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2016


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Ab initio theory for ultrafast magnetization dynamics with a dynamic band structure

Müller, B. Y., Haag, M., Fähnle, M.

{Journal of Magnetism and Magnetic Materials}, 414, pages: 14-18, North-Holland, Amsterdam, 2016 (article)

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DOI [BibTex]

2016


DOI [BibTex]


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High-resolution analysis of currents at low-angle grain boundaries in YBCO thin films using magnetooptics and magnetic x-ray microscopy

Ruoß, S., Stahl, C., Bayer, J., Schütz, G., Albrecht, J., Laviano, F.

{IEEE Transactions on Applied Superconductivity}, 26(3), IEEE, New York, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Three-dimensional character of the magnetization dynamics in magnetic vortex structures: Hybridization of flexure gyromodes with spin waves

Noske, M., Stoll, H., Fähnle, M., Gangwar, A., Woltersdorf, G., Slavin, A., Weigand, M., Dieterle, G., Förster, J., Back, C. H., Schütz, G.

{Physical Review Letters}, 117(3), American Physical Society, Woodbury, N.Y., 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Coercivity scaling in antidot lattices in Fe, Ni, and NiFe thin films

Gräfe, J., Schütz, G., Goering, E. J.

{Journal of Magnetism and Magnetic Materials}, 419, pages: 517-520, North-Holland, Amsterdam, 2016 (article)

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DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Nanostructured materials for solid-state hydrogen storage: A review of the achievement of COST Action MP1103

Callini, E., Aguey-Zinsou, K., Ahuja, R., Ares, J. R., Bals, S., Biliskov, N., Chakraborty, S., Charalambopoulou, G., Chaudhary, A., Cuevas, F., Dam, B., de Jongh, P., Dornheim, M., Filinchuk, Y., Grbovic-Novakovic, J., Hirscher, M., Jensen, T. R., Jensen, P. B., Novakovic, N., Lai, Q., Leardini, F., Gattia, D. M., Pasquini, L., Steriotis, T., Turner, S., Vegge, T., Züttel, A., Montone, A.

{International Journal of Hydrogen Energy}, 41(32):14404-14428, Elsevier, Amsterdam, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic X-ray microscopy at low temperatures - Visualization of flux distributions in superconductors

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

{AIP Conference Proceedings}, 1696, AIP Publishing, Melville, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Enhanced non-adiabaticity in vortex cores due to the emergent Hall effect

Bisig, A., Akosa, C. A., Moon, J., Rhensius, J., Moutafis, C., von Bieren, A., Heidler, J., Kiliani, G., Kammerer, M., Curcic, M., Weigand, M., Tyliszczak, T., Van Waeyenberge, B., Stoll, H., Schütz, G., Lee, K., Manchon, A., Kläui, M.

{Physical Review Letters}, 117(27), American Physical Society, Woodbury, N.Y., 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Quantitative magneto-optical analysis of the role of finite temperatures on the critical state in YBCO thin films

Albrecht, J., Brück, S., Stahl, C., Ruoß, S.

{Superconductor Science and Technology}, 29(11), IOP Pub., Bristol, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Bioinspired Motor Control for Articulated Robots [From the Guest Editors]

Vitiello, Nicola, Ijspeert, Auke J, Schaal, S.

IEEE Robotics {\&} Automation Magazine, 23(1):20-21, 2016 (article)

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[BibTex]

[BibTex]


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Bio-inspired feedback-circuit implementation of discrete, free energy optimizing, winner-take-all computations

Genewein, T, Braun, DA

Biological Cybernetics, 110(2):135–150, June 2016 (article)

Abstract
Bayesian inference and bounded rational decision-making require the accumulation of evidence or utility, respectively, to transform a prior belief or strategy into a posterior probability distribution over hypotheses or actions. Crucially, this process cannot be simply realized by independent integrators, since the different hypotheses and actions also compete with each other. In continuous time, this competitive integration process can be described by a special case of the replicator equation. Here we investigate simple analog electric circuits that implement the underlying differential equation under the constraint that we only permit a limited set of building blocks that we regard as biologically interpretable, such as capacitors, resistors, voltage-dependent conductances and voltage- or current-controlled current and voltage sources. The appeal of these circuits is that they intrinsically perform normalization without requiring an explicit divisive normalization. However, even in idealized simulations, we find that these circuits are very sensitive to internal noise as they accumulate error over time. We discuss in how far neural circuits could implement these operations that might provide a generic competitive principle underlying both perception and action.

ei

DOI [BibTex]

DOI [BibTex]


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Collective modes in three-dimensional magnonic vortex crystals

Hänze, M., Adolff, C. F., Schulte, B., Möller, J., Weigand, M., Meier, G.

{Scientific Reports}, 6, Nature Publishing Group, London, UK, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Spin wave mediated unidirectional vortex core reversal by two orthogonal monopolar field pulses: The essential role of three-dimensional magnetization dynamics

Noske, M., Stoll, H., Fähnle, M., Gangwar, A., Woltersdorf, G., Slavin, A., Weigand, M., Dieterle, G., Förster, J., Back, C. H., Schütz, G.

{Journal of Applied Physics}, 119(17), AIP Publishing, New York, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic vortex cores as tunable spin-wave emitters

Wintz, S., Tiberkevich, V., Weigand, M., Raabe, J., Lindner, J., Erbe, A., Slavin, A., Fassbender, J.

{Nature Nanotechnology}, 11(11):948-953, Nature Publishing Group, London, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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The usable capacity of porous materials for hydrogen storage

Schlichtenmayer, M., Hirscher, M.

{Applied Physics A}, 122(4), Springer-Verlag Heidelberg, Heidelberg, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Ferromagnetic behaviour of ZnO: the role of grain boundaries

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

{Beilstein Journal of Nanotechnology}, 7, pages: 1936-1947, Beilstein-Institut, Frankfurt am Main, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Localized domain wall nucleation dynamics in asymmetric ferromagnetic rings revealed by direct time-resolved magnetic imaging

Richter, K., Krone, A., Mawass, M., Krüger, B., Weigand, M., Stoll, H., Schütz, G., Kläui, M.

{Physical Review B}, 94(2), American Physical Society, Woodbury, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Observation of room-temperature magnetic skyrmions and their current-driven dynamics in ultrathin metallic ferromagnets

Woo, S., Litzius, K., Krüger, B., Im, M., Caretta, L., Richter, K., Mann, M., Krone, A., Reeve, R. M., Weigand, M., Agrawal, P., Lemesh, I., Mawass, M., Fischer, P., Kläui, M., Beach, G. S. D.

{Nature Materials}, 15(5):501-506, Nature Pub. Group, London, UK, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Decision-Making under Ambiguity Is Modulated by Visual Framing, but Not by Motor vs. Non-Motor Context: Experiments and an Information-Theoretic Ambiguity Model

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

PLoS ONE, 11(4):1-21, April 2016 (article)

Abstract
A number of recent studies have investigated differences in human choice behavior depending on task framing, especially comparing economic decision-making to choice behavior in equivalent sensorimotor tasks. Here we test whether decision-making under ambiguity exhibits effects of task framing in motor vs. non-motor context. In a first experiment, we designed an experience-based urn task with varying degrees of ambiguity and an equivalent motor task where subjects chose between hitting partially occluded targets. In a second experiment, we controlled for the different stimulus design in the two tasks by introducing an urn task with bar stimuli matching those in the motor task. We found ambiguity attitudes to be mainly influenced by stimulus design. In particular, we found that the same subjects tended to be ambiguity-preferring when choosing between ambiguous bar stimuli, but ambiguity-avoiding when choosing between ambiguous urn sample stimuli. In contrast, subjects’ choice pattern was not affected by changing from a target hitting task to a non-motor context when keeping the stimulus design unchanged. In both tasks subjects’ choice behavior was continuously modulated by the degree of ambiguity. We show that this modulation of behavior can be explained by an information-theoretic model of ambiguity that generalizes Bayes-optimal decision-making by combining Bayesian inference with robust decision-making under model uncertainty. Our results demonstrate the benefits of information-theoretic models of decision-making under varying degrees of ambiguity for a given context, but also demonstrate the sensitivity of ambiguity attitudes across contexts that theoretical models struggle to explain.

ei

DOI [BibTex]


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Outlook and challenges for hydrogen storage in nanoporous materials

Broom, D. P., Webb, C. J., Hurst, K. E., Parilla, P. A., Gennett, T., Brown, C. M., Zacharia, R., Tylianakis, E., Klontzas, E., Froudakis, G. E., Steriotis, T. A., Trikalitis, P. N., Anton, D. L., Hardy, B., Tamburello, D., Corgnale, C., van Hassel, B. A., Cossement, D., Chahine, R., Hirscher, M.

{Applied Physics A}, 122(3), Springer-Verlag Heidelberg, Heidelberg, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Quantum sieving for separation of hydrogen isotopes using MOFs

Oh, H., Hirscher, M.

{European Journal of Inorganic Chemistry}, 2016(27):4278-4289, Wiley-VCH, Weinheim, Germany, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Direct patterning of vortex generators on a fiber tip using a focused ion beam

Vayalamkuzhi, P., Bhattacharya, S., Eigenthaler, U., Keskinbora, K., Salman, C. T., Hirscher, M., Spatz, J. P., Viswanathan, N. K.

{Optics Letters}, 41(10):2133-2136, Optical Society of America, Washington, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Two-body problem of core-region coupled magnetic vortex stacks

Hänze, M., Adolff, C. F., Velten, S., Weigand, M., Meier, G.

{Physical Review B}, 93(5), American Physical Society, Woodbury, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Irreproducibility in hydrogen storage material research

Broom, D. P., Hirscher, M.

{Energy \& Environmental Science}, 9(11):3368-3380, Royal Society of Chemistry, Cambridge, UK, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Effect of surface configurations on the room-temperature magnetism of pure ZnO

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

{Journal of Materials Chemistry C}, 4(19):4166-4175, Royal Society of Chemistry, London, UK, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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On the synthesis and microstructure analysis of high performance MnBi

Chen, Y., Sawatzki, S., Ener, S., Sepehri-Amin, H., Leineweber, A., Gregori, G., Qu, F., Muralidhar, S., Ohkubo, T., Hono, K., Gutfleisch, O., Kronmüller, H., Schütz, G., Goering, E.

{AIP Advances}, 6(12), 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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The role of individual defects on the magnetic screening of HTSC films

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

{New Journal of Physics}, 18(10), IOP Publishing, Bristol, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Magnetic switching of nanoscale antidot lattices

Wiedwald, U., Gräfe, J., Lebecki, K. M., Skripnik, M., Haering, F., Schütz, G., Ziemann, P., Goering, E., Nowak, U.

{Beilstein Journal of Nanotechnology}, 7, pages: 733-750, Beilstein-Institut, Frankfurt am Main, 2016 (article)

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DOI Project Page [BibTex]

DOI Project Page [BibTex]


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Hydrogen-based energy storage (IEA-HIA Task 32)

Buckley, C. E., Chen, P., van Hassel, B. A., Hirscher, M.

{Applied Physics A}, 122(2), Springer-Verlag Heidelberg, Heidelberg, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Local domain-wall velocity engineering via tailored potential landscapes in ferromagnetic rings

Richter, K., Krone, A., Mawass, M., Krüger, B., Weigand, M., Stoll, H., Schütz, G., Kläui, M.

{Physical Review Applied}, 5(2), American Physical Society, College Park, Md. [u.a.], 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Geometric control of the magnetization reversal in antidot lattices with perpendicular magnetic anisotropy

Gräfe, J., Weigand, M., Träger, N., Schütz, G., Goering, E. J., Skripnik, M., Nowak, U., Haering, F., Ziemann, P., Wiedwald, U.

{Physical Review B}, 93(10), American Physical Society, Woodbury, NY, 2016 (article)

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DOI Project Page Project Page [BibTex]

DOI Project Page Project Page [BibTex]


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Growth and characterizationof large weak topological insulator Bi2Tel single crystal by Bismuth self-flux method

Ryu, G., Son, K., Schütz, G.

{Journal of Crystal Growth}, 440, pages: 26-30, North-Holland, Amsterdam, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Additive interfacial chiral interaction in multilayers for stabilization of small individual skyrmions at room temperature

Moreau-Luchaire, C., Moutafis, C., Reyren, N., Sampaio, J., Vaz, C. A. F., Van Horne, N., Bouzehouane, K., Garcia, K., Deranlot, C., Warnicke, P., Wohlhüter, P., George, J.-M., Weigand, M., Raabe, J., Cros, V., Fert, A.

{Nature Nanotechnology}, 11(5):444-448, Nature Publishing Group, London, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Surface defect free growth of a spin dimer TlCuCl3 compound crystals and investigations on its optical and magnetic properties

Ryu, G., Son, K.

{Journal of Solid State Chemistry}, 237, pages: 358-363, Academic Press, Orlando, Fla., 2016 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Physical and mathematical justification of the numerical Brillouin zone integration of the Boltzmann rate equation by Gaussian smearing

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

{Journal of Theoretical and Applied Physics}, 10(1):1-6, Springer, Berlin, Heidelberg, Tehran, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Pinned orbital moments - A new contribution to magnetic anisotropy

Audehm, P., Schmidt, M., Brück, S., Tietze, T., Gräfe, J., Macke, S., Schütz, G., Goering, E.

{Scientific Reports}, 6, Nature Publishing Group, London, UK, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Comparative study of ALD SiO2 thin films for optical applications

Pfeiffer, K., Shestaeva, S., Bingel, A., Munzert, P., Ghazaryan, L., van Helvoirt, C., Kessels, W. M. M., Sanli, U. T., Grévent, C., Schütz, G., Putkonen, M., Buchanan, I., Jensen, L., Ristau, D., Tünnermann, A., Szeghalmi, A.

{Optical materials express}, 6(2):660-670, OSA, Washington, DC, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Combined first-order reversal curve and x-ray microscopy investigation of magnetization reversal mechanisms in hexagonal antidot lattices

Gräfe, J., Weigand, M., Stahl, C., Träger, N., Kopp, M., Schütz, G., Goering, E. J., Haering, F., Ziemann, P., Wiedwald, U.

{Physical Review B}, 93(1), American Physical Society, Woodbury, NY, 2016 (article)

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DOI Project Page Project Page [BibTex]

DOI Project Page Project Page [BibTex]


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Switching probabilities of magnetic vortex core reversal studied by table top magneto optic Kerr microscopy

Dieterle, G., Gangwar, A., Gräfe, J., Noske, M., Förster, J., Woltersdorf, G., Stoll, H., Back, C. H., Schütz, G.

{Applied Physics Letters}, 108(2), American Institute of Physics, Melville, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Ultrafast demagnetization after femtosecond laser pulses: Transfer of angular momentum from the electronic system to magnetoelastic spin-phonon modes

Tsatsoulis, T., Illg, C., Haag, M., Müller, B. Y., Zhang, L., Fähnle, M.

{Physical Review B}, 93(13), American Physical Society, Woodbury, NY, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Developments in the Ni-Nb-Zr amorphous alloy membranes

Sarker, S., Chandra, D., Hirscher, M., Dolan, M., Isheim, D., Wermer, J., Viano, D., Baricco, M., Udovic, T. J., Grant, D., Palumbo, O., Paolone, A., Cantelli, R.

{Applied Physics A}, 122(3), Springer-Verlag Heidelberg, Heidelberg, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Resistance to the transport of H2 through the external surface of as-made and modified silicalite-1 (MFI)

Kalantzopoulos, G. N., Policicchio, A., Maccallini, E., Krkljus, I., Ciuchi, F., Hirscher, M., Agostino, R. G., Golemme, G.

{Microporous and Mesoporous Materials}, 220, pages: 290-297, Elsevier, Amsterdam, 2016 (article)

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DOI [BibTex]

DOI [BibTex]


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Observation of pseudopartial grain boundary wetting in the NdFeB-based alloy

Straumal, B. B., Mazilkin, A. A., Protasova, S. G., Schütz, G., Straumal, A. B., Baretzky, B.

{Journal of Materials Engineering and Performance}, 25(8):3303-3309, 2016 (article)

mms

DOI [BibTex]

DOI [BibTex]

2007


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A Tutorial on Spectral Clustering

von Luxburg, U.

Statistics and Computing, 17(4):395-416, December 2007 (article)

Abstract
In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. On the first glance spectral clustering appears slightly mysterious, and it is not obvious to see why it works at all and what it really does. The goal of this tutorial is to give some intuition on those questions. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.

ei

PDF PDF DOI [BibTex]

2007


PDF PDF DOI [BibTex]


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A Tutorial on Kernel Methods for Categorization

Jäkel, F., Schölkopf, B., Wichmann, F.

Journal of Mathematical Psychology, 51(6):343-358, December 2007 (article)

Abstract
The abilities to learn and to categorize are fundamental for cognitive systems, be it animals or machines, and therefore have attracted attention from engineers and psychologists alike. Modern machine learning methods and psychological models of categorization are remarkably similar, partly because these two fields share a common history in artificial neural networks and reinforcement learning. However, machine learning is now an independent and mature field that has moved beyond psychologically or neurally inspired algorithms towards providing foundations for a theory of learning that is rooted in statistics and functional analysis. Much of this research is potentially interesting for psychological theories of learning and categorization but also hardly accessible for psychologists. Here, we provide a tutorial introduction to a popular class of machine learning tools, called kernel methods. These methods are closely related to perceptrons, radial-basis-function neural networks and exemplar theories of catego rization. Recent theoretical advances in machine learning are closely tied to the idea that the similarity of patterns can be encapsulated in a positive definite kernel. Such a positive definite kernel can define a reproducing kernel Hilbert space which allows one to use powerful tools from functional analysis for the analysis of learning algorithms. We give basic explanations of some key concepts—the so-called kernel trick, the representer theorem and regularization—which may open up the possibility that insights from machine learning can feed back into psychology.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Accurate Splice site Prediction Using Support Vector Machines

Sonnenburg, S., Schweikert, G., Philips, P., Behr, J., Rätsch, G.

BMC Bioinformatics, 8(Supplement 10):1-16, December 2007 (article)

Abstract
Background: For splice site recognition, one has to solve two classification problems: discriminating true from decoy splice sites for both acceptor and donor sites. Gene finding systems typically rely on Markov Chains to solve these tasks. Results: In this work we consider Support Vector Machines for splice site recognition. We employ the so-called weighted degree kernel which turns out well suited for this task, as we will illustrate in several experiments where we compare its prediction accuracy with that of recently proposed systems. We apply our method to the genome-wide recognition of splice sites in Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, Danio rerio, and Homo sapiens. Our performance estimates indicate that splice sites can be recognized very accurately in these genomes and that our method outperforms many other methods including Markov Chains, GeneSplicer and SpliceMachine. We provide genome-wide predictions of splice sites and a stand-alone prediction tool ready to be used for incorporation in a gene finder. Availability: Data, splits, additional information on the model selection, the whole genome predictions, as well as the stand-alone prediction tool are available for download at http:// www.fml.mpg.de/raetsch/projects/splice.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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A unifying framework for robot control with redundant DOFs

Peters, J., Mistry, M., Udwadia, F., Nakanishi, J., Schaal, S.

Autonomous Robots, 24(1):1-12, October 2007 (article)

Abstract
Recently, Udwadia (Proc. R. Soc. Lond. A 2003:1783–1800, 2003) suggested to derive tracking controllers for mechanical systems with redundant degrees-of-freedom (DOFs) using a generalization of Gauss’ principle of least constraint. This method allows reformulating control problems as a special class of optimal controllers. In this paper, we take this line of reasoning one step further and demonstrate that several well-known and also novel nonlinear robot control laws can be derived from this generic methodology. We show experimental verifications on a Sarcos Master Arm robot for some of the derived controllers. The suggested approach offers a promising unification and simplification of nonlinear control law design for robots obeying rigid body dynamics equations, both with or without external constraints, with over-actuation or underactuation, as well as open-chain and closed-chain kinematics.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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The Need for Open Source Software in Machine Learning

Sonnenburg, S., Braun, M., Ong, C., Bengio, S., Bottou, L., Holmes, G., LeCun, Y., Müller, K., Pereira, F., Rasmussen, C., Rätsch, G., Schölkopf, B., Smola, A., Vincent, P., Weston, J., Williamson, R.

Journal of Machine Learning Research, 8, pages: 2443-2466, October 2007 (article)

Abstract
Open source tools have recently reached a level of maturity which makes them suitable for building large-scale real-world systems. At the same time, the field of machine learning has developed a large body of powerful learning algorithms for diverse applications. However, the true potential of these methods is not realized, since existing implementations are not openly shared, resulting in software with low usability, and weak interoperability. We argue that this situation can be significantly improved by increasing incentives for researchers to publish their software under an open source model. Additionally, we outline the problems authors are faced with when trying to publish algorithmic implementations of machine learning methods. We believe that a resource of peer reviewed software accompanied by short articles would be highly valuable to both the machine learning and the general scientific community.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Some observations on the masking effects of Mach bands

Curnow, T., Cowie, DA., Henning, GB., Hill, NJ.

Journal of the Optical Society of America A, 24(10):3233-3241, October 2007 (article)

Abstract
There are 8 cycle / deg ripples or oscillations in performance as a function of location near Mach bands in experiments measuring Mach bands’ masking effects on random polarity signal bars. The oscillations with increments are 180 degrees out of phase with those for decrements. The oscillations, much larger than the measurement error, appear to relate to the weighting function of the spatial-frequency-tuned channel detecting the broad- band signals. The ripples disappear with step maskers and become much smaller at durations below 25 ms, implying either that the site of masking has changed or that the weighting function and hence spatial-frequency tuning is slow to develop.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Mining complex genotypic features for predicting HIV-1 drug resistance

Saigo, H., Uno, T., Tsuda, K.

Bioinformatics, 23(18):2455-2462, September 2007 (article)

Abstract
Human immunodeficiency virus type 1 (HIV-1) evolves in human body, and its exposure to a drug often causes mutations that enhance the resistance against the drug. To design an effective pharmacotherapy for an individual patient, it is important to accurately predict the drug resistance based on genotype data. Notably, the resistance is not just the simple sum of the effects of all mutations. Structural biological studies suggest that the association of mutations is crucial: Even if mutations A or B alone do not affect the resistance, a significant change might happen when the two mutations occur together. Linear regression methods cannot take the associations into account, while decision tree methods can reveal only limited associations. Kernel methods and neural networks implicitly use all possible associations for prediction, but cannot select salient associations explicitly. Our method, itemset boosting, performs linear regression in the complete space of power sets of mutations. It implements a forward feature selection procedure where, in each iteration, one mutation combination is found by an efficient branch-and-bound search. This method uses all possible combinations, and salient associations are explicitly shown. In experiments, our method worked particularly well for predicting the resistance of nucleotide reverse transcriptase inhibitors (NRTIs). Furthermore, it successfully recovered many mutation associations known in biological literature.

ei

Web DOI [BibTex]

Web DOI [BibTex]