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2008


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ISD: A Software Package for Bayesian NMR Structure Calculation

Rieping, W., Nilges, M., Habeck, M.

Bioinformatics, 24(8):1104-1105, February 2008 (article)

Abstract
SUMMARY: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The Inferential Structure Determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology. AVAILABILITY: The program is available at http://www.bioc.cam.ac.uk/isd

ei

Web DOI [BibTex]

2008


Web DOI [BibTex]


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Probabilistic Structure Calculation

Nilges, M., Habeck, M., Rieping, W.

Comptes Rendus Chimie, 11(4-5):356-369, February 2008 (article)

Abstract
Molecular structures are usually calculated from experimental data with some method of energy minimisation or non-linear optimisation. Key aims of a structure calculation are to estimate the coordinate uncertainty, and to provide a meaningful measure of the quality of the fit to the data. We discuss approaches to optimally combine prior information and experimental data and the connection to probability theory. We analyse the appropriate statistics for NOEs and NOE-derived distances, and the related question of restraint potentials. Finally, we will discuss approaches to determine the appropriate weight on the experimental evidence and to obtain in this way an estimate of the data quality from the structure calculation. Whereas objective estimates of coordinates and their uncertainties can only be obtained by a full Bayesian treatment of the problem, standard structure calculation methods continue to play an important role. To obtain the full benefit of these methods, they should be founded on a rigorous Baye sian analysis.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Fast Projection-based Methods for the Least Squares Nonnegative Matrix Approximation Problem

Kim, D., Sra, S., Dhillon, I.

Statistical Analysis and Data Mining, 1(1):38-51, February 2008 (article)

Abstract
Nonnegative matrix approximation (NNMA) is a popular matrix decomposition technique that has proven to be useful across a diverse variety of fields with applications ranging from document analysis and image processing to bioinformatics and signal processing. Over the years, several algorithms for NNMA have been proposed, e.g. Lee and Seung‘s multiplicative updates, alternating least squares (ALS), and gradient descent-based procedures. However, most of these procedures suffer from either slow convergence, numerical instability, or at worst, serious theoretical drawbacks. In this paper, we develop a new and improved algorithmic framework for the least-squares NNMA problem, which is not only theoretically well-founded, but also overcomes many deficiencies of other methods. Our framework readily admits powerful optimization techniques and as concrete realizations we present implementations based on the Newton, BFGS and conjugate gradient methods. Our algorithms provide numerical resu lts supe rior to both Lee and Seung‘s method as well as to the alternating least squares heuristic, which was reported to work well in some situations but has no theoretical guarantees[1]. Our approach extends naturally to include regularization and box-constraints without sacrificing convergence guarantees. We present experimental results on both synthetic and real-world datasets that demonstrate the superiority of our methods, both in terms of better approximations as well as computational efficiency.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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A Unifying Probabilistic Framework for Analyzing Residual Dipolar Couplings

Habeck, M., Nilges, M., Rieping, W.

Journal of Biomolecular NMR, 40(2):135-144, February 2008 (article)

Abstract
Residual dipolar couplings provide complementary information to the nuclear Overhauser effect measurements that are traditionally used in biomolecular structure determination by NMR. In a de novo structure determination, however, lack of knowledge about the degree and orientation of molecular alignment complicates the analysis of dipolar coupling data. We present a probabilistic framework for analyzing residual dipolar couplings and demonstrate that it is possible to estimate the atomic coordinates, the complete molecular alignment tensor, and the error of the couplings simultaneously. As a by-product, we also obtain estimates of the uncertainty in the coordinates and the alignment tensor. We show that our approach encompasses existing methods for determining the alignment tensor as special cases, including least squares estimation, histogram fitting, and elimination of an explicit alignment tensor in the restraint energy.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Contour-propagation Algorithms for Semi-automated Reconstruction of Neural Processes

Macke, J., Maack, N., Gupta, R., Denk, W., Schölkopf, B., Borst, A.

Journal of Neuroscience Methods, 167(2):349-357, January 2008 (article)

Abstract
A new technique, ”Serial Block Face Scanning Electron Microscopy” (SBFSEM), allows for automatic sectioning and imaging of biological tissue with a scanning electron microscope. Image stacks generated with this technology have a resolution sufficient to distinguish different cellular compartments, including synaptic structures, which should make it possible to obtain detailed anatomical knowledge of complete neuronal circuits. Such an image stack contains several thousands of images and is recorded with a minimal voxel size of 10-20nm in the x and y- and 30nm in z-direction. Consequently, a tissue block of 1mm3 (the approximate volume of the Calliphora vicina brain) will produce several hundred terabytes of data. Therefore, highly automated 3D reconstruction algorithms are needed. As a first step in this direction we have developed semiautomated segmentation algorithms for a precise contour tracing of cell membranes. These algorithms were embedded into an easy-to-operate user interface, which allows direct 3D observation of the extracted objects during the segmentation of image stacks. Compared to purely manual tracing, processing time is greatly accelerated.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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A Quantum-Statistical-Mechanical Extension of Gaussian Mixture Model

Tanaka, K., Tsuda, K.

Journal of Physics: Conference Series, 95(012023):1-9, January 2008 (article)

Abstract
We propose an extension of Gaussian mixture models in the statistical-mechanical point of view. The conventional Gaussian mixture models are formulated to divide all points in given data to some kinds of classes. We introduce some quantum states constructed by superposing conventional classes in linear combinations. Our extension can provide a new algorithm in classifications of data by means of linear response formulas in the statistical mechanics.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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Learning to control in operational space

Peters, J., Schaal, S.

International Journal of Robotics Research, 27, pages: 197-212, 2008, clmc (article)

Abstract
One of the most general frameworks for phrasing control problems for complex, redundant robots is operational space control. However, while this framework is of essential importance for robotics and well-understood from an analytical point of view, it can be prohibitively hard to achieve accurate control in face of modeling errors, which are inevitable in com- plex robots, e.g., humanoid robots. In this paper, we suggest a learning approach for opertional space control as a direct inverse model learning problem. A first important insight for this paper is that a physically cor- rect solution to the inverse problem with redundant degrees-of-freedom does exist when learning of the inverse map is performed in a suitable piecewise linear way. The second crucial component for our work is based on the insight that many operational space controllers can be understood in terms of a constrained optimal control problem. The cost function as- sociated with this optimal control problem allows us to formulate a learn- ing algorithm that automatically synthesizes a globally consistent desired resolution of redundancy while learning the operational space controller. From the machine learning point of view, this learning problem corre- sponds to a reinforcement learning problem that maximizes an immediate reward. We employ an expectation-maximization policy search algorithm in order to solve this problem. Evaluations on a three degrees of freedom robot arm are used to illustrate the suggested approach. The applica- tion to a physically realistic simulator of the anthropomorphic SARCOS Master arm demonstrates feasibility for complex high degree-of-freedom robots. We also show that the proposed method works in the setting of learning resolved motion rate control on real, physical Mitsubishi PA-10 medical robotics arm.

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link (url) DOI [BibTex]

link (url) DOI [BibTex]


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Adaptation to a sub-optimal desired trajectory

M. Mistry, E. A. G. L. T. Y. S. S. M. K.

Advances in Computational Motor Control VII, Symposium at the Society for Neuroscience Meeting, Washington DC, 2008, 2008, clmc (article)

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PDF [BibTex]

PDF [BibTex]


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Human movement generation based on convergent flow fields: A computational model and a behavioral experiment

Hoffmann, H., Schaal, S.

In Advances in Computational Motor Control VII, Symposium at the Society for Neuroscience Meeting, Washington DC, 2008, 2008, clmc (inproceedings)

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link (url) [BibTex]

link (url) [BibTex]


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Operational space control: A theoretical and emprical comparison

Nakanishi, J., Cory, R., Mistry, M., Peters, J., Schaal, S.

International Journal of Robotics Research, 27(6):737-757, 2008, clmc (article)

Abstract
Dexterous manipulation with a highly redundant movement system is one of the hallmarks of hu- man motor skills. From numerous behavioral studies, there is strong evidence that humans employ compliant task space control, i.e., they focus control only on task variables while keeping redundant degrees-of-freedom as compliant as possible. This strategy is robust towards unknown disturbances and simultaneously safe for the operator and the environment. The theory of operational space con- trol in robotics aims to achieve similar performance properties. However, despite various compelling theoretical lines of research, advanced operational space control is hardly found in actual robotics imple- mentations, in particular new kinds of robots like humanoids and service robots, which would strongly profit from compliant dexterous manipulation. To analyze the pros and cons of different approaches to operational space control, this paper focuses on a theoretical and empirical evaluation of different methods that have been suggested in the literature, but also some new variants of operational space controllers. We address formulations at the velocity, acceleration and force levels. First, we formulate all controllers in a common notational framework, including quaternion-based orientation control, and discuss some of their theoretical properties. Second, we present experimental comparisons of these approaches on a seven-degree-of-freedom anthropomorphic robot arm with several benchmark tasks. As an aside, we also introduce a novel parameter estimation algorithm for rigid body dynamics, which ensures physical consistency, as this issue was crucial for our successful robot implementations. Our extensive empirical results demonstrate that one of the simplified acceleration-based approaches can be advantageous in terms of task performance, ease of parameter tuning, and general robustness and compliance in face of inevitable modeling errors.

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link (url) [BibTex]

link (url) [BibTex]


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Movement reproduction and obstacle avoidance with dynamic movement primitives and potential fields

Park, D., Hoffmann, H., Pastor, P., Schaal, S.

In IEEE International Conference on Humanoid Robots, 2008., 2008, clmc (inproceedings)

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PDF [BibTex]

PDF [BibTex]


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The dual role of uncertainty in force field learning

Mistry, M., Theodorou, E., Hoffmann, H., Schaal, S.

In Abstracts of the Eighteenth Annual Meeting of Neural Control of Movement (NCM), Naples, Florida, April 29-May 4, 2008, clmc (inproceedings)

Abstract
Force field experiments have been a successful paradigm for studying the principles of planning, execution, and learning in human arm movements. Subjects have been shown to cope with the disturbances generated by force fields by learning internal models of the underlying dynamics to predict disturbance effects or by increasing arm impedance (via co-contraction) if a predictive approach becomes infeasible. Several studies have addressed the issue uncertainty in force field learning. Scheidt et al. demonstrated that subjects exposed to a viscous force field of fixed structure but varying strength (randomly changing from trial to trial), learn to adapt to the mean disturbance, regardless of the statistical distribution. Takahashi et al. additionally show a decrease in strength of after-effects after learning in the randomly varying environment. Thus they suggest that the nervous system adopts a dual strategy: learning an internal model of the mean of the random environment, while simultaneously increasing arm impedance to minimize the consequence of errors. In this study, we examine what role variance plays in the learning of uncertain force fields. We use a 7 degree-of-freedom exoskeleton robot as a manipulandum (Sarcos Master Arm, Sarcos, Inc.), and apply a 3D viscous force field of fixed structure and strength randomly selected from trial to trial. Additionally, in separate blocks of trials, we alter the variance of the randomly selected strength multiplier (while keeping a constant mean). In each block, after sufficient learning has occurred, we apply catch trials with no force field and measure the strength of after-effects. As expected in higher variance cases, results show increasingly smaller levels of after-effects as the variance is increased, thus implying subjects choose the robust strategy of increasing arm impedance to cope with higher levels of uncertainty. Interestingly, however, subjects show an increase in after-effect strength with a small amount of variance as compared to the deterministic (zero variance) case. This result implies that a small amount of variability aides in internal model formation, presumably a consequence of the additional amount of exploration conducted in the workspace of the task.

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[BibTex]

[BibTex]


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Dynamic movement primitives for movement generation motivated by convergent force fields in frog

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

In Adaptive Motion of Animals and Machines (AMAM), 2008, clmc (inproceedings)

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PDF [BibTex]

PDF [BibTex]


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Behavioral experiments on reinforcement learning in human motor control

Hoffmann, H., Theodorou, E., Schaal, S.

In Abstracts of the Eighteenth Annual Meeting of Neural Control of Movement (NCM), Naples, Florida, April 29-May 4, 2008, clmc (inproceedings)

Abstract
Reinforcement learning (RL) - learning solely based on reward or cost feedback - is widespread in robotics control and has been also suggested as computational model for human motor control. In human motor control, however, hardly any experiment studied reinforcement learning. Here, we study learning based on visual cost feedback in a reaching task and did three experiments: (1) to establish a simple enough experiment for RL, (2) to study spatial localization of RL, and (3) to study the dependence of RL on the cost function. In experiment (1), subjects sit in front of a drawing tablet and look at a screen onto which the drawing pen's position is projected. Beginning from a start point, their task is to move with the pen through a target point presented on screen. Visual feedback about the pen's position is given only before movement onset. At the end of a movement, subjects get visual feedback only about the cost of this trial. We choose as cost the squared distance between target and virtual pen position at the target line. Above a threshold value, the cost was fixed at this value. In the mapping of the pen's position onto the screen, we added a bias (unknown to subject) and Gaussian noise. As result, subjects could learn the bias, and thus, showed reinforcement learning. In experiment (2), we randomly altered the target position between three different locations (three different directions from start point: -45, 0, 45). For each direction, we chose a different bias. As result, subjects learned all three bias values simultaneously. Thus, RL can be spatially localized. In experiment (3), we varied the sensitivity of the cost function by multiplying the squared distance with a constant value C, while keeping the same cut-off threshold. As in experiment (2), we had three target locations. We assigned to each location a different C value (this assignment was randomized between subjects). Since subjects learned the three locations simultaneously, we could directly compare the effect of the different cost functions. As result, we found an optimal C value; if C was too small (insensitive cost), learning was slow; if C was too large (narrow cost valley), the exploration time was longer and learning delayed. Thus, reinforcement learning in human motor control appears to be sen

am

[BibTex]

[BibTex]


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Movement generation by learning from demonstration and generalization to new targets

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

In Adaptive Motion of Animals and Machines (AMAM), 2008, clmc (inproceedings)

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PDF [BibTex]

PDF [BibTex]


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Combining dynamic movement primitives and potential fields for online obstacle avoidance

Park, D., Hoffmann, H., Schaal, S.

In Adaptive Motion of Animals and Machines (AMAM), Cleveland, Ohio, 2008, 2008, clmc (inproceedings)

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link (url) [BibTex]

link (url) [BibTex]


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A library for locally weighted projection regression

Klanke, S., Vijayakumar, S., Schaal, S.

Journal of Machine Learning Research, 9, pages: 623-626, 2008, clmc (article)

Abstract
In this paper we introduce an improved implementation of locally weighted projection regression (LWPR), a supervised learning algorithm that is capable of handling high-dimensional input data. As the key features, our code supports multi-threading, is available for multiple platforms, and provides wrappers for several programming languages.

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link (url) [BibTex]

link (url) [BibTex]


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Computational model for movement learning under uncertain cost

Theodorou, E., Hoffmann, H., Mistry, M., Schaal, S.

In Abstracts of the Society of Neuroscience Meeting (SFN 2008), Washington, DC 2008, 2008, clmc (inproceedings)

Abstract
Stochastic optimal control is a framework for computing control commands that lead to an optimal behavior under a given cost. Despite the long history of optimal control in engineering, it has been only recently applied to describe human motion. So far, stochastic optimal control has been mainly used in tasks that are already learned, such as reaching to a target. For learning, however, there are only few cases where optimal control has been applied. The main assumptions of stochastic optimal control that restrict its application to tasks after learning are the a priori knowledge of (1) a quadratic cost function (2) a state space model that captures the kinematics and/or dynamics of musculoskeletal system and (3) a measurement equation that models the proprioceptive and/or exteroceptive feedback. Under these assumptions, a sequence of control gains is computed that is optimal with respect to the prespecified cost function. In our work, we relax the assumption of the a priori known cost function and provide a computational framework for modeling tasks that involve learning. Typically, a cost function consists of two parts: one part that models the task constraints, like squared distance to goal at movement endpoint, and one part that integrates over the squared control commands. In learning a task, the first part of this cost function will be adapted. We use an expectation-maximization scheme for learning: the expectation step optimizes the task constraints through gradient descent of a reward function and the maximizing step optimizes the control commands. Our computational model is tested and compared with data given from a behavioral experiment. In this experiment, subjects sit in front of a drawing tablet and look at a screen onto which the drawing-pen's position is projected. Beginning from a start point, their task is to move with the pen through a target point presented on screen. Visual feedback about the pen's position is given only before movement onset. At the end of a movement, subjects get visual feedback only about the cost of this trial. In the mapping of the pen's position onto the screen, we added a bias (unknown to subject) and Gaussian noise. Therefore the cost is a function of this bias. The subjects were asked to reach to the target and minimize this cost over trials. In this behavioral experiment, subjects could learn the bias and thus showed reinforcement learning. With our computational model, we could model the learning process over trials. Particularly, the dependence on parameters of the reward function (Gaussian width) and the modulation of movement variance over time were similar in experiment and model.

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[BibTex]

[BibTex]


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Optimization strategies in human reinforcement learning

Hoffmann, H., Theodorou, E., Schaal, S.

Advances in Computational Motor Control VII, Symposium at the Society for Neuroscience Meeting, Washington DC, 2008, 2008, clmc (article)

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PDF [BibTex]

PDF [BibTex]


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A Bayesian approach to empirical local linearizations for robotics

Ting, J., D’Souza, A., Vijayakumar, S., Schaal, S.

In International Conference on Robotics and Automation (ICRA2008), Pasadena, CA, USA, May 19-23, 2008, 2008, clmc (inproceedings)

Abstract
Local linearizations are ubiquitous in the control of robotic systems. Analytical methods, if available, can be used to obtain the linearization, but in complex robotics systems where the the dynamics and kinematics are often not faithfully obtainable, empirical linearization may be preferable. In this case, it is important to only use data for the local linearization that lies within a ``reasonable'' linear regime of the system, which can be defined from the Hessian at the point of the linearization -- a quantity that is not available without an analytical model. We introduce a Bayesian approach to solve statistically what constitutes a ``reasonable'' local regime. We approach this problem in the context local linear regression. In contrast to previous locally linear methods, we avoid cross-validation or complex statistical hypothesis testing techniques to find the appropriate local regime. Instead, we treat the parameters of the local regime probabilistically and use approximate Bayesian inference for their estimation. This approach results in an analytical set of iterative update equations that are easily implemented on real robotics systems for real-time applications. As in other locally weighted regressions, our algorithm also lends itself to complete nonlinear function approximation for learning empirical internal models. We sketch the derivation of our Bayesian method and provide evaluations on synthetic data and actual robot data where the analytical linearization was known.

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link (url) [BibTex]

link (url) [BibTex]


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Do humans plan continuous trajectories in kinematic coordinates?

Hoffmann, H., Schaal, S.

In Abstracts of the Society of Neuroscience Meeting (SFN 2008), Washington, DC 2008, 2008, clmc (inproceedings)

Abstract
The planning and execution of human arm movements is still unresolved. An ongoing controversy is whether we plan a movement in kinematic coordinates and convert these coordinates with an inverse internal model into motor commands (like muscle activation) or whether we combine a few muscle synergies or equilibrium points to move a hand, e.g., between two targets. The first hypothesis implies that a planner produces a desired end-effector position for all time points; the second relies on the dynamics of the muscular-skeletal system for a given control command to produce a continuous end-effector trajectory. To distinguish between these two possibilities, we use a visuomotor adaptation experiment. Subjects moved a pen on a graphics tablet and observed the pen's mapped position onto a screen (subjects quickly adapted to this mapping). The task was to move a cursor between two points in a given time window. In the adaptation test, we manipulated the velocity profile of the cursor feedback such that the shape of the trajectories remained unchanged (for straight paths). If humans would use a kinematic plan and map at each time the desired end-effector position onto control commands, subjects should adapt to the above manipulation. In a similar experiment, Wolpert et al (1995) showed adaptation to changes in the curvature of trajectories. This result, however, cannot rule out a shift of an equilibrium point or an additional synergy activation between start and end point of a movement. In our experiment, subjects did two sessions, one control without and one with velocity-profile manipulation. To skew the velocity profile of the cursor trajectory, we added to the current velocity, v, the function 0.8*v*cos(pi + pi*x), where x is the projection of the cursor position onto the start-goal line divided by the distance start to goal (x=0 at the start point). As result, subjects did not adapt to this manipulation: for all subjects, the true hand motion was not significantly modified in a direction consistent with adaptation, despite that the visually presented motion differed significantly from the control motion. One may still argue that this difference in motion was insufficient to be processed visually. Thus, as a control experiment, we replayed control and modified motions to the subjects and asked which of the two motions appeared 'more natural'. Subjects chose the unperturbed motion as more natural significantly better than chance. In summary, for a visuomotor transformation task, the hypothesis of a planned continuous end-effector trajectory predicts adaptation to a modified velocity profile. The current experiment found no adaptation under such transformation.

am

[BibTex]

[BibTex]

2005


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Kernel Methods for Measuring Independence

Gretton, A., Herbrich, R., Smola, A., Bousquet, O., Schölkopf, B.

Journal of Machine Learning Research, 6, pages: 2075-2129, December 2005 (article)

Abstract
We introduce two new functionals, the constrained covariance and the kernel mutual information, to measure the degree of independence of random variables. These quantities are both based on the covariance between functions of the random variables in reproducing kernel Hilbert spaces (RKHSs). We prove that when the RKHSs are universal, both functionals are zero if and only if the random variables are pairwise independent. We also show that the kernel mutual information is an upper bound near independence on the Parzen window estimate of the mutual information. Analogous results apply for two correlation-based dependence functionals introduced earlier: we show the kernel canonical correlation and the kernel generalised variance to be independence measures for universal kernels, and prove the latter to be an upper bound on the mutual information near independence. The performance of the kernel dependence functionals in measuring independence is verified in the context of independent component analysis.

ei

PDF PostScript PDF [BibTex]

2005


PDF PostScript PDF [BibTex]


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Kernel ICA for Large Scale Problems

Jegelka, S., Gretton, A., Achlioptas, D.

In pages: -, NIPS Workshop on Large Scale Kernel Machines, December 2005 (inproceedings)

ei

Web [BibTex]

Web [BibTex]


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A Unifying View of Sparse Approximate Gaussian Process Regression

Quinonero Candela, J., Rasmussen, C.

Journal of Machine Learning Research, 6, pages: 1935-1959, December 2005 (article)

Abstract
We provide a new unifying view, including all existing proper probabilistic sparse approximations for Gaussian process regression. Our approach relies on expressing the effective prior which the methods are using. This allows new insights to be gained, and highlights the relationship between existing methods. It also allows for a clear theoretically justified ranking of the closeness of the known approximations to the corresponding full GPs. Finally we point directly to designs of new better sparse approximations, combining the best of the existing strategies, within attractive computational constraints.

ei

PDF [BibTex]

PDF [BibTex]


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Training Support Vector Machines with Multiple Equality Constraints

Kienzle, W., Schölkopf, B.

In Proceedings of the 16th European Conference on Machine Learning, Lecture Notes in Computer Science, Vol. 3720, pages: 182-193, (Editors: JG Carbonell and J Siekmann), Springer, Berlin, Germany, ECML, November 2005 (inproceedings)

Abstract
In this paper we present a primal-dual decomposition algorithm for support vector machine training. As with existing methods that use very small working sets (such as Sequential Minimal Optimization (SMO), Successive Over-Relaxation (SOR) or the Kernel Adatron (KA)), our method scales well, is straightforward to implement, and does not require an external QP solver. Unlike SMO, SOR and KA, the method is applicable to a large number of SVM formulations regardless of the number of equality constraints involved. The effectiveness of our algorithm is demonstrated on a more difficult SVM variant in this respect, namely semi-parametric support vector regression.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Measuring Statistical Dependence with Hilbert-Schmidt Norms

Gretton, A., Bousquet, O., Smola, A., Schoelkopf, B.

In Algorithmic Learning Theory, Lecture Notes in Computer Science, Vol. 3734, pages: 63-78, (Editors: S Jain and H-U Simon and E Tomita), Springer, Berlin, Germany, 16th International Conference ALT, October 2005 (inproceedings)

Abstract
We propose an independence criterion based on the eigenspectrum of covariance operators in reproducing kernel Hilbert spaces (RKHSs), consisting of an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator (we term this a Hilbert-Schmidt Independence Criterion, or HSIC). This approach has several advantages, compared with previous kernel-based independence criteria. First, the empirical estimate is simpler than any other kernel dependence test, and requires no user-defined regularisation. Second, there is a clearly defined population quantity which the empirical estimate approaches in the large sample limit, with exponential convergence guaranteed between the two: this ensures that independence tests based on {methodname} do not suffer from slow learning rates. Finally, we show in the context of independent component analysis (ICA) that the performance of HSIC is competitive with that of previously published kernel-based criteria, and of other recently published ICA methods.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Maximal Margin Classification for Metric Spaces

Hein, M., Bousquet, O., Schölkopf, B.

Journal of Computer and System Sciences, 71(3):333-359, October 2005 (article)

Abstract
In order to apply the maximum margin method in arbitrary metric spaces, we suggest to embed the metric space into a Banach or Hilbert space and to perform linear classification in this space. We propose several embeddings and recall that an isometric embedding in a Banach space is always possible while an isometric embedding in a Hilbert space is only possible for certain metric spaces. As a result, we obtain a general maximum margin classification algorithm for arbitrary metric spaces (whose solution is approximated by an algorithm of Graepel. Interestingly enough, the embedding approach, when applied to a metric which can be embedded into a Hilbert space, yields the SVM algorithm, which emphasizes the fact that its solution depends on the metric and not on the kernel. Furthermore we give upper bounds of the capacity of the function classes corresponding to both embeddings in terms of Rademacher averages. Finally we compare the capacities of these function classes directly.

ei

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


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An Analysis of the Anti-Learning Phenomenon for the Class Symmetric Polyhedron

Kowalczyk, A., Chapelle, O.

In Algorithmic Learning Theory: 16th International Conference, pages: 78-92, Algorithmic Learning Theory, October 2005 (inproceedings)

Abstract
This paper deals with an unusual phenomenon where most machine learning algorithms yield good performance on the training set but systematically worse than random performance on the test set. This has been observed so far for some natural data sets and demonstrated for some synthetic data sets when the classification rule is learned from a small set of training samples drawn from some high dimensional space. The initial analysis presented in this paper shows that anti-learning is a property of data sets and is quite distinct from overfitting of a training data. Moreover, the analysis leads to a specification of some machine learning procedures which can overcome anti-learning and generate ma- chines able to classify training and test data consistently.

ei

PDF [BibTex]

PDF [BibTex]


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Selective integration of multiple biological data for supervised network inference

Kato, T., Tsuda, K., Asai, K.

Bioinformatics, 21(10):2488 , October 2005 (article)

ei

PDF [BibTex]

PDF [BibTex]


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Assessing Approximate Inference for Binary Gaussian Process Classification

Kuss, M., Rasmussen, C.

Journal of Machine Learning Research, 6, pages: 1679 , October 2005 (article)

Abstract
Gaussian process priors can be used to define flexible, probabilistic classification models. Unfortunately exact Bayesian inference is analytically intractable and various approximation techniques have been proposed. In this work we review and compare Laplace‘s method and Expectation Propagation for approximate Bayesian inference in the binary Gaussian process classification model. We present a comprehensive comparison of the approximations, their predictive performance and marginal likelihood estimates to results obtained by MCMC sampling. We explain theoretically and corroborate empirically the advantages of Expectation Propagation compared to Laplace‘s method.

ei

PDF PDF [BibTex]

PDF PDF [BibTex]


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Clustering on the Unit Hypersphere using von Mises-Fisher Distributions

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

Journal of Machine Learning Research, 6, pages: 1345-1382, September 2005 (article)

Abstract
Several large scale data mining applications, such as text categorization and gene expression analysis, involve high-dimensional data that is also inherently directional in nature. Often such data is L2 normalized so that it lies on the surface of a unit hypersphere. Popular models such as (mixtures of) multi-variate Gaussians are inadequate for characterizing such data. This paper proposes a generative mixture-model approach to clustering directional data based on the von Mises-Fisher (vMF) distribution, which arises naturally for data distributed on the unit hypersphere. In particular, we derive and analyze two variants of the Expectation Maximization (EM) framework for estimating the mean and concentration parameters of this mixture. Numerical estimation of the concentration parameters is non-trivial in high dimensions since it involves functional inversion of ratios of Bessel functions. We also formulate two clustering algorithms corresponding to the variants of EM that we derive. Our approach provides a theoretical basis for the use of cosine similarity that has been widely employed by the information retrieval community, and obtains the spherical kmeans algorithm (kmeans with cosine similarity) as a special case of both variants. Empirical results on clustering of high-dimensional text and gene-expression data based on a mixture of vMF distributions show that the ability to estimate the concentration parameter for each vMF component, which is not present in existing approaches, yields superior results, especially for difficult clustering tasks in high-dimensional spaces.

ei

PDF [BibTex]

PDF [BibTex]


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Support Vector Machines for 3D Shape Processing

Steinke, F., Schölkopf, B., Blanz, V.

Computer Graphics Forum, 24(3, EUROGRAPHICS 2005):285-294, September 2005 (article)

Abstract
We propose statistical learning methods for approximating implicit surfaces and computing dense 3D deformation fields. Our approach is based on Support Vector (SV) Machines, which are state of the art in machine learning. It is straightforward to implement and computationally competitive; its parameters can be automatically set using standard machine learning methods. The surface approximation is based on a modified Support Vector regression. We present applications to 3D head reconstruction, including automatic removal of outliers and hole filling. In a second step, we build on our SV representation to compute dense 3D deformation fields between two objects. The fields are computed using a generalized SVMachine enforcing correspondence between the previously learned implicit SV object representations, as well as correspondences between feature points if such points are available. We apply the method to the morphing of 3D heads and other objects.

ei

PDF [BibTex]

PDF [BibTex]


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Fast Protein Classification with Multiple Networks

Tsuda, K., Shin, H., Schölkopf, B.

Bioinformatics, 21(Suppl. 2):59-65, September 2005 (article)

Abstract
Support vector machines (SVM) have been successfully used to classify proteins into functional categories. Recently, to integrate multiple data sources, a semidefinite programming (SDP) based SVM method was introduced Lanckriet et al (2004). In SDP/SVM, multiple kernel matrices corresponding to each of data sources are combined with weights obtained by solving an SDP. However, when trying to apply SDP/SVM to large problems, the computational cost can become prohibitive, since both converting the data to a kernel matrix for the SVM and solving the SDP are time and memory demanding. Another application-specific drawback arises when some of the data sources are protein networks. A common method of converting the network to a kernel matrix is the diffusion kernel method, which has time complexity of O(n^3), and produces a dense matrix of size n x n. We propose an efficient method of protein classification using multiple protein networks. Available protein networks, such as a physical interaction network or a metabolic network, can be directly incorporated. Vectorial data can also be incorporated after conversion into a network by means of neighbor point connection. Similarly to the SDP/SVM method, the combination weights are obtained by convex optimization. Due to the sparsity of network edges, the computation time is nearly linear in the number of edges of the combined network. Additionally, the combination weights provide information useful for discarding noisy or irrelevant networks. Experiments on function prediction of 3588 yeast proteins show promising results: the computation time is enormously reduced, while the accuracy is still comparable to the SDP/SVM method.

ei

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Iterative Kernel Principal Component Analysis for Image Modeling

Kim, K., Franz, M., Schölkopf, B.

IEEE Transactions on Pattern Analysis and Machine Intelligence, 27(9):1351-1366, September 2005 (article)

Abstract
In recent years, Kernel Principal Component Analysis (KPCA) has been suggested for various image processing tasks requiring an image model such as, e.g., denoising or compression. The original form of KPCA, however, can be only applied to strongly restricted image classes due to the limited number of training examples that can be processed. We therefore propose a new iterative method for performing KPCA, the Kernel Hebbian Algorithm which iteratively estimates the Kernel Principal Components with only linear order memory complexity. In our experiments, we compute models for complex image classes such as faces and natural images which require a large number of training examples. The resulting image models are tested in single-frame super-resolution and denoising applications. The KPCA model is not specifically tailored to these tasks; in fact, the same model can be used in super-resolution with variable input resolution, or denoising with unknown noise characteristics. In spite of this, both super-resolution a nd denoising performance are comparable to existing methods.

ei

Web DOI [BibTex]

Web DOI [BibTex]


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Phenotypic characterization of chondrosarcoma-derived cell lines

Schorle, C., Finger, F., Zien, A., Block, J., Gebhard, P., Aigner, T.

Cancer Letters, 226(2):143-154, August 2005 (article)

Abstract
Gene expression profiling of three chondrosarcoma derived cell lines (AD, SM, 105KC) showed an increased proliferative activity and a reduced expression of chondrocytic-typical matrix products compared to primary chondrocytes. The incapability to maintain an adequate matrix synthesis as well as a notable proliferative activity at the same time is comparable to neoplastic chondrosarcoma cells in vivo which cease largely cartilage matrix formation as soon as their proliferative activity increases. Thus, the investigated cell lines are of limited value as substitute of primary chondrocytes but might have a much higher potential to investigate the behavior of neoplastic chondrocytes, i.e. chondrosarcoma biology.

ei

Web [BibTex]

Web [BibTex]


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Local Rademacher Complexities

Bartlett, P., Bousquet, O., Mendelson, S.

The Annals of Statistics, 33(4):1497-1537, August 2005 (article)

Abstract
We propose new bounds on the error of learning algorithms in terms of a data-dependent notion of complexity. The estimates we establish give optimal rates and are based on a local and empirical version of Rademacher averages, in the sense that the Rademacher averages are computed from the data, on a subset of functions with small empirical error. We present some applications to classification and prediction with convex function classes, and with kernel classes in particular.

ei

PDF PostScript Web [BibTex]

PDF PostScript Web [BibTex]


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Building Sparse Large Margin Classifiers

Wu, M., Schölkopf, B., BakIr, G.

In Proceedings of the 22nd International Conference on Machine Learning, pages: 996-1003, (Editors: L De Raedt and S Wrobel ), ACM, New York, NY, USA, ICML , August 2005 (inproceedings)

Abstract
This paper presents an approach to build Sparse Large Margin Classifiers (SLMC) by adding one more constraint to the standard Support Vector Machine (SVM) training problem. The added constraint explicitly controls the sparseness of the classifier and an approach is provided to solve the formulated problem. When considering the dual of this problem, it can be seen that building an SLMC is equivalent to constructing an SVM with a modified kernel function. Further analysis of this kernel function indicates that the proposed approach essentially finds a discriminating subspace that can be spanned by a small number of vectors, and in this subspace different classes of data are linearly well separated. Experimental results over several classification benchmarks show that in most cases the proposed approach outperforms the state-of-art sparse learning algorithms.

ei

PDF DOI [BibTex]

PDF DOI [BibTex]


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Learning from Labeled and Unlabeled Data on a Directed Graph

Zhou, D., Huang, J., Schölkopf, B.

In Proceedings of the 22nd International Conference on Machine Learning, pages: 1041 -1048, (Editors: L De Raedt and S Wrobel), ACM, New York, NY, USA, ICML, August 2005 (inproceedings)

Abstract
We propose a general framework for learning from labeled and unlabeled data on a directed graph in which the structure of the graph including the directionality of the edges is considered. The time complexity of the algorithm derived from this framework is nearly linear due to recently developed numerical techniques. In the absence of labeled instances, this framework can be utilized as a spectral clustering method for directed graphs, which generalizes the spectral clustering approach for undirected graphs. We have applied our framework to real-world web classification problems and obtained encouraging results.

ei

PostScript PDF [BibTex]

PostScript PDF [BibTex]


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Regularization on Discrete Spaces

Zhou, D., Schölkopf, B.

In Pattern Recognition, Lecture Notes in Computer Science, Vol. 3663, pages: 361-368, (Editors: WG Kropatsch and R Sablatnig and A Hanbury), Springer, Berlin, Germany, 27th DAGM Symposium, August 2005 (inproceedings)

Abstract
We consider the classification problem on a finite set of objects. Some of them are labeled, and the task is to predict the labels of the remaining unlabeled ones. Such an estimation problem is generally referred to as transductive inference. It is well-known that many meaningful inductive or supervised methods can be derived from a regularization framework, which minimizes a loss function plus a regularization term. In the same spirit, we propose a general discrete regularization framework defined on finite object sets, which can be thought of as the discrete analogue of classical regularization theory. A family of transductive inference schemes is then systemically derived from the framework, including our earlier algorithm for transductive inference, with which we obtained encouraging results on many practical classification problems. The discrete regularization framework is built on the discrete analysis and geometry developed by ourselves, in which a number of discrete differential operators of various orders are constructed, which can be thought of as the discrete analogue of their counterparts in the continuous case.

ei

PDF PostScript DOI [BibTex]

PDF PostScript DOI [BibTex]


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Large Margin Non-Linear Embedding

Zien, A., Candela, J.

In ICML 2005, pages: 1065-1072, (Editors: De Raedt, L. , S. Wrobel), ACM Press, New York, NY, USA, 22nd International Conference on Machine Learning, August 2005 (inproceedings)

Abstract
It is common in classification methods to first place data in a vector space and then learn decision boundaries. We propose reversing that process: for fixed decision boundaries, we ``learn‘‘ the location of the data. This way we (i) do not need a metric (or even stronger structure) -- pairwise dissimilarities suffice; and additionally (ii) produce low-dimensional embeddings that can be analyzed visually. We achieve this by combining an entropy-based embedding method with an entropy-based version of semi-supervised logistic regression. We present results for clustering and semi-supervised classification.

ei

PDF PostScript Web DOI [BibTex]

PDF PostScript Web DOI [BibTex]


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Face Detection: Efficient and Rank Deficient

Kienzle, W., BakIr, G., Franz, M., Schölkopf, B.

In Advances in Neural Information Processing Systems 17, pages: 673-680, (Editors: LK Saul and Y Weiss and L Bottou), MIT Press, Cambridge, MA, USA, 18th Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
This paper proposes a method for computing fast approximations to support vector decision functions in the field of object detection. In the present approach we are building on an existing algorithm where the set of support vectors is replaced by a smaller, so-called reduced set of synthesized input space points. In contrast to the existing method that finds the reduced set via unconstrained optimization, we impose a structural constraint on the synthetic points such that the resulting approximations can be evaluated via separable filters. For applications that require scanning an entire image, this decreases the computational complexity of a scan by a significant amount. We present experimental results on a standard face detection database.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Methods Towards Invasive Human Brain Computer Interfaces

Lal, T., Hinterberger, T., Widman, G., Schröder, M., Hill, J., Rosenstiel, W., Elger, C., Schölkopf, B., Birbaumer, N.

In Advances in Neural Information Processing Systems 17, pages: 737-744, (Editors: LK Saul and Y Weiss and L Bottou), MIT Press, Cambridge, MA, USA, 18th Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
During the last ten years there has been growing interest in the development of Brain Computer Interfaces (BCIs). The field has mainly been driven by the needs of completely paralyzed patients to communicate. With a few exceptions, most human BCIs are based on extracranial electroencephalography (EEG). However, reported bit rates are still low. One reason for this is the low signal-to-noise ratio of the EEG. We are currently investigating if BCIs based on electrocorticography (ECoG) are a viable alternative. In this paper we present the method and examples of intracranial EEG recordings of three epilepsy patients with electrode grids placed on the motor cortex. The patients were asked to repeatedly imagine movements of two kinds, e.g., tongue or finger movements. We analyze the classifiability of the data using Support Vector Machines (SVMs) and Recursive Channel Elimination (RCE).

ei

PDF Web [BibTex]

PDF Web [BibTex]


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A Machine Learning Approach to Conjoint Analysis

Chapelle, O., Harchaoui, Z.

In Advances in Neural Information Processing Systems 17, pages: 257-264, (Editors: Saul, L.K. , Y. Weiss, L. Bottou), MIT Press, Cambridge, MA, USA, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
Choice-based conjoint analysis builds models of consumers preferences over products with answers gathered in questionnaires. Our main goal is to bring tools from the machine learning community to solve more efficiently this problem. Thus, we propose two algorithms to estimate quickly and accurately consumer preferences.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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An Auditory Paradigm for Brain-Computer Interfaces

Hill, N., Lal, T., Bierig, K., Birbaumer, N., Schölkopf, B.

In Advances in Neural Information Processing Systems 17, pages: 569-576, (Editors: LK Saul and Y Weiss and L Bottou), MIT Press, Cambridge, MA, USA, 18th Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
Motivated by the particular problems involved in communicating with "locked-in" paralysed patients, we aim to develop a brain-computer interface that uses auditory stimuli. We describe a paradigm that allows a user to make a binary decision by focusing attention on one of two concurrent auditory stimulus sequences. Using Support Vector Machine classification and Recursive Channel Elimination on the independent components of averaged event-related potentials, we show that an untrained user's EEG data can be classified with an encouragingly high level of accuracy. This suggests that it is possible for users to modulate EEG signals in a single trial by the conscious direction of attention, well enough to be useful in BCI.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection

Tsuda, K., Rätsch, G., Warmuth, M.

In Advances in Neural Information Processing Systems 17, pages: 1425-1432, (Editors: Saul, L.K. , Y. Weiss, L. Bottou), MIT Press, Cambridge, MA, USA, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
We address the problem of learning a symmetric positive definite matrix. The central issue is to design parameter updates that preserve positive definiteness. Our updates are motivated with the von Neumann divergence. Rather than treating the most general case, we focus on two key applications that exemplify our methods: On-line learning with a simple square loss and finding a symmetric positive definite matrix subject to symmetric linear constraints. The updates generalize the Exponentiated Gradient (EG) update and AdaBoost, respectively: the parameter is now a symmetric positive definite matrix of trace one instead of a probability vector (which in this context is a diagonal positive definite matrix with trace one). The generalized updates use matrix logarithms and exponentials to preserve positive definiteness. Most importantly, we show how the analysis of each algorithm generalizes to the non-diagonal case. We apply both new algorithms, called the Matrix Exponentiated Gradient (MEG) update and DefiniteBoost, to learn a kernel matrix from distance measurements.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Machine Learning Applied to Perception: Decision Images for Classification

Wichmann, F., Graf, A., Simoncelli, E., Bülthoff, H., Schölkopf, B.

In Advances in Neural Information Processing Systems 17, pages: 1489-1496, (Editors: LK, Saul and Y, Weiss and L, Bottou), MIT Press, Cambridge, MA, USA, 18th Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
We study gender discrimination of human faces using a combination of psychophysical classification and discrimination experiments together with methods from machine learning. We reduce the dimensionality of a set of face images using principal component analysis, and then train a set of linear classifiers on this reduced representation (linear support vector machines (SVMs), relevance vector machines (RVMs), Fisher linear discriminant (FLD), and prototype (prot) classifiers) using human classification data. Because we combine a linear preprocessor with linear classifiers, the entire system acts as a linear classifier, allowing us to visualise the decision-image corresponding to the normal vector of the separating hyperplanes (SH) of each classifier. We predict that the female-to-maleness transition along the normal vector for classifiers closely mimicking human classification (SVM and RVM 1) should be faster than the transition along any other direction. A psychophysical discrimination experiment using the decision images as stimuli is consistent with this prediction.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Learning the Kernel with Hyperkernels

Ong, CS., Smola, A., Williamson, R.

Journal of Machine Learning Research, 6, pages: 1043-1071, July 2005 (article)

Abstract
This paper addresses the problem of choosing a kernel suitable for estimation with a Support Vector Machine, hence further automating machine learning. This goal is achieved by defining a Reproducing Kernel Hilbert Space on the space of kernels itself. Such a formulation leads to a statistical estimation problem similar to the problem of minimizing a regularized risk functional. We state the equivalent representer theorem for the choice of kernels and present a semidefinite programming formulation of the resulting optimization problem. Several recipes for constructing hyperkernels are provided, as well as the details of common machine learning problems. Experimental results for classification, regression and novelty detection on UCI data show the feasibility of our approach.

ei

PDF [BibTex]

PDF [BibTex]


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Breaking SVM Complexity with Cross-Training

Bakir, G., Bottou, L., Weston, J.

In Advances in Neural Information Processing Systems 17, pages: 81-88, (Editors: Saul, L.K. , Y. Weiss, L. Bottou), MIT Press, Cambridge, MA, USA, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
We propose an algorithm for selectively removing examples from the training set using probabilistic estimates related to editing algorithms (Devijver and Kittler82). The procedure creates a separable distribution of training examples with minimal impact on the decision boundary position. It breaks the linear dependency between the number of SVs and the number of training examples, and sharply reduces the complexity of SVMs during both the training and prediction stages.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Implicit Wiener series for higher-order image analysis

Franz, M., Schölkopf, B.

In Advances in Neural Information Processing Systems 17, pages: 465-472, (Editors: LK Saul and Y Weiss and L Bottou), MIT Press, Cambridge, MA, USA, 18th Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
The computation of classical higher-order statistics such as higher-order moments or spectra is difficult for images due to the huge number of terms to be estimated and interpreted. We propose an alternative approach in which multiplicative pixel interactions are described by a series of Wiener functionals. Since the functionals are estimated implicitly via polynomial kernels, the combinatorial explosion associated with the classical higher-order statistics is avoided. First results show that image structures such as lines or corners can be predicted correctly, and that pixel interactions up to the order of five play an important role in natural images.

ei

PDF Web [BibTex]

PDF Web [BibTex]


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Limits of Spectral Clustering

von Luxburg, U., Bousquet, O., Belkin, M.

In Advances in Neural Information Processing Systems 17, pages: 857-864, (Editors: Saul, L. K., Y. Weiss, L. Bottou), MIT Press, Cambridge, MA, USA, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS), July 2005 (inproceedings)

Abstract
An important aspect of clustering algorithms is whether the partitions constructed on finite samples converge to a useful clustering of the whole data space as the sample size increases. This paper investigates this question for normalized and unnormalized versions of the popular spectral clustering algorithm. Surprisingly, the convergence of unnormalized spectral clustering is more difficult to handle than the normalized case. Even though recently some first results on the convergence of normalized spectral clustering have been obtained, for the unnormalized case we have to develop a completely new approach combining tools from numerical integration, spectral and perturbation theory, and probability. It turns out that while in the normalized case, spectral clustering usually converges to a nice partition of the data space, in the unnormalized case the same only holds under strong additional assumptions which are not always satisfied. We conclude that our analysis gives strong evidence for the superiority of normalized spectral clustering. It also provides a basis for future exploration of other Laplacian-based methods.

ei

PDF Web [BibTex]

PDF Web [BibTex]