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2009


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Constructing Sparse Kernel Machines Using Attractors

Lee, D., Jung, K., Lee, J.

IEEE Transactions on Neural Networks, 20(4):721-729, April 2009 (article)

Abstract
In this brief, a novel method that constructs a sparse kernel machine is proposed. The proposed method generates attractors as sparse solutions from a built-in kernel machine via a dynamical system framework. By readjusting the corresponding coefficients and bias terms, a sparse kernel machine that approximates a conventional kernel machine is constructed. The simulation results show that the constructed sparse kernel machine improves the efficiency of testing phase while maintaining comparable test error.

ei

Web DOI [BibTex]

2009


Web DOI [BibTex]


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Optimal construction of k-nearest-neighbor graphs for identifying noisy clusters

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

Theoretical Computer Science, 410(19):1749-1764, April 2009 (article)

Abstract
We study clustering algorithms based on neighborhood graphs on a random sample of data points. The question we ask is how such a graph should be constructed in order to obtain optimal clustering results. Which type of neighborhood graph should one choose, mutual k-nearest-neighbor or symmetric k-nearest-neighbor? What is the optimal parameter k? In our setting, clusters are defined as connected components of the t-level set of the underlying probability distribution. Clusters are said to be identified in the neighborhood graph if connected components in the graph correspond to the true underlying clusters. Using techniques from random geometric graph theory, we prove bounds on the probability that clusters are identified successfully, both in a noise-free and in a noisy setting. Those bounds lead to several conclusions. First, k has to be chosen surprisingly high (rather of the order n than of the order logn) to maximize the probability of cluster identification. Secondly, the major difference between the mutual and the symmetric k-nearest-neighbor graph occurs when one attempts to detect the most significant cluster only.

ei

PDF PDF DOI [BibTex]


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Overlap and refractory effects in a Brain-Computer Interface speller based on the visual P300 Event-Related Potential

Martens, S., Hill, N., Farquhar, J., Schölkopf, B.

Journal of Neural Engineering, 6(2):1-9, April 2009 (article)

Abstract
We reveal the presence of refractory and overlap effects in the event-related potentials in visual P300 speller datasets, and we show their negative impact on the performance of the system. This finding has important implications for how to encode the letters that can be selected for communication. However, we show that such effects are dependent on stimulus parameters: an alternative stimulus type based on apparent motion suffers less from the refractory effects and leads to an improved letter prediction performance.

ei

PDF DOI [BibTex]


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Nearest Neighbor Clustering: A Baseline Method for Consistent Clustering with Arbitrary Objective Functions

Bubeck, S., von Luxburg, U.

Journal of Machine Learning Research, 10, pages: 657-698, March 2009 (article)

Abstract
Clustering is often formulated as a discrete optimization problem. The objective is to find, among all partitions of the data set, the best one according to some quality measure. However, in the statistical setting where we assume that the finite data set has been sampled from some underlying space, the goal is not to find the best partition of the given sample, but to approximate the true partition of the underlying space. We argue that the discrete optimization approach usually does not achieve this goal, and instead can lead to inconsistency. We construct examples which provably have this behavior. As in the case of supervised learning, the cure is to restrict the size of the function classes under consideration. For appropriate “small” function classes we can prove very general consistency theorems for clustering optimization schemes. As one particular algorithm for clustering with a restricted function space we introduce “nearest neighbor clustering”. Similar to the k-nearest neighbor classifier in supervised learning, this algorithm can be seen as a general baseline algorithm to minimize arbitrary clustering objective functions. We prove that it is statistically consistent for all commonly used clustering objective functions.

ei

PDF Web [BibTex]


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Protein Functional Class Prediction With a Combined Graph

Shin, H., Tsuda, K., Schölkopf, B.

Expert Systems with Applications, 36(2):3284-3292, March 2009 (article)

Abstract
In bioinformatics, there exist multiple descriptions of graphs for the same set of genes or proteins. For instance, in yeast systems, graph edges can represent different relationships such as protein–protein interactions, genetic interactions, or co-participation in a protein complex, etc. Relying on similarities between nodes, each graph can be used independently for prediction of protein function. However, since different graphs contain partly independent and partly complementary information about the problem at hand, one can enhance the total information extracted by combining all graphs. In this paper, we propose a method for integrating multiple graphs within a framework of semi-supervised learning. The method alternates between minimizing the objective function with respect to network output and with respect to combining weights. We apply the method to the task of protein functional class prediction in yeast. The proposed method performs significantly better than the same algorithm trained on any singl e graph.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Gaussian Process Dynamic Programming

Deisenroth, M., Rasmussen, C., Peters, J.

Neurocomputing, 72(7-9):1508-1524, March 2009 (article)

Abstract
Reinforcement learning (RL) and optimal control of systems with contin- uous states and actions require approximation techniques in most interesting cases. In this article, we introduce Gaussian process dynamic programming (GPDP), an approximate value-function based RL algorithm. We consider both a classic optimal control problem, where problem-specific prior knowl- edge is available, and a classic RL problem, where only very general priors can be used. For the classic optimal control problem, GPDP models the unknown value functions with Gaussian processes and generalizes dynamic programming to continuous-valued states and actions. For the RL problem, GPDP starts from a given initial state and explores the state space using Bayesian active learning. To design a fast learner, available data has to be used efficiently. Hence, we propose to learn probabilistic models of the a priori unknown transition dynamics and the value functions on the fly. In both cases, we successfully apply the resulting continuous-valued controllers to the under-actuated pendulum swing up and analyze the performances of the suggested algorithms. It turns out that GPDP uses data very efficiently and can be applied to problems, where classic dynamic programming would be cumbersome.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Towards quantitative PET/MRI: a review of MR-based attenuation correction techniques

Hofmann, M., Pichler, B., Schölkopf, B., Beyer, T.

European Journal of Nuclear Medicine and Molecular Imaging, 36(Supplement 1):93-104, March 2009 (article)

Abstract
Introduction Positron emission tomography (PET) is a fully quantitative technology for imaging metabolic pathways and dynamic processes in vivo. Attenuation correction of raw PET data is a prerequisite for quantification and is typically based on separate transmission measurements. In PET/CT attenuation correction, however, is performed routinely based on the available CT transmission data. Objective Recently, combined PET/magnetic resonance (MR) has been proposed as a viable alternative to PET/CT. Current concepts of PET/MRI do not include CT-like transmission sources and, therefore, alternative methods of PET attenuation correction must be found. This article reviews existing approaches to MR-based attenuation correction (MR-AC). Most groups have proposed MR-AC algorithms for brain PET studies and more recently also for torso PET/MR imaging. Most MR-AC strategies require the use of complementary MR and transmission images, or morphology templates generated from transmission images. We review and discuss these algorithms and point out challenges for using MR-AC in clinical routine. Discussion MR-AC is work-in-progress with potentially promising results from a template-based approach applicable to both brain and torso imaging. While efforts are ongoing in making clinically viable MR-AC fully automatic, further studies are required to realize the potential benefits of MR-based motion compensation and partial volume correction of the PET data.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Generating Spike Trains with Specified Correlation Coefficients

Macke, J., Berens, P., Ecker, A., Tolias, A., Bethge, M.

Neural Computation, 21(2):397-423, February 2009 (article)

Abstract
Spike trains recorded from populations of neurons can exhibit substantial pairwise correlations between neurons and rich temporal structure. Thus, for the realistic simulation and analysis of neural systems, it is essential to have efficient methods for generating artificial spike trains with specified correlation structure. Here we show how correlated binary spike trains can be simulated by means of a latent multivariate gaussian model. Sampling from the model is computationally very efficient and, in particular, feasible even for large populations of neurons. The entropy of the model is close to the theoretical maximum for a wide range of parameters. In addition, this framework naturally extends to correlations over time and offers an elegant way to model correlated neural spike counts with arbitrary marginal distributions.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Automatic detection of preclinical neurodegeneration: Presymptomatic Huntington disease

Klöppel, S., Chu, C., Tan, G., Draganski, B., Johnson, H., Paulsen, J., Kienzle, W., Tabrizi, S., Ashburner, J., Frackowiak, R.

Neurology, 72(5):426-431, February 2009 (article)

Abstract
Background: Treatment of neurodegenerative diseases is likely to be most beneficial in the very early, possibly preclinical stages of degeneration. We explored the usefulness of fully automatic structural MRI classification methods for detecting subtle degenerative change. The availability of a definitive genetic test for Huntington disease (HD) provides an excellent metric for judging the performance of such methods in gene mutation carriers who are free of symptoms. Methods: Using the gray matter segment of MRI scans, this study explored the usefulness of a multivariate support vector machine to automatically identify presymptomatic HD gene mutation carriers (PSCs) in the absence of any a priori information. A multicenter data set of 96 PSCs and 95 age- and sex-matched controls was studied. The PSC group was subclassified into three groups based on time from predicted clinical onset, an estimate that is a function of DNA mutation size and age. Results: Subjects with at least a 33% chance of developing unequivocal signs of HD in 5 years were correctly assigned to the PSC group 69% of the time. Accuracy improved to 83% when regions affected by the disease were selected a priori for analysis. Performance was at chance when the probability of developing symptoms in 5 years was less than 10%. Conclusions: Presymptomatic Huntington disease gene mutation carriers close to estimated diagnostic onset were successfully separated from controls on the basis of single anatomic scans, without additional a priori information. Prior information is required to allow separation when degenerative changes are either subtle or variable.

ei

Web [BibTex]

Web [BibTex]


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Enumeration of condition-dependent dense modules in protein interaction networks

Georgii, E., Dietmann, S., Uno, T., Pagel, P., Tsuda, K.

Bioinformatics, 25(7):933-940, February 2009 (article)

Abstract
Motivation: Modern systems biology aims at understanding how the different molecular components of a biological cell interact. Often, cellular functions are performed by complexes consisting of many different proteins. The composition of these complexes may change according to the cellular environment, and one protein may be involved in several different processes. The automatic discovery of functional complexes from protein interaction data is challenging. While previous approaches use approximations to extract dense modules, our approach exactly solves the problem of dense module enumeration. Furthermore, constraints from additional information sources such as gene expression and phenotype data can be integrated, so we can systematically mine for dense modules with interesting profiles. Results: Given a weighted protein interaction network, our method discovers all protein sets that satisfy a user-defined minimum density threshold. We employ a reverse search strategy, which allows us to exploit the density criterion in an efficient way. Our experiments show that the novel approach is feasible and produces biologically meaningful results. In comparative validation studies using yeast data, the method achieved the best overall prediction performance with respect to confirmed complexes. Moreover, by enhancing the yeast network with phenotypic and phylogenetic profiles and the human network with tissue-specific expression data, we identified condition-dependent complex variants.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Prototype Classification: Insights from Machine Learning

Graf, A., Bousquet, O., Rätsch, G., Schölkopf, B.

Neural Computation, 21(1):272-300, January 2009 (article)

Abstract
We shed light on the discrimination between patterns belonging to two different classes by casting this decoding problem into a generalized prototype framework. The discrimination process is then separated into two stages: a projection stage that reduces the dimensionality of the data by projecting it on a line and a threshold stage where the distributions of the projected patterns of both classes are separated. For this, we extend the popular mean-of-class prototype classification using algorithms from machine learning that satisfy a set of invariance properties. We report a simple yet general approach to express different types of linear classification algorithms in an identical and easy-to-visualize formal framework using generalized prototypes where these prototypes are used to express the normal vector and offset of the hyperplane. We investigate nonmargin classifiers such as the classical prototype classifier, the Fisher classifier, and the relevance vector machine. We then study hard and soft margin cl assifiers such as the support vector machine and a boosted version of the prototype classifier. Subsequently, we relate mean-of-class prototype classification to other classification algorithms by showing that the prototype classifier is a limit of any soft margin classifier and that boosting a prototype classifier yields the support vector machine. While giving novel insights into classification per se by presenting a common and unified formalism, our generalized prototype framework also provides an efficient visualization and a principled comparison of machine learning classification.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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The DICS repository: module-assisted analysis of disease-related gene lists

Dietmann, S., Georgii, E., Antonov, A., Tsuda, K., Mewes, H.

Bioinformatics, 25(6):830-831, January 2009 (article)

Abstract
The DICS database is a dynamic web repository of computationally predicted functional modules from the human protein–protein interaction network. It provides references to the CORUM, DrugBank, KEGG and Reactome pathway databases. DICS can be accessed for retrieving sets of overlapping modules and protein complexes that are significantly enriched in a gene list, thereby providing valuable information about the functional context.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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mGene: accurate SVM-based gene finding with an application to nematode genomes

Schweikert, G., Zien, A., Zeller, G., Behr, J., Dieterich, C., Ong, C., Philips, P., De Bona, F., Hartmann, L., Bohlen, A., Krüger, N., Sonnenburg, S., Rätsch, G.

Genome Research, 19(11):2133-43, 2009 (article)

Abstract
We present a highly accurate gene-prediction system for eukaryotic genomes, called mGene. It combines in an unprecedented manner the flexibility of generalized hidden Markov models (gHMMs) with the predictive power of modern machine learning methods, such as Support Vector Machines (SVMs). Its excellent performance was proved in an objective competition based on the genome of the nematode Caenorhabditis elegans. Considering the average of sensitivity and specificity, the developmental version of mGene exhibited the best prediction performance on nucleotide, exon, and transcript level for ab initio and multiple-genome gene-prediction tasks. The fully developed version shows superior performance in 10 out of 12 evaluation criteria compared with the other participating gene finders, including Fgenesh++ and Augustus. An in-depth analysis of mGene's genome-wide predictions revealed that approximately 2200 predicted genes were not contained in the current genome annotation. Testing a subset of 57 of these genes by RT-PCR and sequencing, we confirmed expression for 24 (42%) of them. mGene missed 300 annotated genes, out of which 205 were unconfirmed. RT-PCR testing of 24 of these genes resulted in a success rate of merely 8%. These findings suggest that even the gene catalog of a well-studied organism such as C. elegans can be substantially improved by mGene's predictions. We also provide gene predictions for the four nematodes C. briggsae, C. brenneri, C. japonica, and C. remanei. Comparing the resulting proteomes among these organisms and to the known protein universe, we identified many species-specific gene inventions. In a quality assessment of several available annotations for these genomes, we find that mGene's predictions are most accurate.

ei

DOI [BibTex]

DOI [BibTex]


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Structure and activity of the N-terminal substrate recognition domains in proteasomal ATPases

Djuranovic, S., Hartmann, MD., Habeck, M., Ursinus, A., Zwickl, P., Martin, J., Lupas, AN., Zeth, K.

Molecular Cell, 34(5):580-590, 2009 (article)

Abstract
The proteasome forms the core of the protein quality control system in archaea and eukaryotes and also occurs in one bacterial lineage, the Actinobacteria. Access to its proteolytic compartment is controlled by AAA ATPases, whose N-terminal domains (N domains) are thought to mediate substrate recognition. The N domains of an archaeal proteasomal ATPase, Archaeoglobus fulgidus PAN, and of its actinobacterial homolog, Rhodococcus erythropolis ARC, form hexameric rings, whose subunits consist of an N-terminal coiled coil and a C-terminal OB domain. In ARC-N, the OB domains are duplicated and form separate rings. PAN-N and ARC-N can act as chaperones, preventing the aggregation of heterologous proteins in vitro, and this activity is preserved in various chimeras, even when these include coiled coils and OB domains from unrelated proteins. The structures suggest a molecular mechanism for substrate processing based on concerted radial motions of the coiled coils relative to the OB rings.

ei

DOI [BibTex]

DOI [BibTex]


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Discussion of: Brownian Distance Covariance

Gretton, A., Fukumizu, K., Sriperumbudur, B.

The Annals of Applied Statistics, 3(4):1285-1294, 2009 (article)

ei

[BibTex]

[BibTex]


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Non-linear System Identification: Visual Saliency Inferred from Eye-Movement Data

Wichmann, F., Kienzle, W., Schölkopf, B., Franz, M.

Journal of Vision, 9(8):article 32, 2009 (article)

Abstract
For simple visual patterns under the experimenter's control we impose which information, or features, an observer can use to solve a given perceptual task. For natural vision tasks, however, there are typically a multitude of potential features in a given visual scene which the visual system may be exploiting when analyzing it: edges, corners, contours, etc. Here we describe a novel non-linear system identification technique based on modern machine learning methods that allows the critical features an observer uses to be inferred directly from the observer's data. The method neither requires stimuli to be embedded in noise nor is it limited to linear perceptive fields (classification images). We demonstrate our technique by deriving the critical image features observers fixate in natural scenes (bottom-up visual saliency). Unlike previous studies where the relevant structure is determined manually—e.g. by selecting Gabors as visual filters—we do not make any assumptions in this regard, but numerically infer number and properties them from the eye-movement data. We show that center-surround patterns emerge as the optimal solution for predicting saccade targets from local image structure. The resulting model, a one-layer feed-forward network with contrast gain-control, is surprisingly simple compared to previously suggested saliency models. Nevertheless, our model is equally predictive. Furthermore, our findings are consistent with neurophysiological hardware in the superior colliculus. Bottom-up visual saliency may thus not be computed cortically as has been thought previously.

ei

Web DOI [BibTex]


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mGene.web: a web service for accurate computational gene finding

Schweikert, G., Behr, J., Zien, A., Zeller, G., Ong, C., Sonnenburg, S., Rätsch, G.

Nucleic Acids Research, 37, pages: W312-6, 2009 (article)

Abstract
We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to train the system with their own data for other organisms on the push of a button, a functionality that will greatly accelerate the annotation of newly sequenced genomes. The system is built in a highly modular way, such that individual components of the framework, like the promoter prediction tool or the splice site predictor, can be used autonomously. The underlying gene finding system mGene is based on discriminative machine learning techniques and its high accuracy has been demonstrated in an international competition on nematode genomes. mGene.web is available at http://www.mgene.org/web, it is free of charge and can be used for eukaryotic genomes of small to moderate size (several hundred Mbp).

ei

DOI [BibTex]

DOI [BibTex]


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Full phase and amplitude control in computer-generated holography

Fratz, M., Fischer, P., Giel, D. M.

OPTICS LETTERS, 34(23):3659-3661, 2009 (article)

Abstract
We report what we believe to be the first realization of a computer-generated complex-valued hologram recorded in a single film of photoactive polymer. Complex-valued holograms give rise to a diffracted optical field with control over its amplitude and phase. The holograms are generated by a one-step direct laser writing process in which a spatial light modulator (SLM) is imaged onto a polymer film. Temporal modulation of the SLM during exposure controls both the strength of the induced birefringence and the orientation of the fast axis. We demonstrate that complex holograms can be used to impart arbitrary amplitude and phase profiles onto a beam and thereby open new possibilities in the control of optical beams. (C) 2009 Optical Society of America

pf

[BibTex]

[BibTex]


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Digital polarization holograms with defined magnitude and orientation of each pixel’s birefringence

Fratz, M., Giel, D. M., Fischer, P.

OPTICS LETTERS, 34(8):1270-1272, 2009 (article)

Abstract
A new form of digital polarization holography is demonstrated that permits both the amplitude and the phase of a diffracted beam to be independently controlled. This permits two independent intensity images to be stored in the same hologram. To fabricate the holograms, a birefringence with defined retardance and orientation of the fast axis is recorded into a photopolymer film. The holograms are selectively read out by choosing the polarization state of the read beam. Polarization holograms of this kind increase the data density in holographic data storage and allow higher quality diffractive optical elements to be written. (C) 2009 Optical Society of America

pf

[BibTex]


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Controlled Propulsion of Artificial Magnetic Nanostructured Propellers

Ghosh, A., Fischer, P.

NANO LETTERS, 9(6):2243-2245, 2009, Featured highlight ‘Nanotechnology: The helix that delivers’ Nature 459, 13 (2009). (article)

Abstract
For biomedical applications, such as targeted drug delivery and microsurgery, it is essential to develop a system of swimmers that can be propelled wirelessly in fluidic environments with good control. Here, we report the construction and operation of chiral colloidal propellers that can be navigated in water with micrometer-level precision using homogeneous magnetic fields. The propellers are made via nanostructured surfaces and can be produced in large numbers. The nanopropellers can carry chemicals, push loads, and act as local probes in rheological measurements.

Featured highlight ‘Nanotechnology: The helix that delivers’ Nature 459, 13 (2009).

pf

Video - Nanospropellers DOI [BibTex]

Video - Nanospropellers DOI [BibTex]


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Absolute Asymmetric Reduction Based on the Relative Orientation of Achiral Reactants

Kuhn, A., Fischer, P.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 48(37):6857-6860, 2009 (article)

pf

DOI [BibTex]

DOI [BibTex]


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Magnetic mobile micro-robots

Pawashe, C., Floyd, S., Sitti, M.

7eme Journees Nationales de la Recherche en Robotique, 2009 (article)

pi

[BibTex]

[BibTex]


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Gecko-Inspired Directional and Controllable Adhesion

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

Small, 5(2):170-175, WILEY-VCH Verlag, 2009 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Multiple magnetic microrobot control using electrostatic anchoring

Pawashe, C., Floyd, S., Sitti, M.

Applied Physics Letters, 94(16):164108, AIP, 2009 (article)

pi

[BibTex]

[BibTex]


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Wet self-cleaning of biologically inspired elastomer mushroom shaped microfibrillar adhesives

Kim, S., Cheung, E., Sitti, M.

Langmuir, 25(13):7196-7199, ACS Publications, 2009 (article)

pi

[BibTex]

[BibTex]


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One-dimensional phthalocyanine nanostructures directed by gold templates

Krauss, T. N., Barrena, E., Lohmüller, T., Kelsch, M., Breitling, A., Van Aken, P. A., Spatz, J., Dosch, H.

{Chemistry of Materials}, 21, pages: 5010-5015, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Near-edge X-ray absorption fine-structure microscopy of organic and magnetic materials

Ade, H., Stoll, H.

{Nature Materials}, 8, pages: 281-290, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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X-ray imaging of the dynamic magnetic vortex core deformation

Vansteenkiste, A., Chou, K. W., Weigand, M., Curcic, M., Sackmann, V., Stoll, H., Tyliszczak, T., Woltersdorf, G., Back, C. H., Schütz, G., Van Waeyenberge, B.

{Nature Physics}, 5, pages: 332-334, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Order\textendashdisorder transition and valence state of ytterbium in YbAuxGa2-x(0.26 \textless\textequalsx \textless\textequals1.31)

Gumeniuk, R., Bischoff, E., Burkhardt, U., Prots, Y., Schnelle, W., Vasylechko, L., Schmidt, M., Kuzma, Y., Grin, Y.

{Journal of Solid State Chemistry}, 182(12):3374-3382, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Coercivity of ledge-type L10-FePt/Fe nanocomposites with perpendicular magnetization

Goll, D., Breitling, A.

{Applied Physics Letters}, 94, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Time-resolved X-ray microscopy of nanoparticle aggregates under oscillatory shear

Auernhammer, G. K., Fauth, K., Ullrich, B., Zhao, J., Weigand, M., Vollmer, D.

{Journal of Synchrotron Radiation}, 16, pages: 307-309, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Micromagnetism of advanced hard magnetic materials

Kronmüller, H., Goll, D.

{International Journal of Materials Research}, 100, pages: 640-651, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Confinement of MgH2 nanoclusters within nanoporous aerogel scaffold materials

Nielsen, T. K., Manickam, K., Hirscher, M., Besenbacher, F., Jensen, T. R.

{American Chemical Society Nano}, 3(11):3521-3528, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Possible definition of atom- and bond-resolved contributions to the magnetocrystalline anisotropy energy

Subkow, S., Fähnle, M.

{Physical Review B}, 80, 2009 (article)

mms

DOI [BibTex]


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Robot ceiling climbers harness new tricks

Marks, Paul

New Scientist, 202(2705):18-19, Reed Business Information, 2009 (article)

pi

[BibTex]

[BibTex]


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Biologically-Inspired Patterned and Coated Adhesives for Medical Devices

Glass, P, Chung, H, Lee, C, Tworkoski, E, Washburn, NR, Sitti, M

Journal of Medical Devices, 3(2):027537, American Society of Mechanical Engineers, 2009 (article)

pi

[BibTex]

[BibTex]


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Modeling and experimental characterization of an untethered magnetic micro-robot

Pawashe, C., Floyd, S., Sitti, M.

The International Journal of Robotics Research, 28(8):1077-1094, Sage Publications, 2009 (article)

pi

[BibTex]

[BibTex]


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Towards automated nanoassembly with the atomic force microscope: A versatile drift compensation procedure

Krohs, F., Onal, C., Sitti, M., Fatikow, S.

Journal of Dynamic Systems, Measurement, and Control, 131(6):061106, American Society of Mechanical Engineers, 2009 (article)

pi

[BibTex]

[BibTex]


Valero-Cuevas, F., Hoffmann, H., Kurse, M. U., Kutch, J. J., Theodorou, E. A.

IEEE Reviews in Biomedical Engineering – (All authors have equally contributed), (2):110?135, 2009, clmc (article)

Abstract
Computational models of the neuromuscular system hold the potential to allow us to reach a deeper understanding of neuromuscular function and clinical rehabilitation by complementing experimentation. By serving as a means to distill and explore specific hypotheses, computational models emerge from prior experimental data and motivate future experimental work. Here we review computational tools used to understand neuromuscular function including musculoskeletal modeling, machine learning, control theory, and statistical model analysis. We conclude that these tools, when used in combination, have the potential to further our understanding of neuromuscular function by serving as a rigorous means to test scientific hypotheses in ways that complement and leverage experimental data.

am

link (url) [BibTex]

link (url) [BibTex]


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Adaptive Frequency Oscillators and Applications

Righetti, L., Buchli, J., Ijspeert, A.

The Open Cybernetics \& Systemics Journal, 3, pages: 64-69, 2009 (article)

Abstract
In this contribution we present a generic mechanism to transform an oscillator into an adaptive frequency oscillator, which can then dynamically adapt its parameters to learn the frequency of any periodic driving signal. Adaptation is done in a dynamic way: it is part of the dynamical system and not an offline process. This mechanism goes beyond entrainment since it works for any initial frequencies and the learned frequency stays encoded in the system even if the driving signal disappears. Interestingly, this mechanism can easily be applied to a large class of oscillators from harmonic oscillators to relaxation types and strange attractors. Several practical applications of this mechanism are then presented, ranging from adaptive control of compliant robots to frequency analysis of signals and construction of limit cycles of arbitrary shape.

mg

link (url) [BibTex]

link (url) [BibTex]


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Complex magnetic phase in submonolayer Fe stripes on Pt(977)

Honolka, J., Lee, T. Y., Kuhnke, K., Repetto, D., Sessi, V., Wahl, P., Buchsbaum, A., Varga, P., Gardonio, S., Carbone, C., Krishnakumar, S. R., Gambardella, P., Komelj, M., Singer, R., Fähnle, M., Fauth, K., Schütz, G., Enders, A., Kern, K.

{Physical Review B}, 79, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Local and nonlocal atomic contributions to unit-cell damping in near-adiabatic collinear magnetization dynamics

Seib, J., Steiauf, D., Fähnle, M.

{Physical Review B}, 79, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Temperature-dependent critical currents in superconducting YBa2Cu3O7-δand ferromagnetic La2/3Ca1/3MnO3 hybrid structures

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

{Physical Review B}, 80, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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High surface area polyHIPEs with hierarchical pore system

Schwab, M. G., Senkovska, I., Rose, M., Klein, N., Koch, M., Pahnke, J., Jonschker, G., Schmitz, B., Hirscher, M., Kaskel, S.

{Soft Matter}, 5, pages: 1055-1059, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Grain boundary wetting phase transformations in the Zn-Sn and Zn-In systems

Gornakova, A. S., Straumal, B. B., Tsurekawa, S., Chang, L.-S., Nekrasov, A. N.

{Reviews on Advanced Materials Science}, 21(1):18-26, 2009 (article)

mms

[BibTex]

[BibTex]


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Magnetization study of nanograined pure and Mn-doped ZnO films: formation of a ferromagnetic grain-boundary foam

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

{Physical Review B}, 79, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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In situ synthesis and hydrogen storage properties of PdNi alloy nanoparticles in an ordered mesoporous carbon template

Campesi, R., Cuevas, F., Leroy, E., Hirscher, M., Gadiou, R., Vix-Guterl, C., Latroche, M.

{Microporous and Mesoporous Materials}, 117, pages: 511-514, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


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On-line learning and modulation of periodic movements with nonlinear dynamical systems

Gams, A., Ijspeert, A., Schaal, S., Lenarčič, J.

Autonomous Robots, 27(1):3-23, 2009, clmc (article)

Abstract
Abstract  The paper presents a two-layered system for (1) learning and encoding a periodic signal without any knowledge on its frequency and waveform, and (2) modulating the learned periodic trajectory in response to external events. The system is used to learn periodic tasks on a humanoid HOAP-2 robot. The first layer of the system is a dynamical system responsible for extracting the fundamental frequency of the input signal, based on adaptive frequency oscillators. The second layer is a dynamical system responsible for learning of the waveform based on a built-in learning algorithm. By combining the two dynamical systems into one system we can rapidly teach new trajectories to robots without any knowledge of the frequency of the demonstration signal. The system extracts and learns only one period of the demonstration signal. Furthermore, the trajectories are robust to perturbations and can be modulated to cope with a dynamic environment. The system is computationally inexpensive, works on-line for any periodic signal, requires no additional signal processing to determine the frequency of the input signal and can be applied in parallel to multiple dimensions. Additionally, it can adapt to changes in frequency and shape, e.g. to non-stationary signals, such as hand-generated signals and human demonstrations.

am

link (url) [BibTex]

link (url) [BibTex]


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The SL simulation and real-time control software package

Schaal, S.

University of Southern California, Los Angeles, CA, 2009, clmc (techreport)

Abstract
SL was originally developed as a Simulation Laboratory software package to allow creating complex rigid-body dynamics simulations with minimal development times. It was meant to complement a real-time robotics setup such that robot programs could first be debugged in simulation before trying them on the actual robot. For this purpose, the motor control setup of SL was copied from our experience with real-time robot setups with vxWorks (Windriver Systems, Inc.)Ñindeed, more than 90% of the code is identical to the actual robot software, as will be explained later in detail. As a result, SL is divided into three software components: 1) the generic code that is shared by the actual robot and the simulation, 2) the robot specific code, and 3) the simulation specific code. The robot specific code is tailored to the robotic environments that we have experienced over the years, in particular towards VME-based multi-processor real-time operating systems. The simulation specific code has all the components for OpenGL graphics simulations and mimics the robot multi-processor environment in simple C-code. Importantly, SL can be used stand-alone for creating graphics an-imationsÑthe heritage from real-time robotics does not restrict the complexity of possible simulations. This technical report describes SL in detail and can serve as a manual for new users of SL.

am

link (url) [BibTex]

link (url) [BibTex]