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2009


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Toward a Theory of Consciousness

Tononi, G., Balduzzi, D.

In The Cognitive Neurosciences, pages: 1201-1220, (Editors: Gazzaniga, M.S.), MIT Press, Cambridge, MA, USA, October 2009 (inbook)

ei

Web [BibTex]

2009


Web [BibTex]


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Text Clustering with Mixture of von Mises-Fisher Distributions

Sra, S., Banerjee, A., Ghosh, J., Dhillon, I.

In Text mining: classification, clustering, and applications, pages: 121-161, Chapman & Hall/CRC data mining and knowledge discovery series, (Editors: Srivastava, A. N. and Sahami, M.), CRC Press, Boca Raton, FL, USA, June 2009 (inbook)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Data Mining for Biologists

Tsuda, K.

In Biological Data Mining in Protein Interaction Networks, pages: 14-27, (Editors: Li, X. and Ng, S.-K.), Medical Information Science Reference, Hershey, PA, USA, May 2009 (inbook)

Abstract
In this tutorial chapter, we review basics about frequent pattern mining algorithms, including itemset mining, association rule mining and graph mining. These algorithms can find frequently appearing substructures in discrete data. They can discover structural motifs, for example, from mutation data, protein structures and chemical compounds. As they have been primarily used for business data, biological applications are not so common yet, but their potential impact would be large. Recent advances in computers including multicore machines and ever increasing memory capacity support the application of such methods to larger datasets. We explain technical aspects of the algorithms, but do not go into details. Current biological applications are summarized and possible future directions are given.

ei

Web [BibTex]

Web [BibTex]


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Large Margin Methods for Part of Speech Tagging

Altun, Y.

In Automatic Speech and Speaker Recognition: Large Margin and Kernel Methods, pages: 141-160, (Editors: Keshet, J. and Bengio, S.), Wiley, Hoboken, NJ, USA, January 2009 (inbook)

ei

Web [BibTex]

Web [BibTex]


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Covariate shift and local learning by distribution matching

Gretton, A., Smola, A., Huang, J., Schmittfull, M., Borgwardt, K., Schölkopf, B.

In Dataset Shift in Machine Learning, pages: 131-160, (Editors: Quiñonero-Candela, J., Sugiyama, M., Schwaighofer, A. and Lawrence, N. D.), MIT Press, Cambridge, MA, USA, 2009 (inbook)

Abstract
Given sets of observations of training and test data, we consider the problem of re-weighting the training data such that its distribution more closely matches that of the test data. We achieve this goal by matching covariate distributions between training and test sets in a high dimensional feature space (specifically, a reproducing kernel Hilbert space). This approach does not require distribution estimation. Instead, the sample weights are obtained by a simple quadratic programming procedure. We provide a uniform convergence bound on the distance between the reweighted training feature mean and the test feature mean, a transductive bound on the expected loss of an algorithm trained on the reweighted data, and a connection to single class SVMs. While our method is designed to deal with the case of simple covariate shift (in the sense of Chapter ??), we have also found benefits for sample selection bias on the labels. Our correction procedure yields its greatest and most consistent advantages when the learning algorithm returns a classifier/regressor that is simpler" than the data might suggest.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Synchronized Oriented Mutations Algorithm for Training Neural Controllers

Berenz, V., Suzuki, K.

In Advances in Neuro-Information Processing: 15th International Conference, ICONIP 2008, Auckland, New Zealand, November 25-28, 2008, Revised Selected Papers, Part II, pages: 244-251, Springer Berlin Heidelberg, Berlin, Heidelberg, 2009 (inbook)

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Integration of Visual Cues for Robotic Grasping

Bergström, N., Bohg, J., Kragic, D.

In Computer Vision Systems, 5815, pages: 245-254, Lecture Notes in Computer Science, Springer Berlin Heidelberg, 2009 (incollection)

Abstract
In this paper, we propose a method that generates grasping actions for novel objects based on visual input from a stereo camera. We are integrating two methods that are advantageous either in predicting how to grasp an object or where to apply a grasp. The first one reconstructs a wire frame object model through curve matching. Elementary grasping actions can be associated to parts of this model. The second method predicts grasping points in a 2D contour image of an object. By integrating the information from the two approaches, we can generate a sparse set of full grasp configurations that are of a good quality. We demonstrate our approach integrated in a vision system for complex shaped objects as well as in cluttered scenes.

am

pdf link (url) DOI [BibTex]

pdf link (url) DOI [BibTex]


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An introduction to Kernel Learning Algorithms

Gehler, P., Schölkopf, B.

In Kernel Methods for Remote Sensing Data Analysis, pages: 25-48, 2, (Editors: Gustavo Camps-Valls and Lorenzo Bruzzone), Wiley, New York, NY, USA, 2009 (inbook)

Abstract
Kernel learning algorithms are currently becoming a standard tool in the area of machine learning and pattern recognition. In this chapter we review the fundamental theory of kernel learning. As the basic building block we introduce the kernel function, which provides an elegant and general way to compare possibly very complex objects. We then review the concept of a reproducing kernel Hilbert space and state the representer theorem. Finally we give an overview of the most prominent algorithms, which are support vector classification and regression, Gaussian Processes and kernel principal analysis. With multiple kernel learning and structured output prediction we also introduce some more recent advancements in the field.

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Visual Object Discovery

Sinha, P., Balas, B., Ostrovsky, Y., Wulff, J.

In Object Categorization: Computer and Human Vision Perspectives, pages: 301-323, (Editors: S. J. Dickinson, A. Leonardis, B. Schiele, M.J. Tarr), Cambridge University Press, 2009 (inbook)

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link (url) [BibTex]

link (url) [BibTex]


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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]


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Carbon Materials

Hirscher, M.

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

mms

[BibTex]

[BibTex]

2008


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New Frontiers in Characterizing Structure and Dynamics by NMR

Nilges, M., Markwick, P., Malliavin, TE., Rieping, W., Habeck, M.

In Computational Structural Biology: Methods and Applications, pages: 655-680, (Editors: Schwede, T. , M. C. Peitsch), World Scientific, New Jersey, NJ, USA, May 2008 (inbook)

Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as the method of choice for studying both the structure and the dynamics of biological macromolecule in solution. Despite the maturity of the NMR method for structure determination, its application faces a number of challenges. The method is limited to systems of relatively small molecular mass, data collection times are long, data analysis remains a lengthy procedure, and it is difficult to evaluate the quality of the final structures. The last years have seen significant advances in experimental techniques to overcome or reduce some limitations. The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time–scales from picoseconds to seconds. NMR is unique in its ability to obtain dynamic information on an atomic scale. The experimental information on structure and dynamics is intricately mixed. It is however difficult to unite both structural and dynamical information into one consistent model, and protocols for the determination of structure and dynamics are performed independently. This chapter deals with the challenges posed by the interpretation of NMR data on structure and dynamics. We will first relate the standard structure calculation methods to Bayesian probability theory. We will then briefly describe the advantages of a fully Bayesian treatment of structure calculation. Then, we will illustrate the advantages of using Bayesian reasoning at least partly in standard structure calculations. The final part will be devoted to interpretation of experimental data on dynamics.

ei

Web [BibTex]

2008


Web [BibTex]


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Measurement-Based Modeling for Haptic Rendering

Okamura, A. M., Kuchenbecker, K. J., Mahvash, M.

In Haptic Rendering: Algorithms and Applications, pages: 443-467, 21, A. K. Peters, May 2008 (incollection)

hi

[BibTex]

[BibTex]


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A Robot System for Biomimetic Navigation: From Snapshots to Metric Embeddings of View Graphs

Franz, MO., Stürzl, W., Reichardt, W., Mallot, HA.

In Robotics and Cognitive Approaches to Spatial Mapping, pages: 297-314, Springer Tracts in Advanced Robotics ; 38, (Editors: Jefferies, M.E. , W.-K. Yeap), Springer, Berlin, Germany, 2008 (inbook)

Abstract
Complex navigation behaviour (way-finding) involves recognizing several places and encoding a spatial relationship between them. Way-finding skills can be classified into a hierarchy according to the complexity of the tasks that can be performed [8]. The most basic form of way-finding is route navigation, followed by topological navigation where several routes are integrated into a graph-like representation. The highest level, survey navigation, is reached when this graph can be embedded into a common reference frame. In this chapter, we present the building blocks for a biomimetic robot navigation system that encompasses all levels of this hierarchy. As a local navigation method, we use scene-based homing. In this scheme, a goal location is characterized either by a panoramic snapshot of the light intensities as seen from the place, or by a record of the distances to the surrounding objects. The goal is found by moving in the direction that minimizes the discrepancy between the recorded intensities or distances and the current sensory input. For learning routes, the robot selects distinct views during exploration that are close enough to be reached by snapshot-based homing. When it encounters already visited places during route learning, it connects the routes and thus forms a topological representation of its environment termed a view graph. The final stage, survey navigation, is achieved by a graph embedding procedure which complements the topologic information of the view graph with odometric position estimates. Calculation of the graph embedding is done with a modified multidimensional scaling algorithm which makes use of distances and angles between nodes.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Hydrogen adsorption (Carbon, Zeolites, Nanocubes)

Hirscher, M., Panella, B.

In Hydrogen as a Future Energy Carrier, pages: 173-188, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, 2008 (incollection)

mms

[BibTex]

[BibTex]


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Ma\ssgeschneiderte Speichermaterialien

Hirscher, M.

In Von Brennstoffzellen bis Leuchtdioden (Energie und Chemie - Ein Bündnis für die Zukunft), pages: 31-33, Deutsche Bunsen-Gesellschaft für Physikalische Chemie e.V., Frankfurt am Main, 2008 (incollection)

mms

[BibTex]

[BibTex]

2004


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Analysis of differential gene expression in healthy and osteoarthritic cartilage and isolated chondrocytes by microarray analysis

Aigner, T., Saas, J., Zien, A., Zimmer, R., Gebhard, P., Knorr, T.

In Volume 1: Cellular and Molecular Tools, pages: 109-128, (Editors: Sabatini, M., P. Pastoureau and F. De Ceuninck), Humana Press, July 2004 (inbook)

Abstract
The regulation of chondrocytes in osteoarthritic cartilage and the expression of specific gene products by these cells during early-onset and late-stage osteoarthritis are not well characterized. With the introduction of cDNA array technology, the measurement of thousands of different genes in one small tissue sample can be carried out. Interpretation of gene expression analyses in articular cartilage is aided by the fact that this tissue contains only one cell type in both normal and diseased conditions. However, care has to be taken not to over- and misinterpret results, and some major challenges must be overcome in order to utilize the potential of this technology properly in the field of osteoarthritis.

ei

Web [BibTex]

2004


Web [BibTex]


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Distributed Command Execution

Stark, S., Berlin, M.

In BSD Hacks: 100 industrial-strength tips & tools, pages: 152-152, (Editors: Lavigne, Dru), O’Reilly, Beijing, May 2004 (inbook)

Abstract
Often you want to execute a command not only on one computer, but on several at once. For example, you might want to report the current statistics on a group of managed servers or update all of your web servers at once.

ei

[BibTex]

[BibTex]


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Local Alignment Kernels for Biological Sequences

Vert, J., Saigo, H., Akutsu, T.

In Kernel Methods in Computational Biology, pages: 131-153, MIT Press, Cambridge, MA,, 2004 (inbook)

ei

Web [BibTex]

Web [BibTex]


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Gaussian Processes in Machine Learning

Rasmussen, CE.

In 3176, pages: 63-71, Lecture Notes in Computer Science, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, 2004, Copyright by Springer (inbook)

Abstract
We give a basic introduction to Gaussian Process regression models. We focus on understanding the role of the stochastic process and how it is used to define a distribution over functions. We present the simple equations for incorporating training data and examine how to learn the hyperparameters using the marginal likelihood. We explain the practical advantages of Gaussian Process and end with conclusions and a look at the current trends in GP work.

ei

PDF PostScript [BibTex]

PDF PostScript [BibTex]


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Protein Classification via Kernel Matrix Completion

Kin, T., Kato, T., Tsuda, K.

In pages: 261-274, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

ei

PDF [BibTex]

PDF [BibTex]


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Introduction to Statistical Learning Theory

Bousquet, O., Boucheron, S., Lugosi, G.

In Lecture Notes in Artificial Intelligence 3176, pages: 169-207, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

ei

PDF [BibTex]

PDF [BibTex]


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A Primer on Kernel Methods

Vert, J., Tsuda, K., Schölkopf, B.

In Kernel Methods in Computational Biology, pages: 35-70, (Editors: B Schölkopf and K Tsuda and JP Vert), MIT Press, Cambridge, MA, USA, 2004 (inbook)

ei

PDF [BibTex]

PDF [BibTex]


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Concentration Inequalities

Boucheron, S., Lugosi, G., Bousquet, O.

In Lecture Notes in Artificial Intelligence 3176, pages: 208-240, (Editors: Bousquet, O., U. von Luxburg and G. Rätsch), Springer, Heidelberg, Germany, 2004 (inbook)

ei

PDF [BibTex]

PDF [BibTex]


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Kernels for graphs

Kashima, H., Tsuda, K., Inokuchi, A.

In pages: 155-170, (Editors: Schoelkopf, B., K. Tsuda and J.P. Vert), MIT Press, Cambridge, MA; USA, 2004 (inbook)

ei

PDF [BibTex]

PDF [BibTex]


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A primer on molecular biology

Zien, A.

In pages: 3-34, (Editors: Schoelkopf, B., K. Tsuda and J. P. Vert), MIT Press, Cambridge, MA, USA, 2004 (inbook)

Abstract
Modern molecular biology provides a rich source of challenging machine learning problems. This tutorial chapter aims to provide the necessary biological background knowledge required to communicate with biologists and to understand and properly formalize a number of most interesting problems in this application domain. The largest part of the chapter (its first section) is devoted to the cell as the basic unit of life. Four aspects of cells are reviewed in sequence: (1) the molecules that cells make use of (above all, proteins, RNA, and DNA); (2) the spatial organization of cells (``compartmentalization''); (3) the way cells produce proteins (``protein expression''); and (4) cellular communication and evolution (of cells and organisms). In the second section, an overview is provided of the most frequent measurement technologies, data types, and data sources. Finally, important open problems in the analysis of these data (bioinformatics challenges) are briefly outlined.

ei

PDF PostScript Web [BibTex]

PDF PostScript Web [BibTex]


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Development of neural motor prostheses for humans

Donoghue, J., Nurmikko, A., Friehs, G., Black, M.

In Advances in Clinical Neurophysiology, (Editors: Hallett, M. and Phillips, L.H. and Schomer, D.L. and Massey, J.M.), Supplements to Clinical Neurophysiology Vol. 57, 2004 (incollection)

ps

pdf [BibTex]

pdf [BibTex]


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Computational approaches to motor learning by imitation

Schaal, S., Ijspeert, A., Billard, A.

In The Neuroscience of Social Interaction, (1431):199-218, (Editors: Frith, C. D.;Wolpert, D.), Oxford University Press, Oxford, 2004, clmc (inbook)

Abstract
Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking - indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions.

am

link (url) [BibTex]

link (url) [BibTex]


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Effect of Grain Boundary Phase Transitions on the Superplasticity in the Al-Zn System

Lopez, G.A., Straumal, B.B., Gust, W., Mittemeijer, E.J.

In Nanomaterials by Severe Plastic Deformation, pages: 642-647, Wiley-VCH Verlag, Weinheim, 2004 (incollection)

mms

[BibTex]

[BibTex]

2003


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Support Vector Machines

Schölkopf, B., Smola, A.

In Handbook of Brain Theory and Neural Networks (2nd edition), pages: 1119-1125, (Editors: MA Arbib), MIT Press, Cambridge, MA, USA, 2003 (inbook)

ei

[BibTex]

2003


[BibTex]


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Extension of the nu-SVM range for classification

Perez-Cruz, F., Weston, J., Herrmann, D., Schölkopf, B.

In Advances in Learning Theory: Methods, Models and Applications, NATO Science Series III: Computer and Systems Sciences, Vol. 190, 190, pages: 179-196, NATO Science Series III: Computer and Systems Sciences, (Editors: J Suykens and G Horvath and S Basu and C Micchelli and J Vandewalle), IOS Press, Amsterdam, 2003 (inbook)

ei

[BibTex]

[BibTex]


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An Introduction to Support Vector Machines

Schölkopf, B.

In Recent Advances and Trends in Nonparametric Statistics , pages: 3-17, (Editors: MG Akritas and DN Politis), Elsevier, Amsterdam, The Netherlands, 2003 (inbook)

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Statistical Learning and Kernel Methods in Bioinformatics

Schölkopf, B., Guyon, I., Weston, J.

In Artificial Intelligence and Heuristic Methods in Bioinformatics, 183, pages: 1-21, 3, (Editors: P Frasconi und R Shamir), IOS Press, Amsterdam, The Netherlands, 2003 (inbook)

ei

[BibTex]

[BibTex]


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Statistical Learning and Kernel Methods

Navia-Vázquez, A., Schölkopf, B.

In Adaptivity and Learning—An Interdisciplinary Debate, pages: 161-186, (Editors: R.Kühn and R Menzel and W Menzel and U Ratsch and MM Richter and I-O Stamatescu), Springer, Berlin, Heidelberg, Germany, 2003 (inbook)

ei

[BibTex]

[BibTex]


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A Short Introduction to Learning with Kernels

Schölkopf, B., Smola, A.

In Proceedings of the Machine Learning Summer School, Lecture Notes in Artificial Intelligence, Vol. 2600, pages: 41-64, LNAI 2600, (Editors: S Mendelson and AJ Smola), Springer, Berlin, Heidelberg, Germany, 2003 (inbook)

ei

[BibTex]

[BibTex]


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Bayesian Kernel Methods

Smola, A., Schölkopf, B.

In Advanced Lectures on Machine Learning, Machine Learning Summer School 2002, Lecture Notes in Computer Science, Vol. 2600, LNAI 2600, pages: 65-117, 0, (Editors: S Mendelson and AJ Smola), Springer, Berlin, Germany, 2003 (inbook)

ei

DOI [BibTex]

DOI [BibTex]


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Stability of ensembles of kernel machines

Elisseeff, A., Pontil, M.

In 190, pages: 111-124, NATO Science Series III: Computer and Systems Science, (Editors: Suykens, J., G. Horvath, S. Basu, C. Micchelli and J. Vandewalle), IOS press, Netherlands, 2003 (inbook)

ei

[BibTex]

[BibTex]


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Investigation of the Initial Oxidation of Surfaces of Quasicrystals by High-Resolution RBS and ERDA

Plachke, D., Khellaf, A., Kurth, M., Szökefalvi-Nagy, A., Carstanjen, H. D.

In Quasicrystals: Structure and Physical Properties, pages: 598-614, Wiley-VCH GmbH & Co. KGaA, Weinheim, 2003 (incollection)

mms

[BibTex]

[BibTex]


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AMOC in positron and positronium chemistry

Stoll, H., Castellaz, P., Siegle, A.

In Principles and Applications of Positron and Positronium Chemistry, pages: 344-366, World Scientific Publishers, Singapore, 2003 (incollection)

mms

[BibTex]

[BibTex]

2002


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Bayesian Inference of Visual Motion Boundaries

Fleet, D. J., Black, M. J., Nestares, O.

In Exploring Artificial Intelligence in the New Millennium, pages: 139-174, (Editors: Lakemeyer, G. and Nebel, B.), Morgan Kaufmann Pub., July 2002 (incollection)

Abstract
This chapter addresses an open problem in visual motion analysis, the estimation of image motion in the vicinity of occlusion boundaries. With a Bayesian formulation, local image motion is explained in terms of multiple, competing, nonlinear models, including models for smooth (translational) motion and for motion boundaries. The generative model for motion boundaries explicitly encodes the orientation of the boundary, the velocities on either side, the motion of the occluding edge over time, and the appearance/disappearance of pixels at the boundary. We formulate the posterior probability distribution over the models and model parameters, conditioned on the image sequence. Approximate inference is achieved with a combination of tools: A Bayesian filter provides for online computation; factored sampling allows us to represent multimodal non-Gaussian distributions and to propagate beliefs with nonlinear dynamics from one time to the next; and mixture models are used to simplify the computation of joint prediction distributions in the Bayesian filter. To efficiently represent such a high-dimensional space, we also initialize samples using the responses of a low-level motion-discontinuity detector. The basic formulation and computational model provide a general probabilistic framework for motion estimation with multiple, nonlinear models.

ps

pdf [BibTex]

2002


pdf [BibTex]


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Learning robot control

Schaal, S.

In The handbook of brain theory and neural networks, 2nd Edition, pages: 983-987, 2, (Editors: Arbib, M. A.), MIT Press, Cambridge, MA, 2002, clmc (inbook)

Abstract
This is a review article on learning control in robots.

am

link (url) [BibTex]

link (url) [BibTex]


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Arm and hand movement control

Schaal, S.

In The handbook of brain theory and neural networks, 2nd Edition, pages: 110-113, 2, (Editors: Arbib, M. A.), MIT Press, Cambridge, MA, 2002, clmc (inbook)

Abstract
This is a review article on computational and biological research on arm and hand control.

am

link (url) [BibTex]

link (url) [BibTex]


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Ion Channeling in Quasicrystals

Plachke, D., Carstanjen, H. D.

In Quasicrystals. An Introduction to Structure, Physical Properties and Applications, 55, pages: 280-304, Springer Series in Materials Science, Springer, Berlin [et al.], 2002 (incollection)

mms

[BibTex]

[BibTex]