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2013


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Self-organized state formation in magnonic vortex crystals

Adolff, C. F., Hänze, M., Vogel, A., Weigand, M., Martens, M., Meier, G.

{Physical Review B}, 88(22), American Physical Society, Woodbury, NY, 2013 (article)

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DOI [BibTex]

2013


DOI [BibTex]


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Erratum: Generalized Gilbert equation including inertial damping: Derivation from an extended breathing Fermi surface model [Phys. Rev. B 84, 172403 (2011)]

Fähnle, M., Steiauf, D., Illg, C.

{Physical Review B}, 88, American Physical Society, Woodbury, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Strain and composition dependence of orbital polarization in nickel oxide superlattices

Wu, M., Benckiser, E., Haverkort, M. W., Franco, A., Lu, J., Nwankwo, U., Brück, S., Audehm, P., Goering, E., Macke, S., Hinkov, V., Wochner, P., Christiani, G., Heinze, S., Logvenov, G., Habermeier, H., Keimer, B.

{Physical Review B}, 88, Published by the American Physical Society through the American Institute of Physics, Woodbury, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Efficient focusing of 8 keV X-rays with multilayer Fresnel zone plates fabricated by atomic layer deposition and focused ion beam milling

Mayer, M., Keskinbora, K., Grévent, C., Szeghalmi, A., Knez, M., Weigand, M., Snigirev, A., Snigereva, I., Schütz, G.

{Journal of Synchrotron Radiation}, 20, pages: 433-440, Published for the International Union of Crystallography by Munksgaard, Copenhagen, Denmark, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Rapid prototyping of Fresnel zone plates via direct Ga+ ion beam lithography for high-resolution x-ray imaging

Keskinbora, K., Grévent, C., Eigenthaler, U., Weigand, M., Schütz, G.

{ACS Nano}, 7(11):9788-9797, American Chemical Society, Washington, DC, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Eine kryoflexible kovalente organische Gerüststruktur für die effiziente Trennung von Wasserstoffisotopien durch Quantensieben

Oh, H., Kalidindi, S. B., Um, Y., Bureekaew, S., Schmid, R., Fischer, R. A., Hirscher, M.

{Angewandte Chemie}, 125(50):13461-13464, Wiley-VCH Verl., Weinheim, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Ultrafast demagnetization after laser irradiation in transition metals: Ab initio calculations of the spin-flip electron-phonon scattering with reduced exchange splitting

Illg, C., Haag, M., Fähnle, M.

{Physical Review B}, 88, American Physical Society, Woodbury, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Phase diagram for magnetic vortex core switching studied by ferromagnetic absorption spectroscopy and time-resolved transmission x-ray microscopy

Martens, M., Kamionka, T., Weigand, M., Stoll, H., Tyliszczak, T., Meier, G.

{Physical Review B}, 87, Published by the American Physical Society through the American Institute of Physics, Woodbury, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Optimal distribution of contact forces with inverse-dynamics control

Righetti, L., Buchli, J., Mistry, M., Kalakrishnan, M., Schaal, S.

The International Journal of Robotics Research, 32(3):280-298, March 2013 (article)

Abstract
The development of legged robots for complex environments requires controllers that guarantee both high tracking performance and compliance with the environment. More specifically the control of the contact interaction with the environment is of crucial importance to ensure stable, robust and safe motions. In this contribution we develop an inverse-dynamics controller for floating-base robots under contact constraints that can minimize any combination of linear and quadratic costs in the contact constraints and the commands. Our main result is the exact analytical derivation of the controller. Such a result is particularly relevant for legged robots as it allows us to use torque redundancy to directly optimize contact interactions. For example, given a desired locomotion behavior, we can guarantee the minimization of contact forces to reduce slipping on difficult terrains while ensuring high tracking performance of the desired motion. The main advantages of the controller are its simplicity, computational efficiency and robustness to model inaccuracies. We present detailed experimental results on simulated humanoid and quadruped robots as well as a real quadruped robot. The experiments demonstrate that the controller can greatly improve the robustness of locomotion of the robots.1

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Thermodynamics as a theory of decision-making with information-processing costs

Ortega, PA, Braun, DA

Proceedings of the Royal Society of London A, 469(2153):1-18, May 2013 (article)

Abstract
Perfectly rational decision-makers maximize expected utility, but crucially ignore the resource costs incurred when determining optimal actions. Here, we propose a thermodynamically inspired formalization of bounded rational decision-making where information processing is modelled as state changes in thermodynamic systems that can be quantified by differences in free energy. By optimizing a free energy, bounded rational decision-makers trade off expected utility gains and information-processing costs measured by the relative entropy. As a result, the bounded rational decision-making problem can be rephrased in terms of well-known variational principles from statistical physics. In the limit when computational costs are ignored, the maximum expected utility principle is recovered. We discuss links to existing decision-making frameworks and applications to human decision-making experiments that are at odds with expected utility theory. Since most of the mathematical machinery can be borrowed from statistical physics, the main contribution is to re-interpret the formalism of thermodynamic free-energy differences in terms of bounded rational decision-making and to discuss its relationship to human decision-making experiments.

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DOI [BibTex]

DOI [BibTex]


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Tank-like module-based climbing robot using passive compliant joints

Seo, T., Sitti, M.

IEEE/ASME Transactions on Mechatronics, 18(1):397-408, 2013 (article)

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[BibTex]

[BibTex]


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Enhanced fabrication and characterization of gecko-inspired mushroom-tipped microfiber adhesives

Song, J., Mengüç, Y., Sitti, M.

Journal of Adhesion Science and Technology, 27(17):1921-1932, Routledge, 2013 (article)

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Project Page [BibTex]

Project Page [BibTex]


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Linear combination of one-step predictive information with an external reward in an episodic policy gradient setting: a critical analysis

Zahedi, K., Martius, G., Ay, N.

Frontiers in Psychology, 4(801), 2013 (article)

Abstract
One of the main challenges in the field of embodied artificial intelligence is the open-ended autonomous learning of complex behaviours. Our approach is to use task-independent, information-driven intrinsic motivation(s) to support task-dependent learning. The work presented here is a preliminary step in which we investigate the predictive information (the mutual information of the past and future of the sensor stream) as an intrinsic drive, ideally supporting any kind of task acquisition. Previous experiments have shown that the predictive information (PI) is a good candidate to support autonomous, open-ended learning of complex behaviours, because a maximisation of the PI corresponds to an exploration of morphology- and environment-dependent behavioural regularities. The idea is that these regularities can then be exploited in order to solve any given task. Three different experiments are presented and their results lead to the conclusion that the linear combination of the one-step PI with an external reward function is not generally recommended in an episodic policy gradient setting. Only for hard tasks a great speed-up can be achieved at the cost of an asymptotic performance lost.

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link (url) DOI [BibTex]


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Switching modes in easy and hard axis magnetic reversal in a self-assembled antidot array

Haering, F., Wiedwald, U., Nothelfer, S., Koslowski, B., Ziemann, P., Lechner, L., Wallucks, A., Lebecki, K., Nowak, U., Gräfe, J., Goering, E., Schütz, G.

{Nanotechnology}, 24, IOP Pub., Bristol, UK, 2013 (article)

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DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Time-resolved imaging of nonlinear magnetic domain-wall dynamics in ferromagnetic nanowires

Stein, F.-U., Bocklage, L., Weigand, M., Meier, G.

{Scientific Reports}, 3, Nature Publishing Group, London, UK, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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A cryogenically flexible covalent organic framework for efficient hydrogen isotrope separation by quantum sieving

Oh, H., Kalidindi, S. B., Um, Y., Bureekaew, S., Schmid, R., Fischer, R. A., Hirscher, M.

{Angewandte Chemie International Edition in English}, 52(50):13219-13222, Wiley-VCH Verlag GmbH & Co. KGaA, D-69451 Weinheim, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Unexpected room-temperature ferromagnetism in bulk ZnO

Chen, Y., Goering, E., Jeurgens, L., Wang, Z., Phillipp, F., Baier, J., Tietze, T., Schütz, G.

{Applied Physics Letters}, (103), American Institute of Physics, Melville, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Large-area hard magnetic L10-FePt and composite L10-FePt based nanopatterns

Goll, D., Bublat, T.

{Physica Status Solidi A-Applications and Materials Science}, 210(7):1261-1271, Wiley-VCH, Weinheim, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Wave modes of collective vortex gyration in dipolar-coupled-dot-array magnonic crystals

Han, D., Vogel, A., Jung, H., Lee, K., Weigand, M., Stoll, H., Schütz, G., Fischer, P., Meier, G., Kim, S.

{Scientific Reports}, 3, Nature Publishing Group, London, UK, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Micro-scale mobile robotics

Diller, E., Sitti, M.

Foundations and Trends in Robotics, 2(3):143-259, Now Publishers Incorporated, 2013 (article)

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[BibTex]

[BibTex]


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Survey and Introduction to the Focused Section on Bio-Inspired Mechatronics

Sitti, M., Menciassi, A., Ijspeert, A., Low, K. H., Kim, S.

Mechatronics, IEEE/ASME Transactions on, 18(2):409-418, DOI: 10.1109/TMECH.2012. 2233492, 2013 (article)

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[BibTex]

[BibTex]


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Robustness of guided self-organization against sensorimotor disruptions

Martius, G.

Advances in Complex Systems, 16(02n03):1350001, 2013 (article)

Abstract
Self-organizing processes are crucial for the development of living beings. Practical applications in robots may benefit from the self-organization of behavior, e.g.~to increase fault tolerance and enhance flexibility, provided that external goals can also be achieved. We present results on the guidance of self-organizing control by visual target stimuli and show a remarkable robustness to sensorimotor disruptions. In a proof of concept study an autonomous wheeled robot is learning an object finding and ball-pushing task from scratch within a few minutes in continuous domains. The robustness is demonstrated by the rapid recovery of the performance after severe changes of the sensor configuration.

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DOI [BibTex]

DOI [BibTex]


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Controlled Reduction with Unactuated Cyclic Variables: Application to 3D Bipedal Walking with Passive Yaw Rotation

Gregg, R., Righetti, L.

IEEE Transactions on Automatic Control, 58(10):2679-2685, October 2013 (article)

Abstract
This technical note shows that viscous damping can shape momentum conservation laws in a manner that stabilizes yaw rotation and enables steering for underactuated 3D walking. We first show that unactuated cyclic variables can be controlled by passively shaped conservation laws given a stabilizing controller in the actuated coordinates. We then exploit this result to realize controlled geometric reduction with multiple unactuated cyclic variables. We apply this underactuated control strategy to a five-link 3D biped to produce exponentially stable straight-ahead walking and steering in the presence of passive yawing.

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Ferromagnetism of zinc oxide nanograined films

Straumal, B. B., Protasova, S. G., Mazilkin, A. A., Schütz, G., Goering, E., Baretzky, B., Straumal, P. B.

{Journal of Experimental and Theoretical Physics Letters}, 97(6):367-377, Pleiades Publishing, Inc., 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Hydrogen adsorption properties of platinum decorated hierarchically structured templated carbons

Oh, H., Gennett, T., Atanassov, P., Kurttepeli, M., Bals, S., Hurst, K. E., Hirscher, M.

{Microporous and Mesoporous Materials}, pages: 66-74, Elsevier, Amsterdam, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Extended s-d models for the dynamics of noncollinear magnetization: Short review of two different approaches

Fähnle, M., Zhang, S.

{Journal of Magnetism and Magnetic Materials}, 326, pages: 232-234, NH, Elsevier, Amsterdam, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Correlation between spin structure oscillations and domain wall velocities

Bisig, A., Stärk, M., Mawass, M., Moutafis, C., Rhensius, J., Heidler, J., Büttner, F., Noske, M., Weigand, M., Eisebitt, S., Tyliszczak, T., Van Wayenberge, B., Stoll, H., Schütz, G., Kläui, M.

{Nature Communications}, 4, Nature Publishing Group, London, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Recent advances in use of atomic layer deposition and focused ion beams for fabrication of Fresnel zone plates for hard x-rays

Keskinbora, K., Robisch, A., Mayer, M., Grévent, C., Szeghalmi, A. V., Knez, M., Weigand, M., Snigireva, I., Snigirev, A., Salditt, T., Schütz, G.

{Proceedings of SPIE (The International Society for Optical Engineering)}, 8851, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic states in low-pinning high-anisotropy material nanostructures suitable for dynamic imaging

Büttner, F., Moutafis, C., Bisig, A., Wohlhüter, P., Günther, C. M., Mohanty, J., Geilhufe, J., Schneider, M., v. Korff Schmising, C., Schaffert, S., Pfau, B., Hantschmann, M., Riemeier, M., Emmel, M., Finizio, S., Jakob, G., Weigand, M., Rhensius, J., Franken, J. H., Lavrijsen, R., Swagten, H. J. M., Stoll, H., Eisebitt, S., Kläui, M.

{Physical Review B}, 87, Published by the American Physical Society through the American Institute of Physics, Woodbury, NY, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Experimental and theoretical study of D2/H2 quantum sieving in a carbon molecular sieve

Gotzias, A., Charalambopoulou, G., Ampoumogli, A., Krkljus, I., Hirscher, M., Steriotis, T.

{Adsorption}, 19(2-4):373-379, Springer Science+Business Media, New York, 2013 (article)

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DOI [BibTex]

DOI [BibTex]


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Non-parametric hand pose estimation with object context

Romero, J., Kjellström, H., Ek, C. H., Kragic, D.

Image and Vision Computing , 31(8):555 - 564, 2013 (article)

Abstract
In the spirit of recent work on contextual recognition and estimation, we present a method for estimating the pose of human hands, employing information about the shape of the object in the hand. Despite the fact that most applications of human hand tracking involve grasping and manipulation of objects, the majority of methods in the literature assume a free hand, isolated from the surrounding environment. Occlusion of the hand from grasped objects does in fact often pose a severe challenge to the estimation of hand pose. In the presented method, object occlusion is not only compensated for, it contributes to the pose estimation in a contextual fashion; this without an explicit model of object shape. Our hand tracking method is non-parametric, performing a nearest neighbor search in a large database (.. entries) of hand poses with and without grasped objects. The system that operates in real time, is robust to self occlusions, object occlusions and segmentation errors, and provides full hand pose reconstruction from monocular video. Temporal consistency in hand pose is taken into account, without explicitly tracking the hand in the high-dim pose space. Experiments show the non-parametric method to outperform other state of the art regression methods, while operating at a significantly lower computational cost than comparable model-based hand tracking methods.

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Publisher site pdf link (url) [BibTex]

Publisher site pdf link (url) [BibTex]

2006


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Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation

Nicastro, G., Habeck, M., Masino, L., Svergun, DI., Pastore, A.

Journal of Biomolecular NMR, 36(4):267-277, December 2006 (article)

Abstract
The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners.

ei

Web DOI [BibTex]

2006


Web DOI [BibTex]


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A Unifying View of Wiener and Volterra Theory and Polynomial Kernel Regression

Franz, M., Schölkopf, B.

Neural Computation, 18(12):3097-3118, December 2006 (article)

Abstract
Volterra and Wiener series are perhaps the best understood nonlinear system representations in signal processing. Although both approaches have enjoyed a certain popularity in the past, their application has been limited to rather low-dimensional and weakly nonlinear systems due to the exponential growth of the number of terms that have to be estimated. We show that Volterra and Wiener series can be represented implicitly as elements of a reproducing kernel Hilbert space by utilizing polynomial kernels. The estimation complexity of the implicit representation is linear in the input dimensionality and independent of the degree of nonlinearity. Experiments show performance advantages in terms of convergence, interpretability, and system sizes that can be handled.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Statistical Analysis of Slow Crack Growth Experiments

Pfingsten, T., Glien, K.

Journal of the European Ceramic Society, 26(15):3061-3065, November 2006 (article)

Abstract
A common approach for the determination of Slow Crack Growth (SCG) parameters are the static and dynamic loading method. Since materials with small Weibull module show a large variability in strength, a correct statistical analysis of the data is indispensable. In this work we propose the use of the Maximum Likelihood method and a Baysian analysis, which, in contrast to the standard procedures, take into account that failure strengths are Weibull distributed. The analysis provides estimates for the SCG parameters, the Weibull module, and the corresponding confidence intervals and overcomes the necessity of manual differentiation between inert and fatigue strength data. We compare the methods to a Least Squares approach, which can be considered the standard procedure. The results for dynamic loading data from the glass sealing of MEMS devices show that the assumptions inherent to the standard approach lead to significantly different estimates.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Mining frequent stem patterns from unaligned RNA sequences

Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.

Bioinformatics, 22(20):2480-2487, October 2006 (article)

Abstract
Motivation: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly. Results: Our method RNAmine employs a graph theoretic representation of RNA sequences, and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis

Aigner, T., Fundel, K., Saas, J., Gebhard, P., Haag, J., Weiss, T., Zien, A., Obermayr, F., Zimmer, R., Bartnik, E.

Arthritis and Rheumatism, 54(11):3533-3544, October 2006 (article)

Abstract
Objective. Despite many research efforts in recent decades, the major pathogenetic mechanisms of osteo- arthritis (OA), including gene alterations occurring during OA cartilage degeneration, are poorly under- stood, and there is no disease-modifying treatment approach. The present study was therefore initiated in order to identify differentially expressed disease-related genes and potential therapeutic targets. Methods. This investigation consisted of a large gene expression profiling study performed based on 78 normal and disease samples, using a custom-made complementar y DNA array covering >4,000 genes. Results. Many differentially expressed genes were identified, including the expected up-regulation of ana- bolic and catabolic matrix genes. In particular, the down-regulation of important oxidative defense genes, i.e., the genes for superoxide dismutases 2 and 3 and glutathione peroxidase 3, was prominent. This indicates that continuous oxidative stress to the cells and the matrix is one major underlying pathogenetic mecha- nism in OA. Also, genes that are involved in the phenot ypic stabilit y of cells, a feature that is greatly reduced in OA cartilage, appeared to be suppressed. Conclusion. Our findings provide a reference data set on gene alterations in OA cartilage and, importantly, indicate major mechanisms underlying central cell bio- logic alterations that occur during the OA disease process. These results identify molecular targets that can be further investigated in the search for therapeutic interventions.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Implicit Surface Modelling with a Globally Regularised Basis of Compact Support

Walder, C., Schölkopf, B., Chapelle, O.

Computer Graphics Forum, 25(3):635-644, September 2006 (article)

Abstract
We consider the problem of constructing a globally smooth analytic function that represents a surface implicitly by way of its zero set, given sample points with surface normal vectors. The contributions of the paper include a novel means of regularising multi-scale compactly supported basis functions that leads to the desirable interpolation properties previously only associated with fully supported bases. We also provide a regularisation framework for simpler and more direct treatment of surface normals, along with a corresponding generalisation of the representer theorem lying at the core of kernel-based machine learning methods. We demonstrate the techniques on 3D problems of up to 14 million data points, as well as 4D time series data and four-dimensional interpolation between three-dimensional shapes.

ei

PDF GZIP DOI [BibTex]


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An Online Support Vector Machine for Abnormal Events Detection

Davy, M., Desobry, F., Gretton, A., Doncarli, C.

Signal Processing, 86(8):2009-2025, August 2006 (article)

Abstract
The ability to detect online abnormal events in signals is essential in many real-world Signal Processing applications. Previous algorithms require an explicit signal statistical model, and interpret abnormal events as statistical model abrupt changes. Corresponding implementation relies on maximum likelihood or on Bayes estimation theory with generally excellent performance. However, there are numerous cases where a robust and tractable model cannot be obtained, and model-free approaches need to be considered. In this paper, we investigate a machine learning, descriptor-based approach that does not require an explicit descriptors statistical model, based on Support Vector novelty detection. A sequential optimization algorithm is introduced. Theoretical considerations as well as simulations on real signals demonstrate its practical efficiency.

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PDF PostScript PDF DOI [BibTex]

PDF PostScript PDF DOI [BibTex]


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Integrating Structured Biological data by Kernel Maximum Mean Discrepancy

Borgwardt, K., Gretton, A., Rasch, M., Kriegel, H., Schölkopf, B., Smola, A.

Bioinformatics, 22(4: ISMB 2006 Conference Proceedings):e49-e57, August 2006 (article)

Abstract
Motivation: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology. Results: We study the practical feasibility of an MMD-based test on three central data integration tasks: Testing cross-platform comparability of microarray data, cancer diagnosis, and data-content based schema matching for two different protein function classification schemas. In all of these experiments, including high-dimensional ones, MMD is very accurate in finding samples that were generated from the same distribution, and outperforms its best competitors. Conclusions: We have defined a novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as confirmed by our experiments.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Large Scale Transductive SVMs

Collobert, R., Sinz, F., Weston, J., Bottou, L.

Journal of Machine Learning Research, 7, pages: 1687-1712, August 2006 (article)

Abstract
We show how the Concave-Convex Procedure can be applied to the optimization of Transductive SVMs, which traditionally requires solving a combinatorial search problem. This provides for the first time a highly scalable algorithm in the nonlinear case. Detailed experiments verify the utility of our approach.

ei

PostScript PDF PDF [BibTex]

PostScript PDF PDF [BibTex]


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Building Support Vector Machines with Reduced Classifier Complexity

Keerthi, S., Chapelle, O., DeCoste, D.

Journal of Machine Learning Research, 7, pages: 1493-1515, July 2006 (article)

Abstract
Support vector machines (SVMs), though accurate, are not preferred in applications requiring great classification speed, due to the number of support vectors being large. To overcome this problem we devise a primal method with the following properties: (1) it decouples the idea of basis functions from the concept of support vectors; (2) it greedily finds a set of kernel basis functions of a specified maximum size ($dmax$) to approximate the SVM primal cost function well; (3) it is efficient and roughly scales as $O(ndmax^2)$ where $n$ is the number of training examples; and, (4) the number of basis functions it requires to achieve an accuracy close to the SVM accuracy is usually far less than the number of SVM support vectors.

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PDF [BibTex]

PDF [BibTex]


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ARTS: Accurate Recognition of Transcription Starts in Human

Sonnenburg, S., Zien, A., Rätsch, G.

Bioinformatics, 22(14):e472-e480, July 2006 (article)

Abstract
Motivation: One of the most important features of genomic DNA are the protein-coding genes. While it is of great value to identify those genes and the encoded proteins, it is also crucial to understand how their transcription is regulated. To this end one has to identify the corresponding promoters and the contained transcription factor binding sites. TSS finders can be used to locate potential promoters. They may also be used in combination with other signal and content detectors to resolve entire gene structures. Results: We have developed a novel kernel based method - called ARTS - that accurately recognizes transcription start sites in human. The application of otherwise too computationally expensive Support Vector Machines was made possible due to the use of efficient training and evaluation techniques using suffix tries. In a carefully designed experimental study, we compare our TSS finder to state-of-the-art methods from the literature: McPromoter, Eponine and FirstEF. For given false positive rates within a reasonable range, we consistently achieve considerably higher true positive rates. For instance, ARTS finds about 24% true positives at a false positive rate of 1/1000, where the other methods find less than half (10.5%). Availability: Datasets, model selection results, whole genome predictions, and additional experimental results are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/arts

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Large Scale Multiple Kernel Learning

Sonnenburg, S., Rätsch, G., Schäfer, C., Schölkopf, B.

Journal of Machine Learning Research, 7, pages: 1531-1565, July 2006 (article)

Abstract
While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lanckriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constrained quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard SVM implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm works for hundred thousands of examples or hundreds of kernels to be combined, and helps for automatic model selection, improving the interpretability of the learning result. In a second part we discuss general speed up mechanism for SVMs, especially when used with sparse feature maps as appear for string kernels, allowing us to train a string kernel SVM on a 10 million real-world splice data set from computational biology. We integrated multiple kernel learning in our machine learning toolbox SHOGUN for which the source code is publicly available at http://www.fml.tuebingen.mpg.de/raetsch/projects/shogun.

ei

PDF [BibTex]

PDF [BibTex]


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Factorial coding of natural images: how effective are linear models in removing higher-order dependencies?

Bethge, M.

Journal of the Optical Society of America A, 23(6):1253-1268, June 2006 (article)

Abstract
The performance of unsupervised learning models for natural images is evaluated quantitatively by means of information theory. We estimate the gain in statistical independence (the multi-information reduction) achieved with independent component analysis (ICA), principal component analysis (PCA), zero-phase whitening, and predictive coding. Predictive coding is translated into the transform coding framework, where it can be characterized by the constraint of a triangular filter matrix. A randomly sampled whitening basis and the Haar wavelet are included into the comparison as well. The comparison of all these methods is carried out for different patch sizes, ranging from 2x2 to 16x16 pixels. In spite of large differences in the shape of the basis functions, we find only small differences in the multi-information between all decorrelation transforms (5% or less) for all patch sizes. Among the second-order methods, PCA is optimal for small patch sizes and predictive coding performs best for large patch sizes. The extra gain achieved with ICA is always less than 2%. In conclusion, the `edge filters‘ found with ICA lead only to a surprisingly small improvement in terms of its actual objective.

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PDF Web [BibTex]


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Classifying EEG and ECoG Signals without Subject Training for Fast BCI Implementation: Comparison of Non-Paralysed and Completely Paralysed Subjects

Hill, N., Lal, T., Schröder, M., Hinterberger, T., Wilhelm, B., Nijboer, F., Mochty, U., Widman, G., Elger, C., Schölkopf, B., Kübler, A., Birbaumer, N.

IEEE Transactions on Neural Systems and Rehabilitation Engineering, 14(2):183-186, June 2006 (article)

Abstract
We summarize results from a series of related studies that aim to develop a motor-imagery-based brain-computer interface using a single recording session of EEG or ECoG signals for each subject. We apply the same experimental and analytical methods to 11 non-paralysed subjects (8 EEG, 3 ECoG), and to 5 paralysed subjects (4 EEG, 1 ECoG) who had been unable to communicate for some time. While it was relatively easy to obtain classifiable signals quickly from most of the non-paralysed subjects, it proved impossible to classify the signals obtained from the paralysed patients by the same methods. This highlights the fact that though certain BCI paradigms may work well with healthy subjects, this does not necessarily indicate success with the target user group. We outline possible reasons for this failure to transfer.

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PDF PDF DOI [BibTex]


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SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments

Tabei, Y., Tsuda, K., Kin, T., Asai, K.

Bioinformatics, 22(14):1723-1729, May 2006 (article)

Abstract
The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but their potential secondary structures. Sankoff‘s algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required. We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable to the much slower existing algorithms.

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The Effect of Artifacts on Dependence Measurement in fMRI

Gretton, A., Belitski, A., Murayama, Y., Schölkopf, B., Logothetis, N.

Magnetic Resonance Imaging, 24(4):401-409, April 2006 (article)

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PDF Web DOI [BibTex]


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Phase noise and the classification of natural images

Wichmann, F., Braun, D., Gegenfurtner, K.

Vision Research, 46(8-9):1520-1529, April 2006 (article)

Abstract
We measured the effect of global phase manipulations on a rapid animal categorization task. The Fourier spectra of our images of natural scenes were manipulated by adding zero-mean random phase noise at all spatial frequencies. The phase noise was the independent variable, uniformly and symmetrically distributed between 0 degree and ±180 degrees. Subjects were remarkably resistant to phase noise. Even with ±120 degree phase noise subjects were still performing at 75% correct. The high resistance of the subjects’ animal categorization rate to phase noise suggests that the visual system is highly robust to such random image changes. The proportion of correct answers closely followed the correlation between original and the phase noise-distorted images. Animal detection rate was higher when the same task was performed with contrast reduced versions of the same natural images, at contrasts where the contrast reduction mimicked that resulting from our phase randomization. Since the subjects’ categorization rate was better in the contrast experiment, reduction of local contrast alone cannot explain the performance in the phase noise experiment. This result obtained with natural images differs from those obtained for simple sinusoidal stimuli were performance changes due to phase changes are attributed to local contrast changes only. Thus the global phasechange accompanying disruption of image structure such as edges and object boundaries at different spatial scales reduces object classification over and above the performance deficit resulting from reducing contrast. Additional colour information improves the categorization performance by 2 %.

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PDF Web DOI [BibTex]

PDF Web DOI [BibTex]