognition of variants of modeled activities is achieved by searching the space of admissible parameterized transformations that these activities can undergo. This formulation iteratively refines the recognition of the class to which the observed activity belongs and the transformation parameters that relate it to the model in its class. We provide several experiments on recognition of articulated and deformable human motions from image motion parameters.

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pdf pdf from publisher DOI [BibTex]

pdf pdf from publisher DOI [BibTex]


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Is imitation learning the route to humanoid robots?

Schaal, S.

Trends in Cognitive Sciences, 3(6):233-242, 1999, clmc (article)

Abstract
This review will focus on two recent developments in artificial intelligence and neural computation: learning from imitation and the development of humanoid robots. It will be postulated that the study of imitation learning offers a promising route to gain new insights into mechanisms of perceptual motor control that could ultimately lead to the creation of autonomous humanoid robots. This hope is justified because imitation learning channels research efforts towards three important issues: efficient motor learning, the connection between action and perception, and modular motor control in form of movement primitives. In order to make these points, first, a brief review of imitation learning will be given from the view of psychology and neuroscience. In these fields, representations and functional connections between action and perception have been explored that contribute to the understanding of motor acts of other beings. The recent discovery that some areas in the primate brain are active during both movement perception and execution provided a first idea of the possible neural basis of imitation. Secondly, computational approaches to imitation learning will be described, initially from the perspective of traditional AI and robotics, and then with a focus on neural network models and statistical learning research. Parallels and differences between biological and computational approaches to imitation will be highlighted. The review will end with an overview of current projects that actually employ imitation learning for humanoid robots.

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link (url) [BibTex]

link (url) [BibTex]


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Segmentation of endpoint trajectories does not imply segmented control

Sternad, D., Schaal, D.

Experimental Brain Research, 124(1):118-136, 1999, clmc (article)

Abstract
While it is generally assumed that complex movements consist of a sequence of simpler units, the quest to define these units of action, or movement primitives, still remains an open question. In this context, two hypotheses of movement segmentation of endpoint trajectories in 3D human drawing movements are re-examined: (1) the stroke-based segmentation hypothesis based on the results that the proportionality coefficient of the 2/3 power law changes discontinuously with each new â??strokeâ?, and (2) the segmentation hypothesis inferred from the observation of piecewise planar endpoint trajectories of 3D drawing movements. In two experiments human subjects performed a set of elliptical and figure-8 patterns of different sizes and orientations using their whole arm in 3D. The kinematic characteristics of the endpoint trajectories and the seven joint angles of the arm were analyzed. While the endpoint trajectories produced similar segmentation features as reported in the literature, analyses of the joint angles show no obvious segmentation but rather continuous oscillatory patterns. By approximating the joint angle data of human subjects with sinusoidal trajectories, and by implementing this model on a 7-degree-of-freedom anthropomorphic robot arm, it is shown that such a continuous movement strategy can produce exactly the same features as observed by the above segmentation hypotheses. The origin of this apparent segmentation of endpoint trajectories is traced back to the nonlinear transformations of the forward kinematics of human arms. The presented results demonstrate that principles of discrete movement generation may not be reconciled with those of rhythmic movement as easily as has been previously suggested, while the generalization of nonlinear pattern generators to arm movements can offer an interesting alternative to approach the question of units of action.

am

link (url) [BibTex]

link (url) [BibTex]