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2010


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Direct imaging of current induced magnetic vortex gyration in an asymmetric potential well

Bisig, A., Rhensius, J., Kammerer, M., Curcic, M., Stoll, H., Schütz, G., Van Waeyenberge, B., Chou, K. W., Tyliszczak, T., Heyderman, L. J., Krzyk, S., von Bieren, A., Kläui, M.

{Applied Physics Letters}, 96, 2010 (article)

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DOI [BibTex]

2010


DOI [BibTex]


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Induced magnetism of carbon atoms at the graphene/Ni(111) interface

Weser, M., Rehder, Y., Horn, K., Sicot, M., Fonin, M., Preobrajenski, A. B., Voloshina, E. N., Goering, E., Dedkov, Y. S.

{Applied Physics Letters}, 96, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Photon counting system for time-resolved experiments in multibunch mode

Puzic, A., Korhonen, T., Kalantari, B., Raabe, J., Quitmann, C., Jüllig, P., Bommer, L., Goll, D., Schütz, G., Wintz, S., Strache, T., Körner, M., Markó, D., Bunce, C., Fassbender, J.

{Synchrotron Radiation News}, 23(2):26-32, 2010 (article)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Coupling of Fe and uncompensated Mn moments in exchange-biased Fe/MnPd

Brück, S., Macke, S., Goering, E., Ji, X., Zhan, Q., Krishnan, K. M.

{Physical Review B}, 81(13), 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Remarks about spillover and hydrogen adsorption - Comments on the contributions of A.V. Talyzin and R.T. Yang

Hirscher, M.

{Microporous and Mesoporous Materials}, 135, pages: 209-210, 2010 (article)

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DOI [BibTex]


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Grain boundary ridges and triple lines

Straumal, B. B., Sursaeva, V. G., Baretzky, B.

{Scripta Materialia}, 62(12):924-927, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Expanding micelle nanolithography to the self-assembly of multicomponent core-shell nanoparticles

Mbenkum, B. N., D\’\iaz-Ortiz, A., Gu, L., van Aken, P. A., Schütz, G.

{Journal of the American Chemical Society}, 132(31):10671-10673, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Learning control in robotics – trajectory-based opitimal control techniques

Schaal, S., Atkeson, C. G.

Robotics and Automation Magazine, 17(2):20-29, 2010, clmc (article)

Abstract
In a not too distant future, robots will be a natural part of daily life in human society, providing assistance in many areas ranging from clinical applications, education and care giving, to normal household environments [1]. It is hard to imagine that all possible tasks can be preprogrammed in such robots. Robots need to be able to learn, either by themselves or with the help of human supervision. Additionally, wear and tear on robots in daily use needs to be automatically compensated for, which requires a form of continuous self-calibration, another form of learning. Finally, robots need to react to stochastic and dynamic environments, i.e., they need to learn how to optimally adapt to uncertainty and unforeseen changes. Robot learning is going to be a key ingredient for the future of autonomous robots. While robot learning covers a rather large field, from learning to perceive, to plan, to make decisions, etc., we will focus this review on topics of learning control, in particular, as it is concerned with learning control in simulated or actual physical robots. In general, learning control refers to the process of acquiring a control strategy for a particular control system and a particular task by trial and error. Learning control is usually distinguished from adaptive control [2] in that the learning system can have rather general optimization objectivesâ??not just, e.g., minimal tracking errorâ??and is permitted to fail during the process of learning, while adaptive control emphasizes fast convergence without failure. Thus, learning control resembles the way that humans and animals acquire new movement strategies, while adaptive control is a special case of learning control that fulfills stringent performance constraints, e.g., as needed in life-critical systems like airplanes. Learning control has been an active topic of research for at least three decades. However, given the lack of working robots that actually use learning components, more work needs to be done before robot learning will make it beyond the laboratory environment. This article will survey some ongoing and past activities in robot learning to assess where the field stands and where it is going. We will largely focus on nonwheeled robots and less on topics of state estimation, as typically explored in wheeled robots [3]â??6], and we emphasize learning in continuous state-action spaces rather than discrete state-action spaces [7], [8]. We will illustrate the different topics of robot learning with examples from our own research with anthropomorphic and humanoid robots.

am

link (url) [BibTex]

link (url) [BibTex]


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Learning, planning, and control for quadruped locomotion over challenging terrain

Kalakrishnan, M., Buchli, J., Pastor, P., Mistry, M., Schaal, S.

International Journal of Robotics Research, 30(2):236-258, 2010, clmc (article)

Abstract
We present a control architecture for fast quadruped locomotion over rough terrain. We approach the problem by decomposing it into many sub-systems, in which we apply state-of-the-art learning, planning, optimization, and control techniques to achieve robust, fast locomotion. Unique features of our control strategy include: (1) a system that learns optimal foothold choices from expert demonstration using terrain templates, (2) a body trajectory optimizer based on the Zero- Moment Point (ZMP) stability criterion, and (3) a floating-base inverse dynamics controller that, in conjunction with force control, allows for robust, compliant locomotion over unperceived obstacles. We evaluate the performance of our controller by testing it on the LittleDog quadruped robot, over a wide variety of rough terrains of varying difficulty levels. The terrain that the robot was tested on includes rocks, logs, steps, barriers, and gaps, with obstacle sizes up to the leg length of the robot. We demonstrate the generalization ability of this controller by presenting results from testing performed by an independent external test team on terrain that has never been shown to us.

am

link (url) Project Page [BibTex]

link (url) Project Page [BibTex]


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Teleoperated 3-D force feedback from the nanoscale with an atomic force microscope

Onal, C. D., Sitti, M.

IEEE Transactions on nanotechnology, 9(1):46-54, IEEE, 2010 (article)

pi

[BibTex]

[BibTex]


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Roll and pitch motion analysis of a biologically inspired quadruped water runner robot

Park, H. S., Floyd, S., Sitti, M.

The International Journal of Robotics Research, 29(10):1281-1297, SAGE Publications Sage UK: London, England, 2010 (article)

pi

[BibTex]

[BibTex]


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Microstructured elastomeric surfaces with reversible adhesion and examples of their use in deterministic assembly by transfer printing

Kim, Seok, Wu, Jian, Carlson, Andrew, Jin, Sung Hun, Kovalsky, Anton, Glass, Paul, Liu, Zhuangjian, Ahmed, Numair, Elgan, Steven L, Chen, Weiqiu, others

Proceedings of the National Academy of Sciences, 107(40):17095-17100, National Acad Sciences, 2010 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Tankbot: A palm-size, tank-like climbing robot using soft elastomer adhesive treads

Unver, O., Sitti, M.

The International Journal of Robotics Research, 29(14):1761-1777, SAGE Publications Sage UK: London, England, 2010 (article)

pi

[BibTex]

[BibTex]


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Hydrogen spillover measurements of unbridged and bridged metal-organic frameworks - revisited

Campesi, R., Cuevas, F., Latroche, M., Hirscher, M.

{Physical Chemistry Chemical Physics}, 12, pages: 10457-10459, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Relating Gilbert damping and ultrafast laser-induced demagnetization

Fähnle, M., Seib, J., Illg, C.

{Physical Review B}, 82, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Ferromagnetic properties of the Mn-doped nanograined ZnO films

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

{Journal of Applied Physics}, 108, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Ubiquity of ferromagnetic signals in common diamagnetic oxide crystals

Khalid, M., Setzer, A., Ziese, M., Esquinazi, P., Spemann, D., Pöppl, A., Goering, E.

{Physical Review B}, 81(21), 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Calculation of the Gilbert damping matrix at low scattering rates in Gd

Seib, J., Fähnle, M.

{Physical Review B}, 82, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Swift heavy ions for controlled modification of soft magnetic properties of Fe0.85N0.15 thin film

Gupta, R., Gupta, A., Bhatt, R., Rüffer, R., Avasthi, D. K.

{Journal of Physics: Condensed Matter}, 22(22), 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Note: Aligned deposition and modal characterization of micron and submicron poly (methyl methacyrlate) fiber cantilevers

Nain, A. S., Filiz, S., Burak Ozdoganlar, O., Sitti, M., Amon, C.

Review of Scientific Instruments, 81(1):016102, AIP, 2010 (article)

pi

[BibTex]

[BibTex]


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Enhanced adhesion of dopamine methacrylamide elastomers via viscoelasticity tuning

Chung, H., Glass, P., Pothen, J. M., Sitti, M., Washburn, N. R.

Biomacromolecules, 12(2):342-347, American Chemical Society, 2010 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


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Laterally driven interfaces in the three-dimensional Ising lattice gas

Smith, T. H. R., Vasilyev, O., Maciolek, A., Schmidt, M.

{Physical Review E}, 82(2), 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Samarium-cobalt 2:17 magnets: identifying Smn+1Co5n-1 phases stabilized by Zr

Stadelmaier, H. H., Kronmüller, H., Goll, D.

{Scripta Materialia}, 63, pages: 843-846, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Planar metamaterial analogue of electromagnetically induced transparancy for plasmonic sensing

Liu, N., Weiss, T., Mesch, M., Langguth, L., Eigenthaler, U., Hirscher, M., Sönnichsen, C., Giessen, H.

{Nano Letters}, 10, pages: 1103-1107, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Explaining the paradoxical diversity of ultrafast last-induced demagnetization

Koopmans, B., Malinowski, G., Dalla Longa, F., Steiauf, D., Fähnle, M., Roth, T., Cinchetti, M., Aeschlimann, M.

{Nature Materials}, 9, pages: 259-265, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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A high heat of adsorption for hydrogen in magnesium formate

Schmitz, B., Krkljus, I., Leung, E., Höffken, H. W., Müller, U., Hirscher, M.

{ChemSusChem}, 3, pages: 758-761, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Force induced destabilization of adhesion complexes at defined integrin spacings on nanostructured surfaces

de Beer, A. G. F., Cavalcanti-Adam, E. A., Majer, G., López-Garc\’\ia, M., Kessler, H., Spatz, J. P.

{Physical Review E}, 81, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Anisotropic damping of the magnetization dynamics in Ni, Co, and Fe

Gilmore, K., Stiles, M. D., Seib, J., Steiauf, D., Fähnle, M.

{Physical Review B}, 81, 2010 (article)

mms

DOI [BibTex]

DOI [BibTex]


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Influence of [Mo6Br8F6]2- cluster inclusion within the mesoporous solid MIL-101 on hydrogen storage performance

Dybtsev, D., Serre, C., Schmitz, B., Panella, B., Hirscher, M., Latroche, M., Llewellyn, P. L., Cordier, S., Molard, Y., Haouas, M., Taulelle, F., Férey, G.

{Langmuir}, 26(13):11283-11290, 2010 (article)

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DOI [BibTex]

DOI [BibTex]


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Grain boundary layers in nanocrystalline ferromagnetic zinc oxide

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

{JETP Letters}, 92(6):396-400, 2010 (article)

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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]


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Real-Time Fetal Heart Monitoring in Biomagnetic Measurements Using Adaptive Real-Time ICA

Waldert, S., Bensch, M., Bogdan, M., Rosenstiel, W., Schölkopf, B., Lowery, C., Eswaran, H., Preissl, H.

IEEE Transactions on Biomedical Engineering, 54(10):1867-1874, September 2007 (article)

Abstract
Electrophysiological signals of the developing fetal brain and heart can be investigated by fetal magnetoencephalography (fMEG). During such investigations, the fetal heart activity and that of the mother should be monitored continuously to provide an important indication of current well-being. Due to physical constraints of an fMEG system, it is not possible to use clinically established heart monitors for this purpose. Considering this constraint, we developed a real-time heart monitoring system for biomagnetic measurements and showed its reliability and applicability in research and for clinical examinations. The developed system consists of real-time access to fMEG data, an algorithm based on Independent Component Analysis (ICA), and a graphical user interface (GUI). The algorithm extracts the current fetal and maternal heart signal from a noisy and artifact-contaminated data stream in real-time and is able to adapt automatically to continuously varying environmental parameters. This algorithm has been na med Adaptive Real-time ICA (ARICA) and is applicable to real-time artifact removal as well as to related blind signal separation problems.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Feature Selection for Trouble Shooting in Complex Assembly Lines

Pfingsten, T., Herrmann, D., Schnitzler, T., Feustel, A., Schölkopf, B.

IEEE Transactions on Automation Science and Engineering, 4(3):465-469, July 2007 (article)

Abstract
The final properties of sophisticated products can be affected by many unapparent dependencies within the manufacturing process, and the products’ integrity can often only be checked in a final measurement. Troubleshooting can therefore be very tedious if not impossible in large assembly lines. In this paper we show that Feature Selection is an efficient tool for serial-grouped lines to reveal causes for irregularities in product attributes. We compare the performance of several methods for Feature Selection on real-world problems in mass-production of semiconductor devices. Note to Practitioners— We present a data based procedure to localize flaws in large production lines: using the results of final quality inspections and information about which machines processed which batches, we are able to identify machines which cause low yield.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Gene selection via the BAHSIC family of algorithms

Song, L., Bedo, J., Borgwardt, K., Gretton, A., Smola, A.

Bioinformatics, 23(13: ISMB/ECCB 2007 Conference Proceedings):i490-i498, July 2007 (article)

Abstract
Motivation: Identifying significant genes among thousands of sequences on a microarray is a central challenge for cancer research in bioinformatics. The ultimate goal is to detect the genes that are involved in disease outbreak and progression. A multitude of methods have been proposed for this task of feature selection, yet the selected gene lists differ greatly between different methods. To accomplish biologically meaningful gene selection from microarray data, we have to understand the theoretical connections and the differences between these methods. In this article, we define a kernel-based framework for feature selection based on the Hilbert–Schmidt independence criterion and backward elimination, called BAHSIC. We show that several well-known feature selectors are instances of BAHSIC, thereby clarifying their relationship. Furthermore, by choosing a different kernel, BAHSIC allows us to easily define novel feature selection algorithms. As a further advantage, feature selection via BAHSIC works directly on multiclass problems. Results: In a broad experimental evaluation, the members of the BAHSIC family reach high levels of accuracy and robustness when compared to other feature selection techniques. Experiments show that features selected with a linear kernel provide the best classification performance in general, but if strong non-linearities are present in the data then non-linear kernels can be more suitable.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Phenotyping of Chondrocytes In Vivo and In Vitro Using cDNA Array Technology

Zien, A., Gebhard, P., Fundel, K., Aigner, T.

Clinical Orthopaedics and Related Research, 460, pages: 226-233, July 2007 (article)

Abstract
The cDNA array technology is a powerful tool to analyze a high number of genes in parallel. We investigated whether large-scale gene expression analysis allows clustering and identification of cellular phenotypes of chondrocytes in different in vivo and in vitro conditions. In 100% of cases, clustering analysis distinguished between in vivo and in vitro samples, suggesting fundamental differences in chondrocytes in situ and in vitro regardless of the culture conditions or disease status. It also allowed us to differentiate between healthy and osteoarthritic cartilage. The clustering also revealed the relative importance of the investigated culturing conditions (stimulation agent, stimulation time, bead/monolayer). We augmented the cluster analysis with a statistical search for genes showing differential expression. The identified genes provided hints to the molecular basis of the differences between the sample classes. Our approach shows the power of modern bioinformatic algorithms for understanding and class ifying chondrocytic phenotypes in vivo and in vitro. Although it does not generate new experimental data per se, it provides valuable information regarding the biology of chondrocytes and may provide tools for diagnosing and staging the osteoarthritic disease process.

ei

DOI [BibTex]

DOI [BibTex]


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Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

Clark, R., Schweikert, G., Toomajian, C., Ossowski, S., Zeller, G., Shinn, P., Warthmann, N., Hu, T., Fu, G., Hinds, D., Chen, H., Frazer, K., Huson, D., Schölkopf, B., Nordborg, M., Rätsch, G., Ecker, J., Weigel, D.

Science, 317(5836):338-342, July 2007 (article)

Abstract
The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and ~4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Graph Laplacians and their Convergence on Random Neighborhood Graphs

Hein, M., Audibert, J., von Luxburg, U.

Journal of Machine Learning Research, 8, pages: 1325-1370, June 2007 (article)

Abstract
Given a sample from a probability measure with support on a submanifold in Euclidean space one can construct a neighborhood graph which can be seen as an approximation of the submanifold. The graph Laplacian of such a graph is used in several machine learning methods like semi-supervised learning, dimensionality reduction and clustering. In this paper we determine the pointwise limit of three different graph Laplacians used in the literature as the sample size increases and the neighborhood size approaches zero. We show that for a uniform measure on the submanifold all graph Laplacians have the same limit up to constants. However in the case of a non-uniform measure on the submanifold only the so called random walk graph Laplacian converges to the weighted Laplace-Beltrami operator.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Bayesian Reconstruction of the Density of States

Habeck, M.

Physical Review Letters, 98(20, 200601):1-4, May 2007 (article)

Abstract
A Bayesian framework is developed to reconstruct the density of states from multiple canonical simulations. The framework encompasses the histogram reweighting method of Ferrenberg and Swendsen. The new approach applies to nonparametric as well as parametric models and does not require simulation data to be discretized. It offers a means to assess the precision of the reconstructed density of states and of derived thermodynamic quantities.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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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]

Web DOI [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.

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PDF Web DOI [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)

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PDF DOI [BibTex]

PDF DOI [BibTex]