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2007


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PALMA: mRNA to Genome Alignments using Large Margin Algorithms

Schulze, U., Hepp, B., Ong, C., Rätsch, G.

Bioinformatics, 23(15):1892-1900, May 2007 (article)

Abstract
Motivation: Despite many years of research on how to properly align sequences in the presence of sequencing errors, alternative splicing and micro-exons, the correct alignment of mRNA sequences to genomic DNA is still a challenging task. Results: We present a novel approach based on large margin learning that combines accurate plice site predictions with common sequence alignment techniques. By solving a convex optimization problem, our algorithm – called PALMA – tunes the parameters of the model such that true alignments score higher than other alignments. We study the accuracy of alignments of mRNAs containing artificially generated micro-exons to genomic DNA. In a carefully designed experiment, we show that our algorithm accurately identifies the intron boundaries as well as boundaries of the optimal local alignment. It outperforms all other methods: for 5702 artificially shortened EST sequences from C. elegans and human it correctly identifies the intron boundaries in all except two cases. The best other method is a recently proposed method called exalin which misaligns 37 of the sequences. Our method also demonstrates robustness to mutations, insertions and deletions, retaining accuracy even at high noise levels. Availability: Datasets for training, evaluation and testing, additional results and a stand-alone alignment tool implemented in C++ and python are available at http://www.fml.mpg.de/raetsch/projects/palma.

ei

Web DOI [BibTex]

2007


Web DOI [BibTex]


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Cluster Identification in Nearest-Neighbor Graphs

Maier, M., Hein, M., von Luxburg, U.

(163), Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany, May 2007 (techreport)

Abstract
Assume we are given a sample of points from some underlying distribution which contains several distinct clusters. Our goal is to construct a neighborhood graph on the sample points such that clusters are ``identified‘‘: that is, the subgraph induced by points from the same cluster is connected, while subgraphs corresponding to different clusters are not connected to each other. We derive bounds on the probability that cluster identification is successful, and use them to predict ``optimal‘‘ values of k for the mutual and symmetric k-nearest-neighbor graphs. We point out different properties of the mutual and symmetric nearest-neighbor graphs related to the cluster identification problem.

ei

PDF [BibTex]

PDF [BibTex]


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Training a Support Vector Machine in the Primal

Chapelle, O.

Neural Computation, 19(5):1155-1178, March 2007 (article)

Abstract
Most literature on Support Vector Machines (SVMs) concentrate on the dual optimization problem. In this paper, we would like to point out that the primal problem can also be solved efficiently, both for linear and non-linear SVMs, and that there is no reason for ignoring this possibilty. On the contrary, from the primal point of view new families of algorithms for large scale SVM training can be investigated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Dirichlet Mixtures of Bayesian Linear Gaussian State-Space Models: a Variational Approach

Chiappa, S., Barber, D.

(161), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, March 2007 (techreport)

Abstract
We describe two related models to cluster multidimensional time-series under the assumption of an underlying linear Gaussian dynamical process. In the first model, times-series are assigned to the same cluster when they show global similarity in their dynamics, while in the second model times-series are assigned to the same cluster when they show simultaneous similarity. Both models are based on Dirichlet Mixtures of Bayesian Linear Gaussian State-Space Models in order to (semi) automatically determine an appropriate number of components in the mixture, and to additionally bias the components to a parsimonious parameterization. The resulting models are formally intractable and to deal with this we describe a deterministic approximation based on a novel implementation of Variational Bayes.

ei

PDF [BibTex]

PDF [BibTex]


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Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Rätsch, G., Sonnenburg, S., Srinivasan, J., Witte, H., Müller, K., Sommer, R., Schölkopf, B.

PLoS Computational Biology, 3(2, e20):0313-0322, February 2007 (article)

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Automatic 3D Face Reconstruction from Single Images or Video

Breuer, P., Kim, K., Kienzle, W., Blanz, V., Schölkopf, B.

(160), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, February 2007 (techreport)

Abstract
This paper presents a fully automated algorithm for reconstructing a textured 3D model of a face from a single photograph or a raw video stream. The algorithm is based on a combination of Support Vector Machines (SVMs) and a Morphable Model of 3D faces. After SVM face detection, individual facial features are detected using a novel regression-and classification-based approach, and probabilistically plausible configurations of features are selected to produce a list of candidates for several facial feature positions. In the next step, the configurations of feature points are evaluated using a novel criterion that is based on a Morphable Model and a combination of linear projections. Finally, the feature points initialize a model-fitting procedure of the Morphable Model. The result is a high-resolution 3D surface model.

ei

PDF [BibTex]

PDF [BibTex]


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Statistical Consistency of Kernel Canonical Correlation Analysis

Fukumizu, K., Bach, F., Gretton, A.

Journal of Machine Learning Research, 8, pages: 361-383, February 2007 (article)

Abstract
While kernel canonical correlation analysis (CCA) has been applied in many contexts, the convergence of finite sample estimates of the associated functions to their population counterparts has not yet been established. This paper gives a mathematical proof of the statistical convergence of kernel CCA, providing a theoretical justification for the method. The proof uses covariance operators defined on reproducing kernel Hilbert spaces, and analyzes the convergence of their empirical estimates of finite rank to their population counterparts, which can have infinite rank. The result also gives a sufficient condition for convergence on the regularization coefficient involved in kernel CCA: this should decrease as n^{-1/3}, where n is the number of data.

ei

PDF [BibTex]

PDF [BibTex]


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Some observations on the pedestal effect

Henning, G., Wichmann, F.

Journal of Vision, 7(1:3):1-15, January 2007 (article)

Abstract
The pedestal or dipper effect is the large improvement in the detectability of a sinusoidal grating observed when it is added to a masking or pedestal grating of the same spatial frequency, orientation, and phase. We measured the pedestal effect in both broadband and notched noiseVnoise from which a 1.5-octave band centered on the signal frequency had been removed. Although the pedestal effect persists in broadband noise, it almost disappears in the notched noise. Furthermore, the pedestal effect is substantial when either high- or low-pass masking noise is used. We conclude that the pedestal effect in the absence of notched noise results principally from the use of information derived from channels with peak sensitivities at spatial frequencies different from that of the signal and the pedestal. We speculate that the spatial-frequency components of the notched noise above and below the spatial frequency of the signal and the pedestal prevent ‘‘off-frequency looking,’’ that is, prevent the use of information about changes in contrast carried in channels tuned to spatial frequencies that are very much different from that of the signal and the pedestal. Thus, the pedestal or dipper effect measured without notched noise appears not to be a characteristic of individual spatial-frequency-tuned channels.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Cue Combination and the Effect of Horizontal Disparity and Perspective on Stereoacuity

Zalevski, AM., Henning, GB., Hill, NJ.

Spatial Vision, 20(1):107-138, January 2007 (article)

Abstract
Relative depth judgments of vertical lines based on horizontal disparity deteriorate enormously when the lines form part of closed configurations (Westheimer, 1979). In studies showing this effect, perspective was not manipulated and thus produced inconsistency between horizontal disparity and perspective. We show that stereoacuity improves dramatically when perspective and horizontal disparity are made consistent. Observers appear to use unhelpful perspective cues in judging the relative depth of the vertical sides of rectangles in a way not incompatible with a form of cue weighting. However, 95% confidence intervals for the weights derived for cues usually exceed the a-priori [0-1] range.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Frequency-domain displacement sensing with a fiber ring-resonator containing a variable gap

Vollmer, F., Fischer, P.

SENSORS AND ACTUATORS A-PHYSICAL, 134(2):410-413, 2007 (article)

Abstract
Ring-resonators are in general not amenable to strain-free (non-contact) displacement measurements. We show that this limitation may be overcome if the ring-resonator, here a fiber-loop, is designed to contain a gap, such that the light traverses a free-space part between two aligned waveguide ends. Displacements are determined with nanometer sensitivity by measuring the associated changes in the resonance frequencies. Miniaturization should increase the sensitivity of the ring-resonator interferometer. Ring geometries that contain an optical circulator can be used to profile reflective samples. (c) 2006 Elsevier B.V. All rights reserved.

pf

DOI [BibTex]

DOI [BibTex]


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Relative Entropy Policy Search

Peters, J.

CLMC Technical Report: TR-CLMC-2007-2, Computational Learning and Motor Control Lab, Los Angeles, CA, 2007, clmc (techreport)

Abstract
This technical report describes a cute idea of how to create new policy search approaches. It directly relates to the Natural Actor-Critic methods but allows the derivation of one shot solutions. Future work may include the application to interesting problems.

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PDF link (url) [BibTex]

PDF link (url) [BibTex]


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Observation of the Faraday effect via beam deflection in a longitudinal magnetic field

Ghosh, A., Hill, W., Fischer, P.

PHYSICAL REVIEW A, 76(5), 2007 (article)

Abstract
We show that magnetic-field-induced circular differential deflection of light can be observed in reflection or refraction at a single interface. The difference in the reflection or refraction angles between the two circular polarization components is a function of the magnetic-field strength and the Verdet constant, and permits the observation of the Faraday effect not via polarization rotation in transmission, but via changes in the propagation direction. Deflection measurements do not suffer from n-pi ambiguities and are shown to be another means to map magnetic fields with high axial resolution, or to determine the sign and magnitude of magnetic-field pulses in a single measurement.

pf

DOI [BibTex]


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Circular differential double diffraction in chiral media

Ghosh, A., Fazal, F. M., Fischer, P.

OPTICS LETTERS, 32(13):1836-1838, 2007 (article)

Abstract
In an optically active liquid the diffraction angle depends on the circular polarization state of the incident light beam. We report the observation of circular differential diffraction in an isotropic chiral medium, and we demonstrate that double diffraction is an alternate means to determine the handedness (enantiomeric excess) of a solution. (c) 2007 Optical Society of America.

pf

DOI [BibTex]

DOI [BibTex]


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Bacterial flagella-based propulsion and on/off motion control of microscale objects

Behkam, B., Sitti, M.

Applied Physics Letters, 90(2):023902, AIP, 2007 (article)

pi

[BibTex]

[BibTex]


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Friction of partially embedded vertically aligned carbon nanofibers inside elastomers

Aksak, B., Sitti, M., Cassell, A., Li, J., Meyyappan, M., Callen, P.

Applied Physics Letters, 91(6):061906, AIP, 2007 (article)

pi

[BibTex]

[BibTex]


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Enhanced friction of elastomer microfiber adhesives with spatulate tips

Kim, S., Aksak, B., Sitti, M.

Applied Physics Letters, 91(22):221913, AIP, 2007 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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The new robotics - towards human-centered machines

Schaal, S.

HFSP Journal Frontiers of Interdisciplinary Research in the Life Sciences, 1(2):115-126, 2007, clmc (article)

Abstract
Research in robotics has moved away from its primary focus on industrial applications. The New Robotics is a vision that has been developed in past years by our own university and many other national and international research instiutions and addresses how increasingly more human-like robots can live among us and take over tasks where our current society has shortcomings. Elder care, physical therapy, child education, search and rescue, and general assistance in daily life situations are some of the examples that will benefit from the New Robotics in the near future. With these goals in mind, research for the New Robotics has to embrace a broad interdisciplinary approach, ranging from traditional mathematical issues of robotics to novel issues in psychology, neuroscience, and ethics. This paper outlines some of the important research problems that will need to be resolved to make the New Robotics a reality.

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link (url) [BibTex]

link (url) [BibTex]


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Hydrogen storage in metal-organic frameworks

Hirscher, M., Panella, B.

{Scripta Materialia}, 56, pages: 809-812, 2007 (article)

mms

[BibTex]

[BibTex]


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Substrate-induced current anisotropy in YBa2Cu3O7-δthin films

Djupmyr, M., Albrecht, J.

{Physica C}, 460-462, pages: 1190-1191, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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A micellar approach to magnetic ultrahigh-density data-storage media: extending the limits of current colloidal methods

Ethirajan, A., Wiedwald, U., Boyen, H.-G., Kern, B., Han, L., Klimmer, A., Weigl, F., Kästle, G., Ziemann, P., Fauth, K., Cai, J., Behm, J., Romanyuk, A., Oelhafen, P., Walther, P., Biskupek, J., Kaiser, U.

{Advanced Materials}, 19, pages: 406-410, 2007 (article)

mms

[BibTex]

[BibTex]


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Size dependence in the magnetization reversal of Fe/Gd multilayers on self-assembled arrays of nanospheres

Amaladass, E., Ludescher, B., Schütz, G., Tyliszczak, T., Eimüller, T.

{Applied Physics Letters}, 91, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Ma\ssgeschneiderte Wasserstoffspeicher

Hirscher, M., Panella, B.

{Nachrichten aus der Gdch-Energieinitiative}, (Sonderheft April 2007):12-13, 2007 (article)

mms

[BibTex]

[BibTex]


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Reconstruction of historical alloys for pipe organs brings true Baroque music back to life.

Baretzky, B., Friesel, M., Straumal, B.

{MRS Bulletin}, 32, pages: 249-255, 2007 (article)

mms

[BibTex]

[BibTex]


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Analysis of results from X-ray magnetic reflectometry for magnetic multilayer systems

Fähnle, M., Steiauf, D., Martosiswoyo, L., Goering, E., Brück, S., Schütz, G.

{Physical Review B}, 75, 2007 (article)

mms

[BibTex]

[BibTex]


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Dramatic role of critical current anisotropy on flux avalanches in MgB2 films

Albrecht, J., Matveev, A. T., Strempfer, J., Habermeier, H.-U., Shantsev, D. V., Galperin, Y. M., Johansen, T. H.

{Physical Review Letters}, 98, 2007 (article)

mms

[BibTex]

[BibTex]


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Transport properties of LCMO/YBCO hybrid structures

Soltan, S., Albrecht, J., Habermeier, H.-U.

{Materials Science and Engineering B}, 144, pages: 15-18, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Microscale and nanoscale robotics systems [grand challenges of robotics]

Sitti, M.

IEEE Robotics \& Automation Magazine, 14(1):53-60, IEEE, 2007 (article)

pi

[BibTex]

[BibTex]


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A new biomimetic adhesive for therapeutic capsule endoscope applications in the gastrointestinal tract

Glass, P., Sitti, M., Appasamy, R.

Gastrointestinal Endoscopy, 65(5):AB91, Mosby, 2007 (article)

pi

[BibTex]

[BibTex]


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Visual servoing-based autonomous 2-D manipulation of microparticles using a nanoprobe

Onal, C. D., Sitti, M.

IEEE Transactions on control systems technology, 15(5):842-852, IEEE, 2007 (article)

pi

[BibTex]

[BibTex]


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Cluster expansions in multicomponent systems: precise expansions from noisy databases

Diaz-Ortiz, A., Dosch, H., Drautz, R.

{Journal of Physics: Condensed Matter}, 19, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Unusual propagation of magnetic avalanches in gold covered MgB2

Albrecht, J., Matveev, A. T., Habermeier, H.-U.

{Physica C}, 460-462, pages: 1245-1246, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Lowering of the L10 ordering temperature of FePt nanoparticles by He+ ion irradiation

Wiedwald, U., Klimmer, A., Kern, B., Han, L., Boyen, H.-G., Ziemann, P., Fauth, K.

{Applied Physics Letters}, 90, 2007 (article)

mms

[BibTex]

[BibTex]


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Magnetic core shell nanoparticles characterized by X-ray absorption and magnetic circular dichroism

Fauth, K.

{Modern Physics Letters B}, 21(18):1179-1187, 2007 (article)

mms

[BibTex]

[BibTex]


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Magnetic moment of Fe in oxide-free FePt nanoparticles

Dmitrieva, O., Spasova, M., Antoniak, C., Acet, M., Dumpich, G., Kästner, J., Farle, M., Fauth, K., Wiedwald, U., Boyen, H.-G., Ziemann, P.

{Physical Review B}, 76, 2007 (article)

mms

[BibTex]

[BibTex]


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The effect of bismuth segregation on the faceting of \Sigma3 and \Sigma9 coincidence boundaries in copper bicrystals

Straumal, B. B., Polyakov, S. A., Chang, L.-S., Mittemeijer, E. J.

{International Journal of Materials Research}, 98, pages: 451-456, 2007 (article)

mms

[BibTex]

[BibTex]


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Hot isostatic pressing of Cu-Bi polycrystals with liquid-like grain boundary layers

Chang, L.-S., Straumal, B., Rabkin, E., Lojkowski, W., Gust, W.

{Acta Materialia}, 55, pages: 335-343, 2007 (article)

mms

[BibTex]

[BibTex]


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Spatially resolved magnetic response in core shell nanoparticles

Fauth, K., Goering, E., Theil Kuhn, L.

{Modern Physics Letters B}, 21(18):1197-1200, 2007 (article)

mms

[BibTex]

[BibTex]


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Interfaces in semiconductor/metal radial superlattices

Deneke, C., Sigle, W., Eigenthaler, U., van Aken, P. A., Schütz, G., Schmidt, O. G.

{Applied Physics Letters}, 90, 2007 (article)

mms

[BibTex]

[BibTex]


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Live cell adhesion assay with attenuated total reflection infrared spectroscopy

Schmidt, M., Wolfram, T., Rumpler, M., Tripp, C. P., Grunze, M.

{Biointerphases}, 2(1):1-5, 2007 (article)

mms

[BibTex]

[BibTex]


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Unusual Co moment reduction in the NiCoO/Co exchange bias system

Brück, S., Goering, E., Tang, Y. J., Schütz, G., Berkowitz, A. E.

{Journal of Magnetism and Magnetic Materials}, 310, pages: 2316-2318, 2007 (article)

mms

[BibTex]

[BibTex]


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Adhesion of biologically inspired vertical and angled polymer microfiber arrays

Aksak, B., Murphy, M. P., Sitti, M.

Langmuir, 23(6):3322-3332, ACS Publications, 2007 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Waalbot: An agile small-scale wall-climbing robot utilizing dry elastomer adhesives

Murphy, M. P., Sitti, M.

IEEE/ASME transactions on Mechatronics, 12(3):330-338, IEEE, 2007 (article)

pi

[BibTex]

[BibTex]


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Ab initio calculations of adiabatic magnon spectra using the atomic-sphere aproximation for the spin direction

Singer, R., Dietermann, F., Steiauf, D., Fähnle, M.

{Physical Review B}, 76, 2007 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Low-temperature thermal-desorption mass spectroscopy applied to investigate the hydrogen adsorption on porous materials

Panella, B., Hirscher, M., Ludescher, B.

{Microporous and Mesoporous Materials}, 103, pages: 230-234, 2007 (article)

mms

[BibTex]


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Dependence of the critical temperature of YBCO thin films on spinpolarized quasiparticle injection

Habermeier, H.-U., Soltan, S., Albrecht, J.

{International Journal of Modern Physics B}, 21(18 \& 19):3303-3306, 2007 (article)

mms

[BibTex]

[BibTex]