Publications | Max Planck Institute for Intelligent Systems

2007

mms Straumal, B. B., Baretzky, B., Kalnins, J., Aslund, A., Friesel, M. Copper alloys for the restoration of reed pipes in historic organs {Journal of Functional Materials}, 1, pages: 4-10, 2007 (article)

Inhomogeneous vortex distribution and magnetic coupling in oxide superconductor-ferromagnet hybrids

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

{New Journal of Physics}, 9, 2007 (article)

mms

mms Albrecht, J., Djupmyr, M., Soltan, S., Habermeier, H.-U., Connolly, M. R., Bending, S. J. Inhomogeneous vortex distribution and magnetic coupling in oxide superconductor-ferromagnet hybrids {New Journal of Physics}, 9, 2007 (article)

Metal hydride materials for solid hydrogen storage: a review

Sakintuna, B., Lamari-Darkrim, F., Hirscher, M.

{International Journal of Hydrogen Energy}, 32, pages: 1121-1140, 2007 (article)

mms

mms Sakintuna, B., Lamari-Darkrim, F., Hirscher, M. Metal hydride materials for solid hydrogen storage: a review {International Journal of Hydrogen Energy}, 32, pages: 1121-1140, 2007 (article)

Thermal reversal of exchange spring composite media in magnetic fields

Goll, D., Macke, S., Bertram, H. N.

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

mms

mms Goll, D., Macke, S., Bertram, H. N. Thermal reversal of exchange spring composite media in magnetic fields {Applied Physics Letters}, 90, 2007 (article)

Magnetism of Co-doped ZnO thin films

Gacic, M., Jakob, G., Herbort, C., Adrian, H., Tietze, T., Brück, S., Goering, E.

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

mms

mms Gacic, M., Jakob, G., Herbort, C., Adrian, H., Tietze, T., Brück, S., Goering, E. Magnetism of Co-doped ZnO thin films {Physical Review B}, 75, 2007 (article)

iCub - The Design and Realization of an Open Humanoid Platform for Cognitive and Neuroscience Research

Tsagarakis, N., Metta, G., Sandini, G., Vernon, D., Beira, R., Becchi, F., Righetti, L., Santos-Victor, J., Ijspeert, A., Carrozza, M., Caldwell, D.

Advanced Robotics, 21(10):1151-1175, 2007 (article)

Abstract

The development of robotic cognition and the advancement of understanding of human cognition form two of the current greatest challenges in robotics and neuroscience, respectively. The RobotCub project aims to develop an embodied robotic child (iCub) with the physical (height 90 cm and mass less than 23 kg) and ultimately cognitive abilities of a 2.5-year-old human child. The iCub will be a freely available open system which can be used by scientists in all cognate disciplines from developmental psychology to epigenetic robotics to enhance understanding of cognitive systems through the study of cognitive development. The iCub will be open both in software, but more importantly in all aspects of the hardware and mechanical design. In this paper the design of the mechanisms and structures forming the basic 'body' of the iCub are described. The papers considers kinematic structures dynamic design criteria, actuator specification and selection, and detailed mechanical and electronic design. The paper concludes with tests of the performance of sample joints, and comparison of these results with the design requirements and simulation projects.

link (url) DOI [BibTex]

mg Tsagarakis, N., Metta, G., Sandini, G., Vernon, D., Beira, R., Becchi, F., Righetti, L., Santos-Victor, J., Ijspeert, A., Carrozza, M., Caldwell, D. iCub - The Design and Realization of an Open Humanoid Platform for Cognitive and Neuroscience Research Advanced Robotics, 21(10):1151-1175, 2007 (article)

link (url) DOI [BibTex]

Subfeature patterning of organic and inorganic materials using robotic assembly

Tafazzoli, A., Cheng, C., Pawashe, C., Sabo, E. K., Trofin, L., Sitti, M., LeDuc, P. R.

Journal of materials research, 22(06):1601-1608, Cambridge University Press, 2007 (article)

pi Tafazzoli, A., Cheng, C., Pawashe, C., Sabo, E. K., Trofin, L., Sitti, M., LeDuc, P. R. Subfeature patterning of organic and inorganic materials using robotic assembly Journal of materials research, 22(06):1601-1608, Cambridge University Press, 2007 (article)

Effect of backing layer thickness on adhesion of single-level elastomer fiber arrays

Kim, S., Sitti, M., Hui, C., Long, R., Jagota, A.

Applied Physics Letters, 91(16):161905, AIP, 2007 (article)

pi Kim, S., Sitti, M., Hui, C., Long, R., Jagota, A. Effect of backing layer thickness on adhesion of single-level elastomer fiber arrays Applied Physics Letters, 91(16):161905, AIP, 2007 (article)

Universal temperature scaling of flux line pinning in high-temperature superconducting thin films

Albrecht, J., Djupmyr, M., Brück, S.

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

mms

mms Albrecht, J., Djupmyr, M., Brück, S. Universal temperature scaling of flux line pinning in high-temperature superconducting thin films {Journal of Physics: Condensed Matter}, 19, 2007 (article)

Dependence of the critical temperature of YBCO thin films on spin-polarized quasiparticle injection

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

{Physica C}, 460-462, pages: 32-35, 2007 (article)

mms

mms Habermeier, H.-U., Soltan, S., Albrecht, J. Dependence of the critical temperature of YBCO thin films on spin-polarized quasiparticle injection {Physica C}, 460-462, pages: 32-35, 2007 (article)

Interaction of ferromagnetic LCMO layers through a superconducting YBCO spacer

Ravikumar, G., Yashwant, G., Singh, M. R., Gupta, S. K., Bhattacharya, S., Soltan, S., Albrecht, J., Habermeier, H.-U.

{Physica C}, 460-462, pages: 1375-1376, 2007 (article)

mms

mms Ravikumar, G., Yashwant, G., Singh, M. R., Gupta, S. K., Bhattacharya, S., Soltan, S., Albrecht, J., Habermeier, H.-U. Interaction of ferromagnetic LCMO layers through a superconducting YBCO spacer {Physica C}, 460-462, pages: 1375-1376, 2007 (article)

Vortex dynamics in Permalloy disks with artificial defects: suppression of the gyrotropic mode

Kuepper, K., Bischoff, L., Akhmadaliev, C., Fassbinder, J., Stoll, H., Chou, K., Puzic, A., Fauth, K., Dolgos, D., Schütz, G., Van Waeyenberge, B., Tyliszczak, T., Neudecker, I., Woltersdorf, G., Back, C.

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

mms

mms Kuepper, K., Bischoff, L., Akhmadaliev, C., Fassbinder, J., Stoll, H., Chou, K., Puzic, A., Fauth, K., Dolgos, D., Schütz, G., Van Waeyenberge, B., Tyliszczak, T., Neudecker, I., Woltersdorf, G., Back, C. Vortex dynamics in Permalloy disks with artificial defects: suppression of the gyrotropic mode {Appplied Physics Letters}, 90, 2007 (article)

Vacancy-interstitial annihilation in titanomagnetite by thermal annealing

Walz, F., Brabers, V. A. M., Brabers, J. H. V. J., Kronmüller, H.

{Physica Status Solidi (A)}, 204(10):3514-3525, 2007 (article)

mms

mms Walz, F., Brabers, V. A. M., Brabers, J. H. V. J., Kronmüller, H. Vacancy-interstitial annihilation in titanomagnetite by thermal annealing {Physica Status Solidi (A)}, 204(10):3514-3525, 2007 (article)

Theory of X-ray absorption spectroscopy in solids: mixing of the core states by the aspherical effective potential

Kostoglou, C., Komelj, M., Fähnle, M.

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

mms

mms Kostoglou, C., Komelj, M., Fähnle, M. Theory of X-ray absorption spectroscopy in solids: mixing of the core states by the aspherical effective potential {Physical Review B}, 75, 2007 (article)

Zinc oxide microcapsules obtained via a bio-inspired approach

Lipowsky, P., Hirscher, M., Hoffmann, R. C., Bill, J., Aldinger, F.

{Nanotechnology}, 18, 2007 (article)

mms

mms Lipowsky, P., Hirscher, M., Hoffmann, R. C., Bill, J., Aldinger, F. Zinc oxide microcapsules obtained via a bio-inspired approach {Nanotechnology}, 18, 2007 (article)

Grain boundary phase observed in Al-5 at.\textpercent Zn alloy by using HREM

Straumal, B. B., Mazilkin, A. A., Kogtenkova, O. A., Protasova, S. G., Baretzky, B.

{Philosophical Magazine Letters}, 87(6):423-430, 2007 (article)

mms

mms Straumal, B. B., Mazilkin, A. A., Kogtenkova, O. A., Protasova, S. G., Baretzky, B. Grain boundary phase observed in Al-5 at.\textpercent Zn alloy by using HREM {Philosophical Magazine Letters}, 87(6):423-430, 2007 (article)

Transport current improvements of in situ MgB2 tapes by the addition of carbon nanotubes, silicon carbide or graphite

Kovac, P., Husek, I., Skakalova, V., Meyer, J., Dobrocka, E., Hirscher, M., Roth, S.

{Superconductor Science and Technology}, 20, pages: 105-111, 2007 (article)

mms

mms Kovac, P., Husek, I., Skakalova, V., Meyer, J., Dobrocka, E., Hirscher, M., Roth, S. Transport current improvements of in situ MgB2 tapes by the addition of carbon nanotubes, silicon carbide or graphite {Superconductor Science and Technology}, 20, pages: 105-111, 2007 (article)

Adhesion and anisotropic friction enhancements of angled heterogeneous micro-fiber arrays with spherical and spatula tips

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

Journal of Adhesion Science and Technology, 21(12-13):1281-1296, Taylor & Francis Group, 2007 (article)

Project Page [BibTex]

pi Murphy, M. P., Aksak, B., Sitti, M. Adhesion and anisotropic friction enhancements of angled heterogeneous micro-fiber arrays with spherical and spatula tips Journal of Adhesion Science and Technology, 21(12-13):1281-1296, Taylor & Francis Group, 2007 (article)

Project Page [BibTex]

Surface-tension-driven biologically inspired water strider robots: Theory and experiments

Song, Y. S., Sitti, M.

IEEE Transactions on robotics, 23(3):578-589, IEEE, 2007 (article)

pi Song, Y. S., Sitti, M. Surface-tension-driven biologically inspired water strider robots: Theory and experiments IEEE Transactions on robotics, 23(3):578-589, IEEE, 2007 (article)

Absorption spectroscopy and XMCD at the Verwey transition of Fe3O4

Goering, E., Lafkioti, M., Gold, S., Schütz, G.

{Journal of Magnetism and Magnetic Materials}, 310, pages: 249-251, 2007 (article)

mms

mms Goering, E., Lafkioti, M., Gold, S., Schütz, G. Absorption spectroscopy and XMCD at the Verwey transition of Fe3O4 {Journal of Magnetism and Magnetic Materials}, 310, pages: 249-251, 2007 (article)

Overcoming the Dipolar Disorder in Dense CoFe Nanoparticle Ensembles: Superferromagnetism

Bedanta, S., Eimüller, T., Kleemann, W., Rhensius, J., Stromberg, F., Amaladass, E., Cardoso, S., Freitas, P. P.

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

mms

mms Bedanta, S., Eimüller, T., Kleemann, W., Rhensius, J., Stromberg, F., Amaladass, E., Cardoso, S., Freitas, P. P. Overcoming the Dipolar Disorder in Dense CoFe Nanoparticle Ensembles: Superferromagnetism {Physical Review Letters}, 98, 2007 (article)

Ultrafast nanomagnetic toggle switching of vortex cores

Hertel, R., Gliga, S., Fähnle, M., Schneider, C. M.

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

mms

mms Hertel, R., Gliga, S., Fähnle, M., Schneider, C. M. Ultrafast nanomagnetic toggle switching of vortex cores {Physical Review Letters}, 98, 2007 (article)

Element-specific spin and orbital momentum dynamics of Fe/Gd multilayers

Bartelt, A. F., Comin, A., Feng, J., Nasiatka, J. R., Eimüller, T., Ludescher, B., Schütz, G., Padmore, H. A., Young, A. T., Scholl, A.

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

mms

mms Bartelt, A. F., Comin, A., Feng, J., Nasiatka, J. R., Eimüller, T., Ludescher, B., Schütz, G., Padmore, H. A., Young, A. T., Scholl, A. Element-specific spin and orbital momentum dynamics of Fe/Gd multilayers {Applied Physics Letters}, 90, 2007 (article)

Slow relaxation of spin reorientation following ultrafast optical excitation

Eimüller, T., Scholl, A., Ludescher, B., Schütz, G., Thiele, J.

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

mms

mms Eimüller, T., Scholl, A., Ludescher, B., Schütz, G., Thiele, J. Slow relaxation of spin reorientation following ultrafast optical excitation {Applied Physics Letters}, 91, 2007 (article)

One-pot synthesis of core-shell FeRh nanoparticles

Ciuculescu, D., Amiens, C., Respaud, M., Falqui, A., Lecante, P., Benfield, R. E., Jiang, L., Fauth, K., Chaudret, B.

{Chemistry of Materials}, 19(19):4624-4626, 2007 (article)

mms

mms Ciuculescu, D., Amiens, C., Respaud, M., Falqui, A., Lecante, P., Benfield, R. E., Jiang, L., Fauth, K., Chaudret, B. One-pot synthesis of core-shell FeRh nanoparticles {Chemistry of Materials}, 19(19):4624-4626, 2007 (article)

Spin-polarized quasiparticles injection effects in the normal state of YBCO thin films

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

{Physica C}, 460-462, pages: 1088-1089, 2007 (article)

mms

mms Soltan, S., Albrecht, J., Habermeier, H.-U. Spin-polarized quasiparticles injection effects in the normal state of YBCO thin films {Physica C}, 460-462, pages: 1088-1089, 2007 (article)

Direct observation of the vortex core magnetization and its dynamics

Chou, K. W., Puzic, A., Stoll, H., Dolgos, D., Schütz, G., Van Waeyenberge, B., Vansteenkiste, A., Tyliszczak, T., Woltersdorf, G., Back, C. H.

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

mms

mms Chou, K. W., Puzic, A., Stoll, H., Dolgos, D., Schütz, G., Van Waeyenberge, B., Vansteenkiste, A., Tyliszczak, T., Woltersdorf, G., Back, C. H. Direct observation of the vortex core magnetization and its dynamics {Applied Physics Letters}, 90, 2007 (article)

Superparamagnetism in small Fe clusters on Cu(111)

Ballentine, G., He\ssler, M., Kinza, M., Fauth, K.

{The European Physical Journal D}, 45, pages: 535-537, 2007 (article)

mms

mms Ballentine, G., He\ssler, M., Kinza, M., Fauth, K. Superparamagnetism in small Fe clusters on Cu(111) {The European Physical Journal D}, 45, pages: 535-537, 2007 (article)

2006

Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation

Nicastro, G., Habeck, M., Masino, L., Svergun, DI., Pastore, A.

Journal of Biomolecular NMR, 36(4):267-277, December 2006 (article)

Abstract

The availability of new and fast tools in structure determination has led to a more than exponential growth of the number of structures solved per year. It is therefore increasingly essential to assess the accuracy of the new structures by reliable approaches able to assist validation. Here, we discuss a specific example in which the use of different complementary techniques, which include Bayesian methods and small angle scattering, resulted essential for validating the two currently available structures of the Josephin domain of ataxin-3, a protein involved in the ubiquitin/proteasome pathway and responsible for neurodegenerative spinocerebellar ataxia of type 3. Taken together, our results demonstrate that only one of the two structures is compatible with the experimental information. Based on the high precision of our refined structure, we show that Josephin contains an open cleft which could be directly implicated in the interaction with polyubiquitin chains and other partners.

2006

ei Nicastro, G., Habeck, M., Masino, L., Svergun, DI., Pastore, A. Structure validation of the Josephin domain of ataxin-3: Conclusive evidence for an open conformation Journal of Biomolecular NMR, 36(4):267-277, December 2006 (article)

A Unifying View of Wiener and Volterra Theory and Polynomial Kernel Regression

Franz, M., Schölkopf, B.

Neural Computation, 18(12):3097-3118, December 2006 (article)

Abstract

Volterra and Wiener series are perhaps the best understood nonlinear system representations in signal processing. Although both approaches have enjoyed a certain popularity in the past, their application has been limited to rather low-dimensional and weakly nonlinear systems due to the exponential growth of the number of terms that have to be estimated. We show that Volterra and Wiener series can be represented implicitly as elements of a reproducing kernel Hilbert space by utilizing polynomial kernels. The estimation complexity of the implicit representation is linear in the input dimensionality and independent of the degree of nonlinearity. Experiments show performance advantages in terms of convergence, interpretability, and system sizes that can be handled.

ei Franz, M., Schölkopf, B. A Unifying View of Wiener and Volterra Theory and Polynomial Kernel Regression Neural Computation, 18(12):3097-3118, December 2006 (article)

Induced Master Motion in Force-Reflecting Teleoperation

Kuchenbecker, K. J., Niemeyer, G.

ASME Journal of Dynamic Systems, Measurement, and Control, 128(4):800-810, December 2006 (article)

hi Kuchenbecker, K. J., Niemeyer, G. Induced Master Motion in Force-Reflecting Teleoperation ASME Journal of Dynamic Systems, Measurement, and Control, 128(4):800-810, December 2006 (article)

Spatial four-alternative forced-choice method is the preferred psychophysical method for naive observers

Jäkel, F., Wichmann, F.

Journal of Vision, 6(11):1307-1322, November 2006 (article)

ei Jäkel, F., Wichmann, F. Spatial four-alternative forced-choice method is the preferred psychophysical method for naive observers Journal of Vision, 6(11):1307-1322, November 2006 (article)

Statistical Analysis of Slow Crack Growth Experiments

Pfingsten, T., Glien, K.

Journal of the European Ceramic Society, 26(15):3061-3065, November 2006 (article)

Abstract

A common approach for the determination of Slow Crack Growth (SCG) parameters are the static and dynamic loading method. Since materials with small Weibull module show a large variability in strength, a correct statistical analysis of the data is indispensable. In this work we propose the use of the Maximum Likelihood method and a Baysian analysis, which, in contrast to the standard procedures, take into account that failure strengths are Weibull distributed. The analysis provides estimates for the SCG parameters, the Weibull module, and the corresponding confidence intervals and overcomes the necessity of manual differentiation between inert and fatigue strength data. We compare the methods to a Least Squares approach, which can be considered the standard procedure. The results for dynamic loading data from the glass sealing of MEMS devices show that the assumptions inherent to the standard approach lead to significantly different estimates.

ei Pfingsten, T., Glien, K. Statistical Analysis of Slow Crack Growth Experiments Journal of the European Ceramic Society, 26(15):3061-3065, November 2006 (article)

An Improved Adaptive Power Line Interference Canceller for Electrocardiography

Martens, SMM., Mischi, M., Oei, SG., Bergmans, JWM.

IEEE Transactions on Biomedical Engineering, 53(11):2220-2231, November 2006 (article)

Abstract

Power line interference may severely corrupt a biomedical recording. Notch filters and adaptive cancellers have been suggested to suppress this interference. We propose an improved adaptive canceller for the reduction of the fundamental power line interference component and harmonics in electrocardiogram (ECG) recordings. The method tracks the amplitude, phase, and frequency of all the interference components for power line frequency deviations up to about 4 Hz. A comparison is made between the performance of our method, former adaptive cancellers, and a narrow and a wide notch filter in suppressing the fundamental power line interference component. For this purpose a real ECG signal is corrupted by an artificial power line interference signal. The cleaned signal after applying all methods is compared with the original ECG signal. Our improved adaptive canceller shows a signal-to-power-line-interference ratio for the fundamental component up to 30 dB higher than that produced by the other methods. Moreover, our method is also effective for the suppression of the harmonics of the power line interference.

ei Martens, SMM., Mischi, M., Oei, SG., Bergmans, JWM. An Improved Adaptive Power Line Interference Canceller for Electrocardiography IEEE Transactions on Biomedical Engineering, 53(11):2220-2231, November 2006 (article)

Donagi-Markman cubic for Hitchin systems

Balduzzi, D.

Mathematical Research Letters, 13(6):923-933, November 2006 (article)

Abstract

The Donagi-Markman cubic is the differential of the period map for algebraic completely integrable systems. Here we prove a formula for the cubic in the case of Hitchin’s system for arbitrary semisimple g. This was originally stated (without proof) by Pantev for sln.

Web [BibTex]

ei Balduzzi, D. Donagi-Markman cubic for Hitchin systems Mathematical Research Letters, 13(6):923-933, November 2006 (article)

Web [BibTex]

Mining frequent stem patterns from unaligned RNA sequences

Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K.

Bioinformatics, 22(20):2480-2487, October 2006 (article)

Abstract

Motivation: In detection of non-coding RNAs, it is often necessary to identify the secondary structure motifs from a set of putative RNA sequences. Most of the existing algorithms aim to provide the best motif or few good motifs, but biologists often need to inspect all the possible motifs thoroughly. Results: Our method RNAmine employs a graph theoretic representation of RNA sequences, and detects all the possible motifs exhaustively using a graph mining algorithm. The motif detection problem boils down to finding frequently appearing patterns in a set of directed and labeled graphs. In the tasks of common secondary structure prediction and local motif detection from long sequences, our method performed favorably both in accuracy and in efficiency with the state-of-the-art methods such as CMFinder.

ei Hamada, M., Tsuda, K., Kudo, T., Kin, T., Asai, K. Mining frequent stem patterns from unaligned RNA sequences Bioinformatics, 22(20):2480-2487, October 2006 (article)

Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis

Aigner, T., Fundel, K., Saas, J., Gebhard, P., Haag, J., Weiss, T., Zien, A., Obermayr, F., Zimmer, R., Bartnik, E.

Arthritis and Rheumatism, 54(11):3533-3544, October 2006 (article)

Abstract

Objective. Despite many research efforts in recent decades, the major pathogenetic mechanisms of osteo- arthritis (OA), including gene alterations occurring during OA cartilage degeneration, are poorly under- stood, and there is no disease-modifying treatment approach. The present study was therefore initiated in order to identify differentially expressed disease-related genes and potential therapeutic targets. Methods. This investigation consisted of a large gene expression profiling study performed based on 78 normal and disease samples, using a custom-made complementar y DNA array covering >4,000 genes. Results. Many differentially expressed genes were identified, including the expected up-regulation of ana- bolic and catabolic matrix genes. In particular, the down-regulation of important oxidative defense genes, i.e., the genes for superoxide dismutases 2 and 3 and glutathione peroxidase 3, was prominent. This indicates that continuous oxidative stress to the cells and the matrix is one major underlying pathogenetic mecha- nism in OA. Also, genes that are involved in the phenot ypic stabilit y of cells, a feature that is greatly reduced in OA cartilage, appeared to be suppressed. Conclusion. Our findings provide a reference data set on gene alterations in OA cartilage and, importantly, indicate major mechanisms underlying central cell bio- logic alterations that occur during the OA disease process. These results identify molecular targets that can be further investigated in the search for therapeutic interventions.

ei Aigner, T., Fundel, K., Saas, J., Gebhard, P., Haag, J., Weiss, T., Zien, A., Obermayr, F., Zimmer, R., Bartnik, E. Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis Arthritis and Rheumatism, 54(11):3533-3544, October 2006 (article)

Walder, C., Schölkopf, B., Chapelle, O.

Implicit Surface Modelling with a Globally Regularised Basis of Compact Support

Computer Graphics Forum, 25(3):635-644, September 2006 (article)

Abstract

We consider the problem of constructing a globally smooth analytic function that represents a surface implicitly by way of its zero set, given sample points with surface normal vectors. The contributions of the paper include a novel means of regularising multi-scale compactly supported basis functions that leads to the desirable interpolation properties previously only associated with fully supported bases. We also provide a regularisation framework for simpler and more direct treatment of surface normals, along with a corresponding generalisation of the representer theorem lying at the core of kernel-based machine learning methods. We demonstrate the techniques on 3D problems of up to 14 million data points, as well as 4D time series data and four-dimensional interpolation between three-dimensional shapes.

PDF GZIP DOI [BibTex]

ei Walder, C., Schölkopf, B., Chapelle, O. Implicit Surface Modelling with a Globally Regularised Basis of Compact Support Computer Graphics Forum, 25(3):635-644, September 2006 (article)

PDF GZIP DOI [BibTex]

From outliers to prototypes: Ordering data

Harmeling, S., Dornhege, G., Tax, D., Meinecke, F., Müller, K.

Neurocomputing, 69(13-15):1608-1618, August 2006 (article)

Abstract

We propose simple and fast methods based on nearest neighbors that order objects from high-dimensional data sets from typical points to untypical points. On the one hand, we show that these easy-to-compute orderings allow us to detect outliers (i.e. very untypical points) with a performance comparable to or better than other often much more sophisticated methods. On the other hand, we show how to use these orderings to detect prototypes (very typical points) which facilitate exploratory data analysis algorithms such as noisy nonlinear dimensionality reduction and clustering. Comprehensive experiments demonstrate the validity of our approach.

ei Harmeling, S., Dornhege, G., Tax, D., Meinecke, F., Müller, K. From outliers to prototypes: Ordering data Neurocomputing, 69(13-15):1608-1618, August 2006 (article)

An Online Support Vector Machine for Abnormal Events Detection

Davy, M., Desobry, F., Gretton, A., Doncarli, C.

Signal Processing, 86(8):2009-2025, August 2006 (article)

Abstract

The ability to detect online abnormal events in signals is essential in many real-world Signal Processing applications. Previous algorithms require an explicit signal statistical model, and interpret abnormal events as statistical model abrupt changes. Corresponding implementation relies on maximum likelihood or on Bayes estimation theory with generally excellent performance. However, there are numerous cases where a robust and tractable model cannot be obtained, and model-free approaches need to be considered. In this paper, we investigate a machine learning, descriptor-based approach that does not require an explicit descriptors statistical model, based on Support Vector novelty detection. A sequential optimization algorithm is introduced. Theoretical considerations as well as simulations on real signals demonstrate its practical efficiency.

PDF PostScript PDF DOI [BibTex]

ei Davy, M., Desobry, F., Gretton, A., Doncarli, C. An Online Support Vector Machine for Abnormal Events Detection Signal Processing, 86(8):2009-2025, August 2006 (article)

PDF PostScript PDF DOI [BibTex]

Integrating Structured Biological data by Kernel Maximum Mean Discrepancy

Borgwardt, K., Gretton, A., Rasch, M., Kriegel, H., Schölkopf, B., Smola, A.

Bioinformatics, 22(4: ISMB 2006 Conference Proceedings):e49-e57, August 2006 (article)

Abstract

Motivation: Many problems in data integration in bioinformatics can be posed as one common question: Are two sets of observations generated by the same distribution? We propose a kernel-based statistical test for this problem, based on the fact that two distributions are different if and only if there exists at least one function having different expectation on the two distributions. Consequently we use the maximum discrepancy between function means as the basis of a test statistic. The Maximum Mean Discrepancy (MMD) can take advantage of the kernel trick, which allows us to apply it not only to vectors, but strings, sequences, graphs, and other common structured data types arising in molecular biology. Results: We study the practical feasibility of an MMD-based test on three central data integration tasks: Testing cross-platform comparability of microarray data, cancer diagnosis, and data-content based schema matching for two different protein function classification schemas. In all of these experiments, including high-dimensional ones, MMD is very accurate in finding samples that were generated from the same distribution, and outperforms its best competitors. Conclusions: We have defined a novel statistical test of whether two samples are from the same distribution, compatible with both multivariate and structured data, that is fast, easy to implement, and works well, as confirmed by our experiments.

ei Borgwardt, K., Gretton, A., Rasch, M., Kriegel, H., Schölkopf, B., Smola, A. Integrating Structured Biological data by Kernel Maximum Mean Discrepancy Bioinformatics, 22(4: ISMB 2006 Conference Proceedings):e49-e57, August 2006 (article)

Bousquet, O., Schölkopf, B.

Comment on “Support vector machines with applications” by J. M. Moguerza and A. Muñoz

Statistical Science, 21(3):337-340, August 2006 (article)

ei Bousquet, O., Schölkopf, B. Comment on “Support vector machines with applications” by J. M. Moguerza and A. Muñoz Statistical Science, 21(3):337-340, August 2006 (article)

Large Scale Transductive SVMs

Collobert, R., Sinz, F., Weston, J., Bottou, L.

Journal of Machine Learning Research, 7, pages: 1687-1712, August 2006 (article)

Abstract

We show how the Concave-Convex Procedure can be applied to the optimization of Transductive SVMs, which traditionally requires solving a combinatorial search problem. This provides for the first time a highly scalable algorithm in the nonlinear case. Detailed experiments verify the utility of our approach.

PostScript PDF PDF [BibTex]

ei Collobert, R., Sinz, F., Weston, J., Bottou, L. Large Scale Transductive SVMs Journal of Machine Learning Research, 7, pages: 1687-1712, August 2006 (article)

PostScript PDF PDF [BibTex]

Building Support Vector Machines with Reduced Classifier Complexity

Keerthi, S., Chapelle, O., DeCoste, D.

Journal of Machine Learning Research, 7, pages: 1493-1515, July 2006 (article)

Abstract

Support vector machines (SVMs), though accurate, are not preferred in applications requiring great classification speed, due to the number of support vectors being large. To overcome this problem we devise a primal method with the following properties: (1) it decouples the idea of basis functions from the concept of support vectors; (2) it greedily finds a set of kernel basis functions of a specified maximum size ($dmax$) to approximate the SVM primal cost function well; (3) it is efficient and roughly scales as $O(ndmax^2)$ where $n$ is the number of training examples; and, (4) the number of basis functions it requires to achieve an accuracy close to the SVM accuracy is usually far less than the number of SVM support vectors.

ei Keerthi, S., Chapelle, O., DeCoste, D. Building Support Vector Machines with Reduced Classifier Complexity Journal of Machine Learning Research, 7, pages: 1493-1515, July 2006 (article)

ARTS: Accurate Recognition of Transcription Starts in Human

Sonnenburg, S., Zien, A., Rätsch, G.

Bioinformatics, 22(14):e472-e480, July 2006 (article)

Abstract

Motivation: One of the most important features of genomic DNA are the protein-coding genes. While it is of great value to identify those genes and the encoded proteins, it is also crucial to understand how their transcription is regulated. To this end one has to identify the corresponding promoters and the contained transcription factor binding sites. TSS finders can be used to locate potential promoters. They may also be used in combination with other signal and content detectors to resolve entire gene structures. Results: We have developed a novel kernel based method - called ARTS - that accurately recognizes transcription start sites in human. The application of otherwise too computationally expensive Support Vector Machines was made possible due to the use of efficient training and evaluation techniques using suffix tries. In a carefully designed experimental study, we compare our TSS finder to state-of-the-art methods from the literature: McPromoter, Eponine and FirstEF. For given false positive rates within a reasonable range, we consistently achieve considerably higher true positive rates. For instance, ARTS finds about 24% true positives at a false positive rate of 1/1000, where the other methods find less than half (10.5%). Availability: Datasets, model selection results, whole genome predictions, and additional experimental results are available at http://www.fml.tuebingen.mpg.de/raetsch/projects/arts

ei Sonnenburg, S., Zien, A., Rätsch, G. ARTS: Accurate Recognition of Transcription Starts in Human Bioinformatics, 22(14):e472-e480, July 2006 (article)

Large Scale Multiple Kernel Learning

Sonnenburg, S., Rätsch, G., Schäfer, C., Schölkopf, B.

Journal of Machine Learning Research, 7, pages: 1531-1565, July 2006 (article)

Abstract

While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lanckriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constrained quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard SVM implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm works for hundred thousands of examples or hundreds of kernels to be combined, and helps for automatic model selection, improving the interpretability of the learning result. In a second part we discuss general speed up mechanism for SVMs, especially when used with sparse feature maps as appear for string kernels, allowing us to train a string kernel SVM on a 10 million real-world splice data set from computational biology. We integrated multiple kernel learning in our machine learning toolbox SHOGUN for which the source code is publicly available at http://www.fml.tuebingen.mpg.de/raetsch/projects/shogun.

ei Sonnenburg, S., Rätsch, G., Schäfer, C., Schölkopf, B. Large Scale Multiple Kernel Learning Journal of Machine Learning Research, 7, pages: 1531-1565, July 2006 (article)

Factorial coding of natural images: how effective are linear models in removing higher-order dependencies?

Bethge, M.

Journal of the Optical Society of America A, 23(6):1253-1268, June 2006 (article)

Abstract

The performance of unsupervised learning models for natural images is evaluated quantitatively by means of information theory. We estimate the gain in statistical independence (the multi-information reduction) achieved with independent component analysis (ICA), principal component analysis (PCA), zero-phase whitening, and predictive coding. Predictive coding is translated into the transform coding framework, where it can be characterized by the constraint of a triangular filter matrix. A randomly sampled whitening basis and the Haar wavelet are included into the comparison as well. The comparison of all these methods is carried out for different patch sizes, ranging from 2x2 to 16x16 pixels. In spite of large differences in the shape of the basis functions, we find only small differences in the multi-information between all decorrelation transforms (5% or less) for all patch sizes. Among the second-order methods, PCA is optimal for small patch sizes and predictive coding performs best for large patch sizes. The extra gain achieved with ICA is always less than 2%. In conclusion, the `edge filters&amp;amp;amp;lsquo; found with ICA lead only to a surprisingly small improvement in terms of its actual objective.

PDF Web [BibTex]

ei Bethge, M. Factorial coding of natural images: how effective are linear models in removing higher-order dependencies? Journal of the Optical Society of America A, 23(6):1253-1268, June 2006 (article)

PDF Web [BibTex]

Classifying EEG and ECoG Signals without Subject Training for Fast BCI Implementation: Comparison of Non-Paralysed and Completely Paralysed Subjects

Hill, N., Lal, T., Schröder, M., Hinterberger, T., Wilhelm, B., Nijboer, F., Mochty, U., Widman, G., Elger, C., Schölkopf, B., Kübler, A., Birbaumer, N.

IEEE Transactions on Neural Systems and Rehabilitation Engineering, 14(2):183-186, June 2006 (article)

Abstract

We summarize results from a series of related studies that aim to develop a motor-imagery-based brain-computer interface using a single recording session of EEG or ECoG signals for each subject. We apply the same experimental and analytical methods to 11 non-paralysed subjects (8 EEG, 3 ECoG), and to 5 paralysed subjects (4 EEG, 1 ECoG) who had been unable to communicate for some time. While it was relatively easy to obtain classifiable signals quickly from most of the non-paralysed subjects, it proved impossible to classify the signals obtained from the paralysed patients by the same methods. This highlights the fact that though certain BCI paradigms may work well with healthy subjects, this does not necessarily indicate success with the target user group. We outline possible reasons for this failure to transfer.

ei Hill, N., Lal, T., Schröder, M., Hinterberger, T., Wilhelm, B., Nijboer, F., Mochty, U., Widman, G., Elger, C., Schölkopf, B., Kübler, A., Birbaumer, N. Classifying EEG and ECoG Signals without Subject Training for Fast BCI Implementation: Comparison of Non-Paralysed and Completely Paralysed Subjects IEEE Transactions on Neural Systems and Rehabilitation Engineering, 14(2):183-186, June 2006 (article)

SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments

Tabei, Y., Tsuda, K., Kin, T., Asai, K.

Bioinformatics, 22(14):1723-1729, May 2006 (article)

Abstract

The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but their potential secondary structures. Sankoff&lsquo;s algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required. We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable to the much slower existing algorithms.

ei Tabei, Y., Tsuda, K., Kin, T., Asai, K. SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments Bioinformatics, 22(14):1723-1729, May 2006 (article)

Response Modeling with Support Vector Machines

Shin, H., Cho, S.

Expert Systems with Applications, 30(4):746-760, May 2006 (article)

Abstract

Support Vector Machine (SVM) employs Structural Risk minimization (SRM) principle to generalize better than conventional machine learning methods employing the traditional Empirical Risk Minimization (ERM) principle. When applying SVM to response modeling in direct marketing,h owever,one has to deal with the practical difficulties: large training data,class imbalance and binary SVM output. This paper proposes ways to alleviate or solve the addressed difficulties through informative sampling,u se of different costs for different classes, and use of distance to decision boundary. This paper also provides various evaluation measures for response models in terms of accuracies,lift chart analysis and computational efficiency.

ei Shin, H., Cho, S. Response Modeling with Support Vector Machines Expert Systems with Applications, 30(4):746-760, May 2006 (article)