Header logo is


2009


no image
Effect of severe plastic deformation on the coercivity of Co-Cu alloys

Straumal, B. B., Protasova, S. G., Mazilkin, A. A., Baretzky, B., Goll, D., Gunderov, D. V., Valiev, R. Z.

{Philosophical Magazine Letters}, 89(10):649-654, 2009 (article)

mms

DOI [BibTex]

2009


DOI [BibTex]


no image
Magnetic properties of cobalt-covered MgB2 films

Treiber, S., Stuhlhofer, B., Habermeier, H.-U., Albrecht, J.

{Superconductor Science and Technology}, 22, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Reconstruction of historic alloys for pipe organs brings true Baroque music back to life

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

{Japan Organist}, 36, pages: 29-38, 2009 (article)

mms

[BibTex]

[BibTex]


no image
Exchange-coupled L10-FePt/Fe composite patterns with perpendicular magnetization

Breitling, A., Bublat, T., Goll, D.

{Physica Status Solidi - Rapid Research Letters}, 3(5):130-132, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Proton NMR studies of the NaAlH4 structure

Valiente-Banuet, L. E., Majer, G., Müller, K.

{Journal of Magnetic Resonance}, 200, pages: 280-284, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
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.)â??indeed, 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-imationsâ??the 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]


no image
Learning and generalization of motor skills by learning from demonstration

Pastor, P., Hoffmann, H., Asfour, T., Schaal, S.

In International Conference on Robotics and Automation (ICRA2009), Kobe, Japan, May 12-19, 2009, 2009, clmc (inproceedings)

Abstract
We provide a general approach for learning robotic motor skills from human demonstration. To represent an observed movement, a non-linear differential equation is learned such that it reproduces this movement. Based on this representation, we build a library of movements by labeling each recorded movement according to task and context (e.g., grasping, placing, and releasing). Our differential equation is formulated such that generalization can be achieved simply by adapting a start and a goal parameter in the equation to the desired position values of a movement. For object manipulation, we present how our framework extends to the control of gripper orientation and finger position. The feasibility of our approach is demonstrated in simulation as well as on a real robot. The robot learned a pick-and-place operation and a water-serving task and could generalize these tasks to novel situations.

am

link (url) [BibTex]

link (url) [BibTex]


no image
Compliant quadruped locomotion over rough terrain

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

In Intelligent Robots and Systems, 2009. IROS 2009. IEEE/RSJ International Conference on, pages: 814-820, 2009, clmc (inproceedings)

Abstract
Many critical elements for statically stable walking for legged robots have been known for a long time, including stability criteria based on support polygons, good foothold selection, recovery strategies to name a few. All these criteria have to be accounted for in the planning as well as the control phase. Most legged robots usually employ high gain position control, which means that it is crucially important that the planned reference trajectories are a good match for the actual terrain, and that tracking is accurate. Such an approach leads to conservative controllers, i.e. relatively low speed, ground speed matching, etc. Not surprisingly such controllers are not very robust - they are not suited for the real world use outside of the laboratory where the knowledge of the world is limited and error prone. Thus, to achieve robust robotic locomotion in the archetypical domain of legged systems, namely complex rough terrain, where the size of the obstacles are in the order of leg length, additional elements are required. A possible solution to improve the robustness of legged locomotion is to maximize the compliance of the controller. While compliance is trivially achieved by reduced feedback gains, for terrain requiring precise foot placement (e.g. climbing rocks, walking over pegs or cracks) compliance cannot be introduced at the cost of inferior tracking. Thus, model-based control and - in contrast to passive dynamic walkers - active balance control is required. To achieve these objectives, in this paper we add two crucial elements to legged locomotion, i.e., floating-base inverse dynamics control and predictive force control, and we show that these elements increase robustness in face of unknown and unanticipated perturbations (e.g. obstacles). Furthermore, we introduce a novel line-based COG trajectory planner, which yields a simpler algorithm than traditional polygon based methods and creates the appropriate input to our control system.We show results from bot- h simulation and real world of a robotic dog walking over non-perceived obstacles and rocky terrain. The results prove the effectivity of the inverse dynamics/force controller. The presented results show that we have all elements needed for robust all-terrain locomotion, which should also generalize to other legged systems, e.g., humanoid robots.

am

link (url) [BibTex]

link (url) [BibTex]


no image
A scaled bilateral control system for experimental one-dimensional teleoperated nanomanipulation

Onal, C. D., Sitti, M.

The International Journal of Robotics Research, 28(4):484-497, Sage Publications, 2009 (article)

pi

[BibTex]

[BibTex]


no image
A Swallowable Tethered Capsule Endoscope for Diagnosing Barrett’s Esophagus

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

Gastrointestinal Endoscopy, 69(5):AB106, Mosby, 2009 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


no image
A miniature ceiling walking robot with flat tacky elastomeric footpads

Unver, O., Sitti, M.

In Robotics and Automation, 2009. ICRA’09. IEEE International Conference on, pages: 2276-2281, 2009 (inproceedings)

pi

[BibTex]

[BibTex]


no image
Adhesion of biologically inspired polymer microfibers on soft surfaces

Cheung, E., Sitti, M.

Langmuir, 25(12):6613-6616, ACS Publications, 2009 (article)

pi

[BibTex]

[BibTex]


no image
Dangling chain elastomers as repeatable fibrillar adhesives

Sitti, M., Cusick, B., Aksak, B., Nese, A., Lee, H., Dong, H., Kowalewski, T., Matyjaszewski, K.

ACS applied materials \& interfaces, 1(10):2277-2287, American Chemical Society, 2009 (article)

pi

[BibTex]

[BibTex]


no image
A Sensor-Based Learning Algorithm for the Self-Organization of Robot Behavior

Hesse, F., Martius, G., Der, R., Herrmann, J. M.

Algorithms, 2(1):398-409, 2009 (article)

Abstract
Ideally, sensory information forms the only source of information to a robot. We consider an algorithm for the self-organization of a controller. At short timescales the controller is merely reactive but the parameter dynamics and the acquisition of knowledge by an internal model lead to seemingly purposeful behavior on longer timescales. As a paradigmatic example, we study the simulation of an underactuated snake-like robot. By interacting with the real physical system formed by the robotic hardware and the environment, the controller achieves a sensitive and body-specific actuation of the robot.

al

link (url) [BibTex]

link (url) [BibTex]


no image
Metal-Organic Frameworks

Panella, B., Hirscher, M.

In Encyclopedia of Electrochemical Power Sources, pages: 493-496, Elsevier, Amsterdam [et al.], 2009 (incollection)

mms

[BibTex]

[BibTex]


no image
In-situ - Untersuchungen zu Interdiffusion und Magnetismus in magnetischen Multilayern

Schmidt, M.

Universität Stuttgart, Stuttgart, 2009 (mastersthesis)

mms

[BibTex]

[BibTex]


no image
Magnetism of FePt surface alloys

Honolka, J., Lee, T. Y., Kuhnke, K., Enders, A., Skomski, R., Bornemann, S., Mankovsky, S., Minár, J., Staunton, J., Ebert, H., Hessler, M., Fauth, K., Schütz, G., Buchsbaum, A., Schmid, M., Varga, P., Kern, K.

{Physical Review Letters}, 102(6), 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Enhanced 95Zr diffusion in grain boundaries of nano-crystalline ZrO2 \mbox⋅ 9.5 mol\textpercent Y2O3

Drings, H., Brossmann, U., Carstanjen, H. D., Szökefalvi-Nagy, A., Noll, C., Schaefer, H.-E.

{Physica Status Solidi (A)}, 206(1):54-58, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Magnetism of nanostructured materials for advanced magnetic recording

Goll, D.

{International Journal of Materials Research}, 100, pages: 652-662, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Vortex core switching by coherent excitation with single in-plane magnetic field pulses

Weigand, M., van Waeyenberge, B., Vansteenkiste, A., Curcic, M., Sackmann, V., Stoll, H., Tyliszczak, T., Kaznatcheev, K., Bertwistle, D., Woltersdorf, G., Back, C. H., Schütz, G.

{Physical Review Letters}, 102, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Increase of Mn solubility with decreasing grain size in ZnO

Straumal, B., Baretzky, B., Mazilkin, A., Protasova, S., Myatiev, A., Straumal, P.

{Journal of the European Ceramic Society}, 29(10):1963-1970, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Fe-C nanograined alloys obtained by high-pressure torsion: Structure and magnetic properties

Straumal, B. B., Mazilkin, A. A., Protasova, S. G., Dobatkin, S. V., Rodin, A. O., Baretzky, B., Goll, D., Schütz, G.

{Materials Science and Engineering A}, 503, pages: 185-189, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Chiral symmetry breaking of magnetic vortices by sample roughness

Vansteenkiste, A., Weigand, M., Curcic, M., Stoll, H., Schütz, G., Van Waeyenberge, B.

{New Journal of Physics}, 11, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Extended s-d model for magnetization dynamics of strongly noncollinear configurations

De Angeli, L., Steiauf, D., Singer, R., Köberle, I., Dietermann, F., Fähnle, M.

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

mms

DOI [BibTex]

DOI [BibTex]


no image
Incorporating Muscle Activation-Contraction dynamics to an optimal control framework for finger movements

Theodorou, Evangelos A., Valero-Cuevas, Francisco J.

Abstracts of Neural Control of Movement Conference (NCM 2009), 2009, clmc (article)

Abstract
Recent experimental and theoretical work [1] investigated the neural control of contact transition between motion and force during tapping with the index finger as a nonlinear optimization problem. Such transitions from motion to well-directed contact force are a fundamental part of dexterous manipulation. There are 3 alternative hypotheses of how this transition could be accomplished by the nervous system as a function of changes in direction and magnitude of the torque vector controlling the finger. These hypotheses are 1) an initial change in direction with a subsequent change in magnitude of the torque vector; 2) an initial change in magnitude with a subsequent directional change of the torque vector; and 3) a simultaneous and proportionally equal change of both direction and magnitude of the torque vector. Experimental work in [2] shows that the nervous system selects the first strategy, and in [1] we suggest that this may in fact be the optimal strategy. In [4] the framework of Iterative Linear Quadratic Optimal Regulator (ILQR) was extended to incorporate motion and force control. However, our prior simulation work assumed direct and instantaneous control of joint torques, which ignores the known delays and filtering properties of skeletal muscle. In this study, we implement an ILQR controller for a more biologically plausible biomechanical model of the index finger than [4], and add activation-contraction dynamics to the system to simulate muscle function. The planar biomechanical model includes the kinematics of the 3 joints while the applied torques are driven by activation?contraction dynamics with biologically plausible time constants [3]. In agreement with our experimental work [2], the task is to, within 500 ms, move the finger from a given resting configuration to target configuration with a desired terminal velocity. ILQR does not only stabilize the finger dynamics according to the objective function, but it also generates smooth joint space trajectories with minimal tuning and without an a-priori initial control policy (which is difficult to find for highly dimensional biomechanical systems). Furthemore, the use of this optimal control framework and the addition of activation-contraction dynamics considers the full nonlinear dynamics of the index finger and produces a sequence of postures which are compatible with experimental motion data [2]. These simulations combined with prior experimental results suggest that optimal control is a strong candidate for the generation of finger movements prior to abrupt motion-to-force transitions. This work is funded in part by grants NIH R01 0505520 and NSF EFRI-0836042 to Dr. Francisco J. Valero- Cuevas 1 Venkadesan M, Valero-Cuevas FJ. 
Effects of neuromuscular lags on controlling contact transitions. 
Philosophical Transactions of the Royal Society A: 2008. 2 Venkadesan M, Valero-Cuevas FJ. 
Neural Control of Motion-to-Force Transitions with the Fingertip. 
J. Neurosci., Feb 2008; 28: 1366 - 1373; 3 Zajac. Muscle and tendon: properties, models, scaling, and application to biomechanics and motor control. Crit Rev Biomed Eng, 17 4. Weiwei Li., Francisco Valero Cuevas: ?Linear Quadratic Optimal Control of Contact Transition with Fingertip ? ACC 2009

am

PDF [BibTex]

PDF [BibTex]


no image
Inertial parameter estimation of floating-base humanoid systems using partial force sensing

Mistry, M., Schaal, S., Yamane, K.

In IEEE-RAS International Conference on Humanoid Robots (Humanoids 2009), Paris, Dec.7-10, 2009, clmc (inproceedings)

Abstract
Recently, several controllers have been proposed for humanoid robots which rely on full-body dynamic models. The estimation of inertial parameters from data is a critical component for obtaining accurate models for control. However, floating base systems, such as humanoid robots, incur added challenges to this task (e.g. contact forces must be measured, contact states can change, etc.) In this work, we outline a theoretical framework for whole body inertial parameter estimation, including the unactuated floating base. Using a least squares minimization approach, conducted within the nullspace of unmeasured degrees of freedom, we are able to use a partial force sensor set for full-body estimation, e.g. using only joint torque sensors, allowing for estimation when contact force measurement is unavailable or unreliable (e.g. due to slipping, rolling contacts, etc.). We also propose how to determine the theoretical minimum force sensor set for full body estimation, and discuss the practical limitations of doing so.

am

link (url) [BibTex]

link (url) [BibTex]


no image
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]


no image
Reversible dry micro-fibrillar adhesives with thermally controllable adhesion

Kim, S., Sitti, M., Xie, T., Xiao, X.

Soft Matter, 5(19):3689-3693, Royal Society of Chemistry, 2009 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


no image
Biologically Inspired Polymer Microfibrillar Arrays for Mask Sealing

Cheung, E., Aksak, B., Sitti, M.

CARNEGIE-MELLON UNIV PITTSBURGH PA, 2009 (techreport)

pi

[BibTex]

[BibTex]


no image
Tankbot: A miniature, peeling based climber on rough and smooth surfaces

Unver, O., Sitti, M.

In Robotics and Automation, 2009. ICRA’09. IEEE International Conference on, pages: 2282-2287, 2009 (inproceedings)

pi

[BibTex]

[BibTex]


no image
Automated 2-D nanoparticle manipulation with an atomic force microscope

Onal, C. D., Ozcan, O., Sitti, M.

In Robotics and Automation, 2009. ICRA’09. IEEE International Conference on, pages: 1814-1819, 2009 (inproceedings)

pi

[BibTex]

[BibTex]


no image
Enhanced reversible adhesion of dopamine methacrylamide-coated elastomer microfibrillar structures under wet conditions

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

Langmuir, 25(12):6607-6612, ACS Publications, 2009 (article)

pi

Project Page [BibTex]

Project Page [BibTex]


no image
Microparticle manipulation using multiple untethered magnetic micro-robots on an electrostatic surface

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

In Intelligent Robots and Systems, 2009. IROS 2009. IEEE/RSJ International Conference on, pages: 528-533, 2009 (inproceedings)

pi

[BibTex]

[BibTex]


no image
Carbon Materials

Hirscher, M.

In Encyclopedia of Electrochemical Power Sources, pages: 484-487, Elsevier, Amsterdam [et al.], 2009 (incollection)

mms

[BibTex]

[BibTex]


no image
Theorie der elektronischen Zustände in oxidischen magnetischen Materialien

Kostoglou, C.

Universität Stuttgart, Stuttgart, 2009 (phdthesis)

mms

[BibTex]

[BibTex]


no image
Magnetooptische Untersuchungen an Ferromagnet- und Supraleiter-Nanosystemen und deren Hybriden

Treiber, S.

Universität Stuttgart, Stuttgart, 2009 (mastersthesis)

mms

[BibTex]

[BibTex]


no image
Superconducting phase formation in random neck syntheses: a study of the Y-Ba-Cu-O system by magneto-optics and magnetometry

Willems, J. B., Albrecht, J., Landau, I. L., Hulliger, J.

{Superconductor Science and Technology}, 22, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Determination of spin moments from magnetic EXAFS

Popescu, V., Gü\ssmann, M., Fähnle, M., Schütz, G.

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

mms

DOI [BibTex]

DOI [BibTex]


no image
Linewidth of ferromagnetic resonance for systems with anisotropic damping

Seib, J., Steiauf, D., Fähnle, M.

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

mms

DOI [BibTex]

DOI [BibTex]


no image
Structural and magnetic deconvolution of FePt/FeOx-nanoparticles using x-ray magnetic circular dichroism

Nolle, D., Goering, E., Tietze, T., Schütz, G., Figuerola, A., Manna, L.

{New Journal of Physics}, 11, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Magnetic imaging with femtosecond temporal resolution

Li, J., Lee, M.-S., He, W., Redeker, B., Remhof, A., Amaladass, E., Hassel, C., Eimüller, T.

{Review of Scientific Instruments}, 80(7), 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]


no image
Elliott-Yafet mechanism and the discussion of femtosecond magnetization dynamics

Steiauf, D., Fähnle, M.

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

mms

DOI [BibTex]

DOI [BibTex]


no image
Investigation of the stability of Mn12 single molecule magnets

Voss, S., Fonin, M., Burova, L., Burgert, M., Dedkov, Y. S., Preobrajenski, A. B., Goering, E., Groth, U., Kaul, A. R., Ruediger, U.

{Applied Physics A}, 94(3):491-495, 2009 (article)

mms

DOI [BibTex]

DOI [BibTex]

2007


no image
Reaction graph kernels for discovering missing enzymes in the plant secondary metabolism

Saigo, H., Hattori, M., Tsuda, K.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
Secondary metabolic pathway in plant is important for finding druggable candidate enzymes. However, there are many enzymes whose functions are still undiscovered especially in organism-specific metabolic pathways. We propose reaction graph kernels for automatically assigning the EC numbers to unknown enzymatic reactions in a metabolic network. Experiments are carried out on KEGG/REACTION database and our method successfully predicted the first three digits of the EC number with 83% accuracy.We also exhaustively predicted missing enzymatic functions in the plant secondary metabolism pathways, and evaluated our results in biochemical validity.

ei

Web [BibTex]

2007


Web [BibTex]


no image
Positional Oligomer Importance Matrices

Sonnenburg, S., Zien, A., Philips, P., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
At the heart of many important bioinformatics problems, such as gene finding and function prediction, is the classification of biological sequences, above all of DNA and proteins. In many cases, the most accurate classifiers are obtained by training SVMs with complex sequence kernels, for instance for transcription starts or splice sites. However, an often criticized downside of SVMs with complex kernels is that it is very hard for humans to understand the learned decision rules and to derive biological insights from them. To close this gap, we introduce the concept of positional oligomer importance matrices (POIMs) and develop an efficient algorithm for their computation. We demonstrate how they overcome the limitations of sequence logos, and how they can be used to find relevant motifs for different biological phenomena in a straight-forward way. Note that the concept of POIMs is not limited to interpreting SVMs, but is applicable to general k−mer based scoring systems.

ei

Web [BibTex]

Web [BibTex]


no image
Machine Learning Algorithms for Polymorphism Detection

Schweikert, G., Zeller, G., Weigel, D., Schölkopf, B., Rätsch, G.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

ei

Web [BibTex]

Web [BibTex]


no image
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]

PDF PDF DOI [BibTex]


no image
An Automated Combination of Kernels for Predicting Protein Subcellular Localization

Zien, A., Ong, C.

NIPS Workshop on Machine Learning in Computational Biology, December 2007 (talk)

Abstract
Protein subcellular localization is a crucial ingredient to many important inferences about cellular processes, including prediction of protein function and protein interactions.We propose a new class of protein sequence kernels which considers all motifs including motifs with gaps. This class of kernels allows the inclusion of pairwise amino acid distances into their computation. We utilize an extension of the multiclass support vector machine (SVM)method which directly solves protein subcellular localization without resorting to the common approach of splitting the problem into several binary classification problems. To automatically search over families of possible amino acid motifs, we optimize over multiple kernels at the same time. We compare our automated approach to four other predictors on three different datasets, and show that we perform better than the current state of the art. Furthermore, our method provides some insights as to which features are most useful for determining subcellular localization, which are in agreement with biological reasoning.

ei

Web [BibTex]

Web [BibTex]


no image
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]


no image
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]