169 results (BibTeX)

2011


Access to Unlabeled Data can Speed up Prediction Time

Urner, R., Shalev-Shwartz, S., Ben-David, S.

In Proceedings of the 28th International Conference on Machine Learning, pages: 641-648, ICML, 2011 (inproceedings)

link (url) [BibTex]

2011

link (url) [BibTex]


Thumb md screen shot 2012 02 23 at 09.35.10
Learning Output Kernels with Block Coordinate Descent

Dinuzzo, F., Ong, C., Gehler, P., Pillonetto, G.

In Proceedings of the 28th International Conference on Machine Learning (ICML-11), pages: 49-56, ICML ’11, (Editors: Getoor, Lise and Scheffer, Tobias), ACM, New York, NY, USA, ICML, June 2011 (inproceedings)

data+code pdf [BibTex]

data+code pdf [BibTex]


Thumb md problem
Recovering Intrinsic Images with a Global Sparsity Prior on Reflectance

Gehler, P., Rother, C., Kiefel, M., Zhang, L., Schölkopf, B.

In Advances in Neural Information Processing Systems 24, pages: 765-773, (Editors: Shawe-Taylor, John and Zemel, Richard S. and Bartlett, Peter L. and Pereira, Fernando C. N. and Weinberger, Kilian Q.), Curran Associates, Inc., Red Hook, NY, USA, Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS), 2011 (inproceedings)

Abstract
We address the challenging task of decoupling material properties from lighting properties given a single image. In the last two decades virtually all works have concentrated on exploiting edge information to address this problem. We take a different route by introducing a new prior on reflectance, that models reflectance values as being drawn from a sparse set of basis colors. This results in a Random Field model with global, latent variables (basis colors) and pixel-accurate output reflectance values. We show that without edge information high-quality results can be achieved, that are on par with methods exploiting this source of information. Finally, we are able to improve on state-of-the-art results by integrating edge information into our model. We believe that our new approach is an excellent starting point for future developments in this field.

website + code pdf poster Project Page [BibTex]

website + code pdf poster Project Page [BibTex]


Fast Convergent Algorithms for Expectation Propagation Approximate Bayesian Inference

Seeger, M., Nickisch, H.

In JMLR Workshop and Conference Proceedings Volume 15: AISTATS 2011, pages: 652-660, (Editors: Gordon, G. , D. Dunson, M. Dudík ), MIT Press, Cambridge, MA, USA, 14th International Conference on Artificial Intelligence and Statistics, April 2011 (inproceedings)

Abstract
We propose a novel algorithm to solve the expectation propagation relaxation of Bayesian inference for continuous-variable graphical models. In contrast to most previous algorithms, our method is provably convergent. By marrying convergent EP ideas from (Opper&Winther, 2005) with covariance decoupling techniques (Wipf&Nagarajan, 2008; Nickisch&Seeger, 2009), it runs at least an order of magnitude faster than the most common EP solver.

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


Policy Search for Motor Primitives in Robotics

Kober, J., Peters, J.

Machine Learning, 84(1-2):171-203, July 2011 (article)

Abstract
Many motor skills in humanoid robotics can be learned using parametrized motor primitives. While successful applications to date have been achieved with imitation learning, most of the interesting motor learning problems are high-dimensional reinforcement learning problems. These problems are often beyond the reach of current reinforcement learning methods. In this paper, we study parametrized policy search methods and apply these to benchmark problems of motor primitive learning in robotics. We show that many well-known parametrized policy search methods can be derived from a general, common framework. This framework yields both policy gradient methods and expectation-maximization (EM) inspired algorithms. We introduce a novel EM-inspired algorithm for policy learning that is particularly well-suited for dynamical system motor primitives. We compare this algorithm, both in simulation and on a real robot, to several well-known parametrized policy search methods such as episodic REINFORCE, ‘Vanilla’ Policy Gradients with optimal baselines, episodic Natural Actor Critic, and episodic Reward-Weighted Regression. We show that the proposed method out-performs them on an empirical benchmark of learning dynamical system motor primitives both in simulation and on a real robot. We apply it in the context of motor learning and show that it can learn a complex Ball-in-a-Cup task on a real Barrett WAM™ robot arm.

PDF PDF DOI Project Page Project Page [BibTex]


Transition from the locked in to the completely locked-in state: A physiological analysis

Ramos Murguialday, A., Hill, J., Bensch, M., Martens, S., Halder, S., Nijboer, F., Schölkopf, B., Birbaumer, N., Gharabaghi, A.

Clinical Neurophysiology, 122(5):925-933 , May 2011 (article)

Abstract
Objective To clarify the physiological and behavioral boundaries between locked-in (LIS) and the completely locked-in state (CLIS) (no voluntary eye movements, no communication possible) through electrophysiological data and to secure brain–computer-interface (BCI) communication. Methods Electromyography from facial muscles, external anal sphincter (EAS), electrooculography and electrocorticographic data during different psychophysiological tests were acquired to define electrophysiological differences in an amyotrophic lateral sclerosis (ALS) patient with an intracranially implanted grid of 112 electrodes for nine months while the patient passed from the LIS to the CLIS. Results At the very end of the LIS there was no facial muscle activity, nor external anal sphincter but eye control. Eye movements were slow and lasted for short periods only. During CLIS event related brain potentials (ERP) to passive limb movements and auditory stimuli were recorded, vibrotactile stimulation of different body parts resulted in no ERP response. Conclusions The results presented contradict the commonly accepted assumption that the EAS is the last remaining muscle under voluntary control and demonstrate complete loss of eye movements in CLIS. The eye muscle was shown to be the last muscle group under voluntary control. The findings suggest ALS as a multisystem disorder, even affecting afferent sensory pathways. Significance Auditory and proprioceptive brain–computer-interface (BCI) systems are the only remaining communication channels in CLIS.

PDF DOI [BibTex]

PDF DOI [BibTex]


What are the Causes of Performance Variation in Brain-Computer Interfacing?

Grosse-Wentrup, M.

International Journal of Bioelectromagnetism, 13(3):115-116, September 2011 (article)

Abstract
While research on brain-computer interfacing (BCI) has seen tremendous progress in recent years, performance still varies substantially between as well as within subjects, with roughly 10 - 20% of subjects being incapable of successfully operating a BCI system. In this short report, I argue that this variation in performance constitutes one of the major obstacles that impedes a successful commercialization of BCI systems. I review the current state of research on the neuro-physiological causes of performance variation in BCI, discuss recent progress and open problems, and delineate potential research programs for addressing this issue.

PDF Web [BibTex]

PDF Web [BibTex]


A graphical model framework for decoding in the visual ERP-based BCI speller

Martens, S., Mooij, J., Hill, N., Farquhar, J., Schölkopf, B.

Neural Computation, 23(1):160-182, January 2011 (article)

Abstract
We present a graphical model framework for decoding in the visual ERP-based speller system. The proposed framework allows researchers to build generative models from which the decoding rules are obtained in a straightforward manner. We suggest two models for generating brain signals conditioned on the stimulus events. Both models incorporate letter frequency information but assume different dependencies between brain signals and stimulus events. For both models, we derive decoding rules and perform a discriminative training. We show on real visual speller data how decoding performance improves by incorporating letter frequency information and using a more realistic graphical model for the dependencies between the brain signals and the stimulus events. Furthermore, we discuss how the standard approach to decoding can be seen as a special case of the graphical model framework. The letter also gives more insight into the discriminative approach for decoding in the visual speller system.

Web DOI Project Page [BibTex]

Web DOI Project Page [BibTex]


Finding dependencies between frequencies with the kernel cross-spectral density

Besserve, M., Janzing, D., Logothetis, N., Schölkopf, B.

In pages: 2080-2083 , IEEE, Piscataway, NJ, USA, IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) , May 2011 (inproceedings)

Abstract
Cross-spectral density (CSD), is widely used to find linear dependency between two real or complex valued time series. We define a non-linear extension of this measure by mapping the time series into two Reproducing Kernel Hilbert Spaces. The dependency is quantified by the Hilbert Schmidt norm of a cross-spectral density operator between these two spaces. We prove that, by choosing a characteristic kernel for the mapping, this quantity detects any pairwise dependency between the time series. Then we provide a fast estimator for the Hilbert-Schmidt norm based on the Fast Fourier Trans form. We demonstrate the interest of this approach to quantify non-linear dependencies between frequency bands of simulated signals and intra-cortical neural recordings.

Web DOI Project Page Project Page [BibTex]

Web DOI Project Page Project Page [BibTex]


Active Exploration for Robot Parameter Selection in Episodic Reinforcement Learning

Kroemer, O., Peters, J.

In Proceedings of the 2011 IEEE Symposium on Adaptive Dynamic Programming and Reinforcement Learning (ADPRL 2011), pages: 25-31, IEEE, Piscataway, NJ, USA, IEEE Symposium on Adaptive Dynamic Programming and Reinforcement Learning (ADPRL), April 2011 (inproceedings)

Abstract
As the complexity of robots and other autonomous systems increases, it becomes more important that these systems can adapt and optimize their settings actively. However, such optimization is rarely trivial. Sampling from the system is often expensive in terms of time and other costs, and excessive sampling should therefore be avoided. The parameter space is also usually continuous and multi-dimensional. Given the inherent exploration-exploitation dilemma of the problem, we propose treating it as an episodic reinforcement learning problem. In this reinforcement learning framework, the policy is defined by the system's parameters and the rewards are given by the system's performance. The rewards accumulate during each episode of a task. In this paper, we present a method for efficiently sampling and optimizing in continuous multidimensional spaces. The approach is based on Gaussian process regression, which can represent continuous non-linear mappings from parameters to system performance. We employ an upper confidence bound policy, which explicitly manages the trade-off between exploration and exploitation. Unlike many other policies for this kind of problem, we do not rely on a discretization of the action space. The presented method was evaluated on a real robot. The robot had to learn grasping parameters in order to adapt its grasping execution to different objects. The proposed method was also tested on a more general gain tuning problem. The results of the experiments show that the presented method can quickly determine suitable parameters and is applicable to real online learning applications.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


Projected Newton-type methods in machine learning

Schmidt, M., Kim, D., Sra, S.

In Optimization for Machine Learning, pages: 305-330, (Editors: Sra, S., Nowozin, S. and Wright, S. J.), MIT Press, Cambridge, MA, USA, December 2011 (inbook)

Abstract
We consider projected Newton-type methods for solving large-scale optimization problems arising in machine learning and related fields. We first introduce an algorithmic framework for projected Newton-type methods by reviewing a canonical projected (quasi-)Newton method. This method, while conceptually pleasing, has a high computation cost per iteration. Thus, we discuss two variants that are more scalable, namely, two-metric projection and inexact projection methods. Finally, we show how to apply the Newton-type framework to handle non-smooth objectives. Examples are provided throughout the chapter to illustrate machine learning applications of our framework.

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


Dynamics of excitable neural networks with heterogeneous connectivity

Chavez, M., Besserve, M., Le Van Quyen, M.

Progress in Biophysics and Molecular Biology, 105(1-2):29-33, March 2011 (article)

Abstract
A central issue of neuroscience is to understand how neural units integrates internal and external signals to create coherent states. Recently, it has been shown that the sensitivity and dynamic range of neural assemblies are optimal at a critical coupling among its elements. Complex architectures of connections seem to play a constructive role on the reliable coordination of neural units. Here we show that, the synchronizability and sensitivity of excitable neural networks can be tuned by diversity in the connections strengths. We illustrate our findings for weighted networks with regular, random and complex topologies. Additional comparisons of real brain networks support previous studies suggesting that heterogeneity in the connectivity may play a constructive role on information processing. These findings provide insights into the relationship between structure and function of neural circuits.

PDF DOI [BibTex]

PDF DOI [BibTex]


A Blind Deconvolution Approach for Improving the Resolution of Cryo-EM Density Maps

Hirsch, M., Schölkopf, B., Habeck, M.

Journal of Computational Biology, 18(3):335-346, March 2011 (article)

Abstract
Cryo-electron microscopy (cryo-EM) plays an increasingly prominent role in structure elucidation of macromolecular assemblies. Advances in experimental instrumentation and computational power have spawned numerous cryo-EM studies of large biomolecular complexes resulting in the reconstruction of three-dimensional density maps at intermediate and low resolution. In this resolution range, identification and interpretation of structural elements and modeling of biomolecular structure with atomic detail becomes problematic. In this article, we present a novel algorithm that enhances the resolution of intermediate- and low-resolution density maps. Our underlying assumption is to model the low-resolution density map as a blurred and possibly noise-corrupted version of an unknown high-resolution map that we seek to recover by deconvolution. By exploiting the nonnegativity of both the high-resolution map and blur kernel, we derive multiplicative updates reminiscent of those used in nonnegative matrix factorization. Our framework allows for easy incorporation of additional prior knowledge such as smoothness and sparseness, on both the sharpened density map and the blur kernel. A probabilistic formulation enables us to derive updates for the hyperparameters; therefore, our approach has no parameter that needs adjustment. We apply the algorithm to simulated three-dimensional electron microscopic data. We show that our method provides better resolved density maps when compared with B-factor sharpening, especially in the presence of noise. Moreover, our method can use additional information provided by homologous structures, which helps to improve the resolution even further.

Web DOI Project Page [BibTex]

Web DOI Project Page [BibTex]


Adaptive nonparametric detection in cryo-electron microscopy

Langovoy, M., Habeck, M., Schölkopf, B.

In Proceedings of the 58th World Statistics Congress, pages: 4456-4461, ISI, August 2011 (inproceedings)

Abstract
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. The objects of interest have unknown varying intensities. No boundary shape constraints are imposed on the objects, only a set of weak bulk conditions is required. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect greyscale objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures. Applications to cryo-electron microscopy are presented.

PDF link (url) [BibTex]

PDF link (url) [BibTex]


Reinforcement Learning to adjust Robot Movements to New Situations

Kober, J., Oztop, E., Peters, J.

In pages: 2650-2655, (Editors: Walsh, T.), AAAI Press, Menlo Park, CA, USA, Twenty-Second International Joint Conference on Artificial Intelligence (IJCAI), July 2011 (inproceedings)

Abstract
Many complex robot motor skills can be represented using elementary movements, and there exist efficient techniques for learning parametrized motor plans using demonstrations and self-improvement. However with current techniques, in many cases, the robot currently needs to learn a new elementary movement even if a parametrized motor plan exists that covers a related situation. A method is needed that modulates the elementary movement through the meta-parameters of its representation. In this paper, we describe how to learn such mappings from circumstances to meta-parameters using reinforcement learning. In particular we use a kernelized version of the reward-weighted regression. We show two robot applications of the presented setup in robotic domains; the generalization of throwing movements in darts, and of hitting movements in table tennis. We demonstrate that both tasks can be learned successfully using simulated and real robots.

PDF Web [BibTex]

PDF Web [BibTex]


Online submodular minimization for combinatorial structures

Jegelka, S., Bilmes, J.

In pages: 345-352, (Editors: Getoor, L. , T. Scheffer), International Machine Learning Society, Madison, WI, USA, 28th International Conference on Machine Learning (ICML), July 2011 (inproceedings)

Abstract
Most results for online decision problems with structured concepts, such as trees or cuts, assume linear costs. In many settings, however, nonlinear costs are more realistic. Owing to their non-separability, these lead to much harder optimization problems. Going beyond linearity, we address online approximation algorithms for structured concepts that allow the cost to be submodular, i.e., nonseparable. In particular, we show regret bounds for three Hannan-consistent strategies that capture different settings. Our results also tighten a regret bound for unconstrained online submodular minimization.

PDF PDF Web Project Page [BibTex]

PDF PDF Web Project Page [BibTex]


PAC-Bayesian Analysis of the Exploration-Exploitation Trade-off

Seldin, Y., Cesa-Bianchi, N., Laviolette, F., Auer, P., Shawe-Taylor, J., Peters, J.

In pages: 1-8, ICML Workshop on Online Trading of Exploration and Exploitation 2, July 2011 (inproceedings)

Abstract
We develop a coherent framework for integrative simultaneous analysis of the exploration-exploitation and model order selection trade-offs. We improve over our preceding results on the same subject (Seldin et al., 2011) by combining PAC-Bayesian analysis with Bernstein-type inequality for martingales. Such a combination is also of independent interest for studies of multiple simultaneously evolving martingales.

PDF Web [BibTex]

PDF Web [BibTex]


Semi-supervised kernel canonical correlation analysis with application to human fMRI

Blaschko, M., Shelton, J., Bartels, A., Lampert, C., Gretton, A.

Pattern Recognition Letters, 32(11):1572-1583 , August 2011 (article)

Abstract
Kernel canonical correlation analysis (KCCA) is a general technique for subspace learning that incorporates principal components analysis (PCA) and Fisher linear discriminant analysis (LDA) as special cases. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying process that generates the data and can ignore high-variance noise directions. However, for data where acquisition in one or more modalities is expensive or otherwise limited, KCCA may suffer from small sample effects. We propose to use semi-supervised Laplacian regularization to utilize data that are present in only one modality. This approach is able to find highly correlated directions that also lie along the data manifold, resulting in a more robust estimate of correlated subspaces. Functional magnetic resonance imaging (fMRI) acquired data are naturally amenable to subspace techniques as data are well aligned. fMRI data of the human brain are a particularly interesting candidate. In this study we implemented various supervised and semi-supervised versions of KCCA on human fMRI data, with regression to single and multi-variate labels (corresponding to video content subjects viewed during the image acquisition). In each variate condition, the semi-supervised variants of KCCA performed better than the supervised variants, including a supervised variant with Laplacian regularization. We additionally analyze the weights learned by the regression in order to infer brain regions that are important to different types of visual processing.

PDF PDF DOI [BibTex]

PDF PDF DOI [BibTex]


ccSVM: correcting Support Vector Machines for confounding factors in biological data classification

Li, L., Rakitsch, B., Borgwardt, K.

Bioinformatics, 27(13: ISMB/ECCB 2011):i342-i348, July 2011 (article)

Abstract
Motivation: Classifying biological data into different groups is a central task of bioinformatics: for instance, to predict the function of a gene or protein, the disease state of a patient or the phenotype of an individual based on its genotype. Support Vector Machines are a wide spread approach for classifying biological data, due to their high accuracy, their ability to deal with structured data such as strings, and the ease to integrate various types of data. However, it is unclear how to correct for confounding factors such as population structure, age or gender or experimental conditions in Support Vector Machine classification. Results: In this article, we present a Support Vector Machine classifier that can correct the prediction for observed confounding factors. This is achieved by minimizing the statistical dependence between the classifier and the confounding factors. We prove that this formulation can be transformed into a standard Support Vector Machine with rescaled input data. In our experiments, our confounder correcting SVM (ccSVM) improves tumor diagnosis based on samples from different labs, tuberculosis diagnosis in patients of varying age, ethnicity and gender, and phenotype prediction in the presence of population structure and outperforms state-of-the-art methods in terms of prediction accuracy.

Web DOI [BibTex]

Web DOI [BibTex]


FaST linear mixed models for genome-wide association studies

Lippert, C. Listgarten, J. Liu, Y. Kadie, CM. Davidson, RI. Heckerman, D.

Nature Methods, 8(10):833–835, October 2011 (article)

Abstract
We describe factored spectrally transformed linear mixed models (FaST-LMM), an algorithm for genome-wide association studies (GWAS) that scales linearly with cohort size in both run time and memory use. On Wellcome Trust data for 15,000 individuals, FaST-LMM ran an order of magnitude faster than current efficient algorithms. Our algorithm can analyze data for 120,000 individuals in just a few hours, whereas current algorithms fail on data for even 20,000 individuals (http://mscompbio.codeplex.com/).

PDF DOI [BibTex]

PDF DOI [BibTex]


Detecting low-complexity unobserved causes

Janzing, D., Sgouritsa, E., Stegle, O., Peters, J., Schölkopf, B.

In pages: 383-391, (Editors: FG Cozman and A Pfeffer), AUAI Press, Corvallis, OR, USA, 27th Conference on Uncertainty in Artificial Intelligence (UAI), July 2011 (inproceedings)

Abstract
We describe a method that infers whether statistical dependences between two observed variables X and Y are due to a \direct" causal link or only due to a connecting causal path that contains an unobserved variable of low complexity, e.g., a binary variable. This problem is motivated by statistical genetics. Given a genetic marker that is correlated with a phenotype of interest, we want to detect whether this marker is causal or it only correlates with a causal one. Our method is based on the analysis of the location of the conditional distributions P(Y jx) in the simplex of all distributions of Y . We report encouraging results on semi-empirical data.

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


Learning anticipation policies for robot table tennis

Wang, Z., Lampert, C., Mülling, K., Schölkopf, B., Peters, J.

In pages: 332-337 , (Editors: NM Amato), IEEE, Piscataway, NJ, USA, IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS), September 2011 (inproceedings)

Abstract
Playing table tennis is a difficult task for robots, especially due to their limitations of acceleration. A key bottleneck is the amount of time needed to reach the desired hitting position and velocity of the racket for returning the incoming ball. Here, it often does not suffice to simply extrapolate the ball's trajectory after the opponent returns it but more information is needed. Humans are able to predict the ball's trajectory based on the opponent's moves and, thus, have a considerable advantage. Hence, we propose to incorporate an anticipation system into robot table tennis players, which enables the robot to react earlier while the opponent is performing the striking movement. Based on visual observation of the opponent's racket movement, the robot can predict the aim of the opponent and adjust its movement generation accordingly. The policies for deciding how and when to react are obtained by reinforcement learning. We conduct experiments with an existing robot player to show that the learned reaction policy can significantly improve the performance of the overall system.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


Estimating integrated information with TMS pulses during wakefulness, sleep and under anesthesia

Balduzzi, D.

In pages: 4717-4720 , IEEE, Piscataway, NJ, USA, 33rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE EMBC), September 2011 (inproceedings)

Abstract
This paper relates a recently proposed measure of information integration to experiments investigating the evoked high-density electroencephalography (EEG) response to transcranial magnetic stimulation (TMS) during wakefulness, early non-rapid eye movement (NREM) sleep and under anesthesia. We show that bistability, arising at the cellular and population level during NREM sleep and under anesthesia, dramatically reduces the brain’s ability to integrate information.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


A Non-Parametric Approach to Dynamic Programming

Kroemer, O., Peters, J.

In Advances in Neural Information Processing Systems 24, pages: 1719-1727, (Editors: J Shawe-Taylor and RS Zemel and P Bartlett and F Pereira and KQ Weinberger), Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS), 2011 (inproceedings)

Abstract
In this paper, we consider the problem of policy evaluation for continuousstate systems. We present a non-parametric approach to policy evaluation, which uses kernel density estimation to represent the system. The true form of the value function for this model can be determined, and can be computed using Galerkin’s method. Furthermore, we also present a unified view of several well-known policy evaluation methods. In particular, we show that the same Galerkin method can be used to derive Least-Squares Temporal Difference learning, Kernelized Temporal Difference learning, and a discrete-state Dynamic Programming solution, as well as our proposed method. In a numerical evaluation of these algorithms, the proposed approach performed better than the other methods.

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


Evaluation and Optimization of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

Mantlik, F., Hofmann, M., Bezrukov, I., Schmidt, H., Kolb, A., Beyer, T., Reimold, M., Schölkopf, B., Pichler, B.

2011(MIC18.M-96), 2011 IEEE Nuclear Science Symposium, Medical Imaging Conference (NSS-MIC), October 2011 (poster)

Abstract
Combined PET/MR provides simultaneous molecular and functional information in an anatomical context with unique soft tissue contrast. However, PET/MR does not support direct derivation of attenuation maps of objects and tissues within the measured PET field-of-view. Valid attenuation maps are required for quantitative PET imaging, specifically for scientific brain studies. Therefore, several methods have been proposed for MR-based attenuation correction (MR-AC). Last year, we performed an evaluation of different MR-AC methods, including simple MR thresholding, atlas- and machine learning-based MR-AC. CT-based AC served as gold standard reference. RoIs from 2 anatomic brain atlases with different levels of detail were used for evaluation of correction accuracy. We now extend our evaluation of different MR-AC methods by using an enlarged dataset of 23 patients from the integrated BrainPET/MR (Siemens Healthcare). Further, we analyze options for improving the MR-AC performance in terms of speed and accuracy. Finally, we assess the impact of ignoring BrainPET positioning aids during the course of MR-AC. This extended study confirms the overall prediction accuracy evaluation results of the first evaluation in a larger patient population. Removing datasets affected by metal artifacts from the Atlas-Patch database helped to improve prediction accuracy, although the size of the database was reduced by one half. Significant improvement in prediction speed can be gained at a cost of only slightly reduced accuracy, while further optimizations are still possible.

Web [BibTex]

Web [BibTex]


Improving Denoising Algorithms via a Multi-scale Meta-procedure

Burger, H., Harmeling, S.

In Pattern Recognition, pages: 206-215, (Editors: Mester, R. , M. Felsberg), Springer, Berlin, Germany, 33rd DAGM Symposium, September 2011 (inproceedings)

Abstract
Many state-of-the-art denoising algorithms focus on recovering high-frequency details in noisy images. However, images corrupted by large amounts of noise are also degraded in the lower frequencies. Thus properly handling all frequency bands allows us to better denoise in such regimes. To improve existing denoising algorithms we propose a meta-procedure that applies existing denoising algorithms across different scales and combines the resulting images into a single denoised image. With a comprehensive evaluation we show that the performance of many state-of-the-art denoising algorithms can be improved.

PDF DOI Project Page [BibTex]

PDF DOI Project Page [BibTex]


Multiple reference genomes and transcriptomes for Arabidopsis thaliana

Gan, X., Stegle, O., Behr, J., Steffen, J., Drewe, P., Hildebrand, K., Lyngsoe, R., Schultheiss, S., Osborne, E., Sreedharan, V., Kahles, A., Bohnert, R., Jean, G., Derwent, P., Kersey, P., Belfield, E., Harberd, N., Kemen, E., Toomajian, C., Kover, P., Clark, R., Rätsch, G., Mott, R.

Nature, 477(7365):419–423, September 2011 (article)

Abstract
Genetic differences between Arabidopsis thaliana accessions underlie the plant’s extensive phenotypic variation, and until now these have been interpreted largely in the context of the annotated reference accession Col-0. Here we report the sequencing, assembly and annotation of the genomes of 18 natural A. thaliana accessions, and their transcriptomes. When assessed on the basis of the reference annotation, one-third of protein-coding genes are predicted to be disrupted in at least one accession. However, re-annotation of each genome revealed that alternative gene models often restore coding potential. Gene expression in seedlings differed for nearly half of expressed genes and was frequently associated with cis variants within 5 kilobases, as were intron retention alternative splicing events. Sequence and expression variation is most pronounced in genes that respond to the biotic environment. Our data further promote evolutionary and functional studies in A. thaliana, especially the MAGIC genetic reference population descended from these accessions.

Web DOI [BibTex]

Web DOI [BibTex]


Weisfeiler-Lehman Graph Kernels

Shervashidze, N., Schweitzer, P., van Leeuwen, E., Mehlhorn, K., Borgwardt, M.

Journal of Machine Learning Research, 12, pages: 2539-2561, September 2011 (article)

Abstract
In this article, we propose a family of efficient kernels for large graphs with discrete node labels. Key to our method is a rapid feature extraction scheme based on the Weisfeiler-Lehman test of isomorphism on graphs. It maps the original graph to a sequence of graphs, whose node attributes capture topological and label information. A family of kernels can be defined based on this Weisfeiler-Lehman sequence of graphs, including a highly efficient kernel comparing subtree-like patterns. Its runtime scales only linearly in the number of edges of the graphs and the length of the Weisfeiler-Lehman graph sequence. In our experimental evaluation, our kernels outperform state-of-the-art graph kernels on several graph classification benchmark data sets in terms of accuracy and runtime. Our kernels open the door to large-scale applications of graph kernels in various disciplines such as computational biology and social network analysis.

PDF Web Project Page [BibTex]

PDF Web Project Page [BibTex]


Support Vector Machines as Probabilistic Models

Franc, V., Zien, A., Schölkopf, B.

In Proceedings of the 28th International Conference on Machine Learning, pages: 665-672, (Editors: L Getoor and T Scheffer), International Machine Learning Society, Madison, WI, USA, ICML, July 2011 (inproceedings)

Abstract
We show how the SVM can be viewed as a maximum likelihood estimate of a class of probabilistic models. This model class can be viewed as a reparametrization of the SVM in a similar vein to the v-SVM reparametrizing the classical (C-)SVM. It is not discriminative, but has a non-uniform marginal. We illustrate the benefits of this new view by rederiving and re-investigating two established SVM-related algorithms.

PDF Web [BibTex]

PDF Web [BibTex]


Statistical estimation for optimization problems on graphs

Langovoy, M., Sra, S.

In pages: 1-6, NIPS Workshop on Discrete Optimization in Machine Learning (DISCML): Uncertainty, Generalization and Feedback , December 2011 (inproceedings)

Abstract
Large graphs abound in machine learning, data mining, and several related areas. A useful step towards analyzing such graphs is that of obtaining certain summary statistics — e.g., or the expected length of a shortest path between two nodes, or the expected weight of a minimum spanning tree of the graph, etc. These statistics provide insight into the structure of a graph, and they can help predict global properties of a graph. Motivated thus, we propose to study statistical properties of structured subgraphs (of a given graph), in particular, to estimate the expected objective function value of a combinatorial optimization problem over these subgraphs. The general task is very difficult, if not unsolvable; so for concreteness we describe a more specific statistical estimation problem based on spanning trees. We hope that our position paper encourages others to also study other types of graphical structures for which one can prove nontrivial statistical estimates.

PDF Web [BibTex]

PDF Web [BibTex]


Reinforcement Learning with Bounded Information Loss

Peters, J., Peters, J., Mülling, K., Altun, Y.

AIP Conference Proceedings, 1305(1):365-372, 2011 (article)

Abstract
Policy search is a successful approach to reinforcement learning. However, policy improvements often result in the loss of information. Hence, it has been marred by premature convergence and implausible solutions. As first suggested in the context of covariant or natural policy gradients, many of these problems may be addressed by constraining the information loss. In this paper, we continue this path of reasoning and suggest two reinforcement learning methods, i.e., a model‐based and a model free algorithm that bound the loss in relative entropy while maximizing their return. The resulting methods differ significantly from previous policy gradient approaches and yields an exact update step. It works well on typical reinforcement learning benchmark problems as well as novel evaluations in robotics. We also show a Bayesian bound motivation of this new approach [8].

Web DOI [BibTex]

Web DOI [BibTex]


Transfer Learning with Copulas

Lopez-Paz, D., Hernandez-Lobato, J.

In pages: 2, NIPS, Workshop on Copulas in Machine Learning, 2011 (inproceedings)

PDF [BibTex]

PDF [BibTex]


Denoising sparse noise via online dictionary learning

Cherian, A., Sra, S., Papanikolopoulos, N.

In Proceedings of the IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2011, pages: 2060 -2063, IEEE, IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2011 (inproceedings)

DOI [BibTex]

DOI [BibTex]


Support Vector Machines for finding deletions and short insertions using paired-end short reads

Grimm, D. Hagmann, J. König, D. Weigel, D. Borgwardt, KM.

International Conference on Intelligent Systems for Molecular Biology (ISMB), 2011 (poster)

Web [BibTex]

Web [BibTex]


What You Expect Is What You Get? Potential Use of Contingent Negative Variation for Passive BCI Systems in Gaze-Based HCI

Ihme, K. Zander, TO.

In Affective Computing and Intelligent Interaction, 6975, pages: 447-456, Lecture Notes in Computer Science, (Editors: D’Mello, S., Graesser, A., Schuller, B. and Martin, J.-C.), Springer, Berlin, Germany, 2011 (inbook)

Abstract
When using eye movements for cursor control in human-computer interaction (HCI), it may be difficult to find an appropriate substitute for the click operation. Most approaches make use of dwell times. However, in this context the so-called Midas-Touch-Problem occurs which means that the system wrongly interprets fixations due to long processing times or spontaneous dwellings of the user as command. Lately it has been shown that brain-computer interface (BCI) input bears good prospects to overcome this problem using imagined hand movements to elicit a selection. The current approach tries to develop this idea further by exploring potential signals for the use in a passive BCI, which would have the advantage that the brain signals used as input are generated automatically without conscious effort of the user. To explore event-related potentials (ERPs) giving information about the user’s intention to select an object, 32-channel electroencephalography (EEG) was recorded from ten participants interacting with a dwell-time-based system. Comparing ERP signals during the dwell time with those occurring during fixations on a neutral cross hair, a sustained negative slow cortical potential at central electrode sites was revealed. This negativity might be a contingent negative variation (CNV) reflecting the participants’ anticipation of the upcoming selection. Offline classification suggests that the CNV is detectable in single trial (mean accuracy 74.9 %). In future, research on the CNV should be accomplished to ensure its stable occurence in human-computer interaction and render possible its use as a potential substitue for the click operation.

DOI [BibTex]

DOI [BibTex]


PILCO: A Model-Based and Data-Efficient Approach to Policy Search

Deisenroth, MP. Rasmussen, CE.

In Proceedings of the 28th International Conference on Machine Learning, ICML 2011, pages: 465-472, (Editors: L Getoor and T Scheffer), Omnipress, 2011 (inproceedings)

Abstract
In this paper, we introduce PILCO, a practical, data-efficient model-based policy search method. PILCO reduces model bias, one of the key problems of model-based reinforcement learning, in a principled way. By learning a probabilistic dynamics model and explicitly incorporating model uncertainty into long-term planning, PILCO can cope with very little data and facilitates learning from scratch in only a few trials. Policy evaluation is performed in closed form using state-of-the-art approximate inference. Furthermore, policy gradients are computed analytically for policy improvement. We report unprecedented learning efficiency on challenging and high-dimensional control tasks.

Web Project Page [BibTex]

Web Project Page [BibTex]


Kernel Bayes’ Rule

Fukumizu, K., Song, L., Gretton, A.

In Advances in Neural Information Processing Systems 24, pages: 1737-1745, (Editors: J Shawe-Taylor and RS Zemel and P Bartlett and F Pereira and KQ Weinberger), Curran Associates, Inc., Red Hook, NY, USA, Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS), 2011 (inproceedings)

PDF Project Page [BibTex]

PDF Project Page [BibTex]


A Novel Active Learning Strategy for Domain Adaptation in the Classification of Remote Sensing Images

Persello, C., Bruzzone, L.

In pages: 3720-3723 , IEEE, Piscataway, NJ, USA, IEEE International Geoscience and Remote Sensing Symposium (IGARSS), July 2011 (inproceedings)

Abstract
We present a novel technique for addressing domain adaptation problems in the classification of remote sensing images with active learning. Domain adaptation is the important problem of adapting a supervised classifier trained on a given image (source domain) to the classification of another similar (but not identical) image (target domain) acquired on a different area, or on the same area at a different time. The main idea of the proposed approach is to iteratively labeling and adding to the training set the minimum number of the most informative samples from target domain, while removing the source-domain samples that does not fit with the distributions of the classes in the target domain. In this way, the classification system exploits already available information, i.e., the labeled samples of source domain, in order to minimize the number of target domain samples to be labeled, thus reducing the cost associated to the definition of the training set for the classification of the target domain. Experimental results obtained in the classification of a hyperspectral image confirm the effectiveness of the proposed technique.

Web DOI [BibTex]

Web DOI [BibTex]


Using brain–computer interfaces to induce neural plasticity and restore function

Grosse-Wentrup, M., Mattia, D., Oweiss, K.

Journal of Neural Engineering, 8(2):1-5, April 2011 (article)

Abstract
Analyzing neural signals and providing feedback in real-time is one of the core characteristics of a brain-computer interface (BCI). As this feature may be employed to induce neural plasticity, utilizing BCI-technology for therapeutic purposes is increasingly gaining popularity in the BCI-community. In this review, we discuss the state-of-the-art of research on this topic, address the principles of and challenges in inducing neural plasticity by means of a BCI, and delineate the problems of study design and outcome evaluation arising in this context. The review concludes with a list of open questions and recommendations for future research in this field.

PDF DOI Project Page [BibTex]

PDF DOI Project Page [BibTex]


Incremental online sparsification for model learning in real-time robot control

Nguyen-Tuong, D., Peters, J.

Neurocomputing, 74(11):1859-1867, May 2011 (article)

Abstract
For many applications such as compliant, accurate robot tracking control, dynamics models learned from data can help to achieve both compliant control performance as well as high tracking quality. Online learning of these dynamics models allows the robot controller to adapt itself to changes in the dynamics (e.g., due to time-variant nonlinearities or unforeseen loads). However, online learning in real-time applications -- as required in control -- cannot be realized by straightforward usage of off-the-shelf machine learning methods such as Gaussian process regression or support vector regression. In this paper, we propose a framework for online, incremental sparsification with a fixed budget designed for fast real-time model learning. The proposed approach employs a sparsification method based on an independence measure. In combination with an incremental learning approach such as incremental Gaussian process regression, we obtain a model approximation method which is applicable in real-time online learning. It exhibits competitive learning accuracy when compared with standard regression techniques. Implementation on a real Barrett WAM robot demonstrates the applicability of the approach in real-time online model learning for real world systems.

PDF DOI [BibTex]


Trajectory Planning for Optimal Robot Catching in Real-Time

Lampariello, R., Nguyen-Tuong, D., Castellini, C., Hirzinger, G., Peters, J.

In Proceedings of the IEEE International Conference on Robotics and Automation (ICRA 2011), pages: 3719-3726 , IEEE, Piscataway, NJ, USA, IEEE International Conference on Robotics and Automation (ICRA), May 2011 (inproceedings)

Abstract
Many real-world tasks require fast planning of highly dynamic movements for their execution in real-time. The success often hinges on quickly finding one of the few plans that can achieve the task at all. A further challenge is to quickly find a plan which optimizes a desired cost. In this paper, we will discuss this problem in the context of catching small flying targets efficiently. This can be formulated as a non-linear optimization problem where the desired trajectory is encoded by an adequate parametric representation. The optimizer generates an energy-optimal trajectory by efficiently using the robot kinematic redundancy while taking into account maximal joint motion, collision avoidance and local minima. To enable the resulting method to work in real-time, examples of the global planner are generalized using nearest neighbour approaches, Support Vector Machines and Gaussian process regression, which are compared in this context. Evaluations indicate that the presented method is highly efficient in complex tasks such as ball-catching.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


Towards Motor Skill Learning for Robotics

Peters, J., Mülling, K., Kober, J., Nguyen-Tuong, D., Kroemer, O.

In Robotics Research, pages: 469-482, (Editors: Pradalier, C. , R. Siegwart, G. Hirzinger), Springer, Berlin, Germany, 14th International Symposium on Robotics Research (ISRR), January 2011 (inproceedings)

Abstract
Learning robots that can acquire new motor skills and refine existing one has been a long standing vision of robotics, artificial intelligence, and the cognitive sciences. Early steps towards this goal in the 1980s made clear that reasoning and human insights will not suffice. Instead, new hope has been offered by the rise of modern machine learning approaches. However, to date, it becomes increasingly clear that off-the-shelf machine learning approaches will not suffice for motor skill learning as these methods often do not scale into the high-dimensional domains of manipulator and humanoid robotics nor do they fulfill the real-time requirement of our domain. As an alternative, we propose to break the generic skill learning problem into parts that we can understand well from a robotics point of view. After designing appropriate learning approaches for these basic components, these will serve as the ingredients of a general approach to motor skill learning. In this paper, we discuss our recent and current progress in this direction. For doing so, we present our work on learning to control, on learning elementary movements as well as our steps towards learning of complex tasks. We show several evaluations both using real robots as well as physically realistic simulations.

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


Combining computational modeling with sparse and low-resolution data

Habeck, M. Nilges, M.

Journal of Structural Biology, 173(3):419, March 2011 (article)

Abstract
Structural biology is moving into a new era by shifting its focus from static structures of single proteins and protein domains to large and often fragile multi-component complexes. Over the past decade, structural genomics initiatives aimed to fill the voids in fold space and to provide a census of all protein structures. Completion of such an atlas of protein structures is still ongoing, but not sufficient for a mechanistic understanding of how living cells function. One of the great challenges is to bridge the gap between atomic resolution detail and the more fuzzy description of the molecular complexes that govern cellular processes or host–pathogen interactions. We want to move from cartoon-like representations of multi-component complexes to atomic resolution structures. To characterize the structures of the increasingly large and often flexible complexes, high resolution structure determination (as was possible for example for the ribosome) will likely stay the exception. Rather, data from many different methods providing information on the shape (X-ray crystallography, electron microscopy, SAXS, AFM, etc.) or on contacts between components (mass spectrometry, co-purification, or spectroscopic methods) need to be integrated with prior structural knowledge to build a consistent model of the complex. A particular difficulty is that the ratio between the number of conformational degrees of freedom and the number of measurements becomes unfavorable as we work with large complexes: data become increasingly sparse. Structural characterization of large molecular assemblies often involves a loss in resolution as well as in number and quality of data. We are good at solving structures of single proteins, but classical high-resolution structure determination by X-ray crystallography and NMR spectroscopy is often facing its limits as we move to higher molecular mass and increased flexibility. Therefore, structural studies on large complexes rely on new experimental techniques that complement the classical high resolution methods. But also computational approaches are becoming more important when it comes to integrating and analyzing structural information of often heterogeneous nature. Cryoelectron microscopy may serve as an example of how experimental methods can benefit from computation. Low-resolution data from cryo-EM show their true power when combined with modeling and bioinformatics methods such rigid docking and secondary structure hunting. Even in high resolution structure determination, molecular modeling is always necessary to calculate structures from data, to complement the missing information and to evaluate and score the obtained structures. With sparse data, all these three aspects become increasingly difficult, and the quality of the modeling approach becomes more important. With data alone, algorithms may not converge any more; scoring against data becomes meaningless; and the potential energy function becomes central not only as a help in making algorithms converge but also to score and evaluate the structures. In addition to the sparsity of the data, hybrid approaches bring the additional difficulty that the different sources of data may have rather different quality, and may be in the extreme case incompatible with each other. In addition to scoring the structures, modeling should also score in some way the data going into the calculation. This special issue brings together some of the numerous efforts to solve the problems that come from sparsity of data and from integrating data from different sources in hybrid approaches. The methods range from predominantly force-field based to mostly data based. Systems of very different sizes, ranging from single domains to multi-component complexes, are treated. We hope that you will enjoy reading the issue and find it a useful and inspiring resource.

PDF DOI [BibTex]

PDF DOI [BibTex]


Statistical Image Analysis and Percolation Theory

Langovoy, M., Habeck, M., Schölkopf, B.

2011 Joint Statistical Meetings (JSM), August 2011 (talk)

Abstract
We develop a novel method for detection of signals and reconstruction of images in the presence of random noise. The method uses results from percolation theory. We specifically address the problem of detection of multiple objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. The objects of interest have unknown varying intensities. No boundary shape constraints are imposed on the objects, only a set of weak bulk conditions is required. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect greyscale objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures. Applications to cryo-electron microscopy are presented.

Web [BibTex]

Web [BibTex]