Publications | Empirical Inference - Max Planck Institute for Intelligent Systems

104 results (View BibTeX file of all listed publications)

2010

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Computationally efficient algorithms for statistical image processing: Implementation in R

Langovoy, M., Wittich, O.

(2010-053), EURANDOM, Technische Universiteit Eindhoven, December 2010 (techreport)

Abstract

In the series of our earlier papers on the subject, we proposed a novel statistical hy- pothesis testing method for detection of objects in noisy images. The method uses results from percolation theory and random graph theory. We developed algorithms that allowed to detect objects of unknown shapes in the presence of nonparametric noise of unknown level and of un- known distribution. No boundary shape constraints were imposed on the objects, only a weak bulk condition for the object's interior was required. Our algorithms have linear complexity and exponential accuracy. In the present paper, we describe an implementation of our nonparametric hypothesis testing method. We provide a program that can be used for statistical experiments in image processing. This program is written in the statistical programming language R.

2010

Langovoy, M., Wittich, O. Computationally efficient algorithms for statistical image processing: Implementation in R (2010-053), EURANDOM, Technische Universiteit Eindhoven, December 2010 (techreport)

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Similarities in resting state and feature-driven activity: Non-parametric evaluation of human fMRI

Shelton, J., Blaschko, M., Gretton, A., Müller, J., Fischer, E., Bartels, A.

NIPS Workshop on Learning and Planning from Batch Time Series Data, December 2010 (poster)

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Shelton, J., Blaschko, M., Gretton, A., Müller, J., Fischer, E., Bartels, A. Similarities in resting state and feature-driven activity: Non-parametric evaluation of human fMRI NIPS Workshop on Learning and Planning from Batch Time Series Data, December 2010 (poster)

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Fast Convergent Algorithms for Expectation Propagation Approximate Bayesian Inference

Seeger, M., Nickisch, H.

Max Planck Institute for Biological Cybernetics, December 2010 (techreport)

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 05) with covariance decoupling techniques (Wipf&Nagarajan 08, Nickisch&Seeger 09), it runs at least an order of magnitude faster than the most commonly used EP solver.

Seeger, M., Nickisch, H. Fast Convergent Algorithms for Expectation Propagation Approximate Bayesian Inference Max Planck Institute for Biological Cybernetics, December 2010 (techreport)

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Augmentation of fMRI Data Analysis using Resting State Activity and Semi-supervised Canonical Correlation Analysis

Shelton, JA., Blaschko, MB., Bartels, A.

NIPS Women in Machine Learning Workshop (WiML), December 2010 (poster)

Abstract

Resting state activity is brain activation that arises in the absence of any task, and is usually measured in awake subjects during prolonged fMRI scanning sessions where the only instruction given is to close the eyes and do nothing. It has been recognized in recent years that resting state activity is implicated in a wide variety of brain function. While certain networks of brain areas have different levels of activation at rest and during a task, there is nevertheless significant similarity between activations in the two cases. This suggests that recordings of resting state activity can be used as a source of unlabeled data to augment kernel canonical correlation analysis (KCCA) in a semisupervised setting. We evaluate this setting empirically yielding three main results: (i) KCCA tends to be improved by the use of Laplacian regularization even when no additional unlabeled data are available, (ii) resting state data seem to have a similar marginal distribution to that recorded during the execution of a visual processing task implying largely similar types of activation, and (iii) this source of information can be broadly exploited to improve the robustness of empirical inference in fMRI studies, an inherently data poor domain.

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Shelton, JA., Blaschko, MB., Bartels, A. Augmentation of fMRI Data Analysis using Resting State Activity and Semi-supervised Canonical Correlation Analysis NIPS Women in Machine Learning Workshop (WiML), December 2010 (poster)

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High frequency phase-spike synchronization of extracellular signals modulates causal interactions in monkey primary visual cortex

Besserve, M., Murayama, Y., Schölkopf, B., Logothetis, N., Panzeri, S.

40(616.2), 40th Annual Meeting of the Society for Neuroscience (Neuroscience), November 2010 (poster)

Abstract

Functional correlates of Rhythms in the gamma band (30-100Hz) are observed in the mammalian brain with a large variety of functional correlates. Nevertheless, their functional role is still debated. One way to disentangle this issue is to go beyond usual correlation analysis and apply causality measures that quantify the directed interactions between the gamma rhythms and other aspects of neural activity. These measures can be further compared with other aspects of neurophysicological signals to find markers of neural interactions. In a recent study, we analyzed extracellular recordings in the primary visual cortex of 4 anesthetized macaques during the presentation of movie stimuli using a causality measure named Transfer Entropy. We found causal interactions between high frequency gamma rhythms (60-100Hz) recorded in different electrodes, involving in particular their phase, and between the gamma phase and spiking activity quantified by the instantaneous envelope of the MUA band (1-3kHz). Here, we further investigate in the same dataset the meaning of these phase-MUA and phase-phase causal interactions by studying the distribution of phases at multiple recording sites at lags around the occurrence of spiking events. First, we found a sharpening of the gamma phase distribution in one electrode when spikes are occurring in other recording site. This phenomena appeared as a form of phase-spike synchronization and was quantified by an information theoretic measure. We found this measure correlates significantly with phase-MUA causal interactions. Additionally, we quantified in a similar way the interplay between spiking and the phase difference between two recording sites (reflecting the well-know concept of phase synchronization). We found that, depending on the couple of recording site, spiking can correlate either with a phase synchronization or with a desynchronization with respect to the baseline. This effect correlates very well with the phase-phase causality measure. These results provide evidence for high frequency phase-spike synchronization to reflect communication between distant neural populations in V1. Conversely, both phase synchronization or desynchronization may favor neural communication between recording sites. This new result, which contrasts with current hypothesis on the role of phase synchronization, could be interpreted as the presence of inhibitory interactions that are suppressed by desynchronization. Finally, our findings give new insights into the role of gamma rhythms in regulating local computation in the visual cortex.

Besserve, M., Murayama, Y., Schölkopf, B., Logothetis, N., Panzeri, S. High frequency phase-spike synchronization of extracellular signals modulates causal interactions in monkey primary visual cortex 40(616.2), 40th Annual Meeting of the Society for Neuroscience (Neuroscience), November 2010 (poster)

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Attenuation Correction for Whole Body PET/MR: Quantitative Evaluation and Lung Attenuation Estimation with Consistency Information

Bezrukov, I., Hofmann, M., Aschoff, P., Beyer, T., Mantlik, F., Pichler, B., Schölkopf, B.

2010(M13-122), 2010 Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), November 2010 (poster)

Bezrukov, I., Hofmann, M., Aschoff, P., Beyer, T., Mantlik, F., Pichler, B., Schölkopf, B. Attenuation Correction for Whole Body PET/MR: Quantitative Evaluation and Lung Attenuation Estimation with Consistency Information 2010(M13-122), 2010 Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), November 2010 (poster)

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Approximate Inference in Graphical Models

University of Cambridge, November 2010 (phdthesis)

Hennig, P. Approximate Inference in Graphical Models University of Cambridge, November 2010 (phdthesis)

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PET/MRI: Observation of Non-Isotropic Positron Distribution in High Magnetic Fields and Its Diagnostic Impact

Kolb, A., Hofmann, M., Sauter, A., Liu, C., Schölkopf, B., Pichler, B.

2010 Nuclear Science Symposium and Medical Imaging Conference, 2010(M18-119):1, November 2010 (poster)

Kolb, A., Hofmann, M., Sauter, A., Liu, C., Schölkopf, B., Pichler, B. PET/MRI: Observation of Non-Isotropic Positron Distribution in High Magnetic Fields and Its Diagnostic Impact 2010 Nuclear Science Symposium and Medical Imaging Conference, 2010(M18-119):1, November 2010 (poster)

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Probabilistic Assignment of Chemical Shift Data for Semi-Automatic Amino Acid Recognition

11(10):30, 11th Conference of Junior Neuroscientists of T{\"u}bingen (NeNa), October 2010 (poster)

Abstract

manner. First the backbone resonances are assigned. This is usually achieved from sequential information provided by three chemical shifts: CA, CB and C’. Once the sequence is solved, the second assignment step takes place. For this purpose, the CA-CB and HA chemical shifts are used as a start point for assignment of the side chain resonances, thus connecting the backbone resonances to their respective side chains. This strategy is unfortunately limited by the size of the protein due to increasing signal overlap and missing signals. Therefore, amino acid recognition is in many cases not possible as the CA-CB chemical shift pattern is not sufficient to discriminate between the 20 amino acids. As a result, the first step of the strategy described above remains tedious and time consuming. The combination of modern NMR techniques with new spectrometers now provide information that was not always accessible in the past, due to sensitivity problems. These experiments can be applied efficiently to measure a protein size up to 45 kDa and furthermore provide a unique combination of sequential carbon spin system information. The assignment process can thus benefit from a maximum knowledge input, containing âallâ backbone and side chain chemical shifts as well as an immediate amino acid recognition from the side chain spin system. We propose to extend the software PASTA (Protein ASsignment by Threshold Accepting) to achieve a general sequential assignment of backbone and side-chain resonances in a semi- to fullautomatic per-residue approach. PASTA will offer the possibility to achieve the sequential assignment using any kind of chemical shifts (carbons and/or protons) that can provide sequential information combined with an amino acid recognition feature based on carbon spin system analysis.

Hooge, J. Probabilistic Assignment of Chemical Shift Data for Semi-Automatic Amino Acid Recognition 11(10):30, 11th Conference of Junior Neuroscientists of T{\"u}bingen (NeNa), October 2010 (poster)

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Generalizing Demonstrated Actions in Manipulation Tasks

Kroemer, O., Detry, R., Piater, J., Peters, J.

IROS 2010 Workshop on Grasp Planning and Task Learning by Imitation, 2010, pages: 1, October 2010 (poster)

Abstract

Programming-by-demonstration promises to significantly reduce the burden of coding robots to perform new tasks. However, service robots will be presented with a variety of different situations that were not specifically demonstrated to it. In such cases, the robot must autonomously generalize its learned motions to these new situations. We propose a system that can generalize movements to new target locations and even new objects. The former is achieved by using a task-specific coordinate system together with dynamical systems motor primitives. Generalizing actions to new objects is a more complex problem, which we solve by treating it as a continuum-armed bandits problem. Using the bandits framework, we can efficiently optimize the learned action for a specific object. The proposed method was implemented on a real robot and succesfully adapted the grasping action to three different objects. Although we focus on grasping as an example of a task, the proposed methods are much more widely applicable to robot manipulation tasks.

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Kroemer, O., Detry, R., Piater, J., Peters, J. Generalizing Demonstrated Actions in Manipulation Tasks IROS 2010 Workshop on Grasp Planning and Task Learning by Imitation, 2010, pages: 1, October 2010 (poster)

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Bayesian Inference and Experimental Design for Large Generalised Linear Models

Biologische Kybernetik, Technische Universität Berlin, Berlin, Germany, September 2010 (phdthesis)

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Nickisch, H. Bayesian Inference and Experimental Design for Large Generalised Linear Models Biologische Kybernetik, Technische Universität Berlin, Berlin, Germany, September 2010 (phdthesis)

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Inhomogeneous Positron Range Effects in High Magnetic Fields might Cause Severe Artefacts in PET/MRI

Kolb, A., Hofmann, M., Sauter, A., Liu, C., Eriksson, L., Pichler, B.

(0305B), 2010 World Molecular Imaging Congress (WMIC), September 2010 (poster)

Abstract

The combination of PET and MRI is an emerging field of current research. It is known that the positron range is shortened in high magnetic fields (MF), leading to an improved resolution in PET images. Interestingly, only the fraction of positron range (PR) orthogonal to the MF is reduced and the fraction along the MF is not affected and yields to a non-isotropic count distribution. We measured the PR effect with PET isotopes like F-18, Cu-64, C-11, N-13 and Ga-68. A piece of paper (1 cm2) was soaked with each isotope and placed in the cFOV of a clinical 3T BrainPET/MR scanner. A polyethylene board (PE) was placed as a positron (β+) stopper with an axial distance of 3 cm from the soaked paper. The area under the peaks of one pixel wide profiles along the z-axis in coronal images was compared. Based on these measurements we confirmed our data in organic tissue. A larynx/trachea and lung of a butchered swine were injected with a mixture of NiSO4 for T1 MRI signals and Ga-68, simulating tumor lesions in the respiratory tract. The trachea/larynx were aligned in 35° to the MF lines and a small mass lesion was inserted to imitate a primary tracheal tumor whereas the larynx was injected submucosally in the lower medial part of the epiglottis. Reconstructed PET data show that the annihilated ratio of β+ at the origin position and in the PE depends on the isotope energy and the direction of the MF. The annihilation ratios of the source and PE are 52.4/47.6 (F-18), 57.5/42.5 (Cu-64), 43.7/56.7 (C-11), 31.1/68.9 (N-13) and 14.9/85.1 (Ga-68). In the swine larynx measurement, an artefact with approximately 39% of the lesion activity formed along MF lines 3cm away from the original injected position (fig.1). The data of the trachea showed two shine artefacts with a symmetric alignment along the MF lines. About 58% of the positrons annihilated at the lesion and 21% formed each artefact. The PR effects areminor in tissue of higher or equal density to water (0.096 cm-1). However, the effect is severe in low density tissue or air and might lead to misinterpretation of clinical data.

Kolb, A., Hofmann, M., Sauter, A., Liu, C., Eriksson, L., Pichler, B. Inhomogeneous Positron Range Effects in High Magnetic Fields might Cause Severe Artefacts in PET/MRI (0305B), 2010 World Molecular Imaging Congress (WMIC), September 2010 (poster)

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A PAC-Bayesian Analysis of Graph Clustering and Pairwise Clustering

Max Planck Institute for Biological Cybernetics, Tübingen, Germany, September 2010 (techreport)

Abstract

We formulate weighted graph clustering as a prediction problem: given a subset of edge weights we analyze the ability of graph clustering to predict the remaining edge weights. This formulation enables practical and theoretical comparison of different approaches to graph clustering as well as comparison of graph clustering with other possible ways to model the graph. We adapt the PAC-Bayesian analysis of co-clustering (Seldin and Tishby, 2008; Seldin, 2009) to derive a PAC-Bayesian generalization bound for graph clustering. The bound shows that graph clustering should optimize a trade-off between empirical data fit and the mutual information that clusters preserve on the graph nodes. A similar trade-off derived from information-theoretic considerations was already shown to produce state-of-the-art results in practice (Slonim et al., 2005; Yom-Tov and Slonim, 2009). This paper supports the empirical evidence by providing a better theoretical foundation, suggesting formal generalization guarantees, and offering a more accurate way to deal with finite sample issues. We derive a bound minimization algorithm and show that it provides good results in real-life problems and that the derived PAC-Bayesian bound is reasonably tight.

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Seldin, Y. A PAC-Bayesian Analysis of Graph Clustering and Pairwise Clustering Max Planck Institute for Biological Cybernetics, Tübingen, Germany, September 2010 (techreport)

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Sparse nonnegative matrix approximation: new formulations and algorithms

Tandon, R., Sra, S.

(193), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, September 2010 (techreport)

Abstract

We introduce several new formulations for sparse nonnegative matrix approximation. Subsequently, we solve these formulations by developing generic algorithms. Further, to help selecting a particular sparse formulation, we briefly discuss the interpretation of each formulation. Finally, preliminary experiments are presented to illustrate the behavior of our formulations and algorithms.

Tandon, R., Sra, S. Sparse nonnegative matrix approximation: new formulations and algorithms (193), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, September 2010 (techreport)

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Robust nonparametric detection of objects in noisy images

Langovoy, M., Wittich, O.

(2010-049), EURANDOM, Technische Universiteit Eindhoven, September 2010 (techreport)

Abstract

We propose a novel statistical hypothesis testing method for detection of objects in noisy images. The method uses results from percolation theory and random graph theory. We present an algorithm that allows to detect objects of unknown shapes in the presence of nonparametric noise of unknown level and of unknown distribution. No boundary shape constraints are imposed on the object, only a weak bulk condition for the object's interior is required. The algorithm has linear complexity and exponential accuracy and is appropriate for real-time systems. In this paper, we develop further the mathematical formalism of our method and explore im- portant connections to the mathematical theory of percolation and statistical physics. We prove results on consistency and algorithmic complexity of our testing procedure. In addition, we address not only an asymptotic behavior of the method, but also a nite sample performance of our test.

Langovoy, M., Wittich, O. Robust nonparametric detection of objects in noisy images (2010-049), EURANDOM, Technische Universiteit Eindhoven, September 2010 (techreport)

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Large Scale Variational Inference and Experimental Design for Sparse Generalized Linear Models

Seeger, M., Nickisch, H.

Max Planck Institute for Biological Cybernetics, August 2010 (techreport)

Abstract

Many problems of low-level computer vision and image processing, such as denoising, deconvolution, tomographic reconstruction or super-resolution, can be addressed by maximizing the posterior distribution of a sparse linear model (SLM). We show how higher-order Bayesian decision-making problems, such as optimizing image acquisition in magnetic resonance scanners, can be addressed by querying the SLM posterior covariance, unrelated to the density's mode. We propose a scalable algorithmic framework, with which SLM posteriors over full, high-resolution images can be approximated for the first time, solving a variational optimization problem which is convex iff posterior mode finding is convex. These methods successfully drive the optimization of sampling trajectories for real-world magnetic resonance imaging through Bayesian experimental design, which has not been attempted before. Our methodology provides new insight into similarities and differences between sparse reconstruction and approximate Bayesian inference, and has important implications for compressive sensing of real-world images.

Seeger, M., Nickisch, H. Large Scale Variational Inference and Experimental Design for Sparse Generalized Linear Models Max Planck Institute for Biological Cybernetics, August 2010 (techreport)

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Cooperative Cuts for Image Segmentation

Jegelka, S., Bilmes, J.

(UWEETR-1020-0003), University of Washington, Washington DC, USA, August 2010 (techreport)

Abstract

We propose a novel framework for graph-based cooperative regularization that uses submodular costs on graph edges. We introduce an efficient iterative algorithm to solve the resulting hard discrete optimization problem, and show that it has a guaranteed approximation factor. The edge-submodular formulation is amenable to the same extensions as standard graph cut approaches, and applicable to a range of problems. We apply this method to the image segmentation problem. Specifically, Here, we apply it to introduce a discount for homogeneous boundaries in binary image segmentation on very difficult images, precisely, long thin objects and color and grayscale images with a shading gradient. The experiments show that significant portions of previously truncated objects are now preserved.

Jegelka, S., Bilmes, J. Cooperative Cuts for Image Segmentation (UWEETR-1020-0003), University of Washington, Washington DC, USA, August 2010 (techreport)

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Inferring High-Dimensional Causal Relations using Free Probability Theory

Zscheischler, J.

Humboldt Universität Berlin, Germany, August 2010 (diplomathesis)

Zscheischler, J. Inferring High-Dimensional Causal Relations using Free Probability Theory Humboldt Universität Berlin, Germany, August 2010 (diplomathesis)

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Fast algorithms for total-variationbased optimization

Barbero, A., Sra, S.

(194), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, August 2010 (techreport)

Abstract

We derive a number of methods to solve efficiently simple optimization problems subject to a totalvariation (TV) regularization, under different norms of the TV operator and both for the case of 1-dimensional and 2-dimensional data. In spite of the non-smooth, non-separable nature of the TV terms considered, we show that a dual formulation with strong structure can be derived. Taking advantage of this structure we develop adaptions of existing algorithms from the optimization literature, resulting in efficient methods for the problem at hand. Experimental results show that for 1-dimensional data the proposed methods achieve convergence within good accuracy levels in practically linear time, both for L1 and L2 norms. For the more challenging 2-dimensional case a performance of order O(N2 log2 N) for N x N inputs is achieved when using the L2 norm. A final section suggests possible extensions and lines of further work.

Barbero, A., Sra, S. Fast algorithms for total-variationbased optimization (194), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, August 2010 (techreport)

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Predictive Representations For Sequential Decision Making Under Uncertainty

Université Laval, Quebec, Canada, July 2010 (phdthesis)

Abstract

The problem of making decisions is ubiquitous in life. This problem becomes even more complex when the decisions should be made sequentially. In fact, the execution of an action at a given time leads to a change in the environment of the problem, and this change cannot be predicted with certainty. The aim of a decision-making process is to optimally select actions in an uncertain environment. To this end, the environment is often modeled as a dynamical system with multiple states, and the actions are executed so that the system evolves toward a desirable state. In this thesis, we proposed a family of stochastic models and algorithms in order to improve the quality of of the decision-making process. The proposed models are alternative to Markov Decision Processes, a largely used framework for this type of problems. In particular, we showed that the state of a dynamical system can be represented more compactly if it is described in terms of predictions of certain future events. We also showed that even the cognitive process of selecting actions, known as policy, can be seen as a dynamical system. Starting from this observation, we proposed a panoply of algorithms, all based on predictive policy representations, in order to solve different problems of decision-making, such as decentralized planning, reinforcement learning, or imitation learning. We also analytically and empirically demonstrated that the proposed approaches lead to a decrease in the computational complexity and an increase in the quality of the decisions, compared to standard approaches for planning and learning under uncertainty.

Boularias, A. Predictive Representations For Sequential Decision Making Under Uncertainty Université Laval, Quebec, Canada, July 2010 (phdthesis)

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Reinforcement Learning by Relative Entropy Policy Search

Peters, J., Mülling, K., Altun, Y.

30th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (MaxEnt 2010), 30, pages: 69, July 2010 (poster)

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 policy gradients, many of these problems may be addressed by constraining the information loss. In this book chapter, we continue this path of reasoning and suggest the Relative Entropy Policy Search (REPS) method. The resulting method differs significantly from previous policy gradient approaches and yields an exact update step. It works well on typical reinforcement learning benchmark problems. We will also present a real-world applications where a robot employs REPS to learn how to return balls in a game of table tennis.

Peters, J., Mülling, K., Altun, Y. Reinforcement Learning by Relative Entropy Policy Search 30th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (MaxEnt 2010), 30, pages: 69, July 2010 (poster)

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Semi-supervised Subspace Learning and Application to Human Functional Magnetic Brain Resonance Imaging Data

Biologische Kybernetik, Eberhard Karls Universität, Tübingen, Germany, July 2010 (diplomathesis)

Shelton, J. Semi-supervised Subspace Learning and Application to Human Functional Magnetic Brain Resonance Imaging Data Biologische Kybernetik, Eberhard Karls Universität, Tübingen, Germany, July 2010 (diplomathesis)

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A Maximum Entropy Approach to Semi-supervised Learning

Erkan, A., Altun, Y.

30th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (MaxEnt 2010), 30, pages: 80, July 2010 (poster)

Abstract

Maximum entropy (MaxEnt) framework has been studied extensively in supervised learning. Here, the goal is to find a distribution p that maximizes an entropy function while enforcing data constraints so that the expected values of some (pre-defined) features with respect to p match their empirical counterparts approximately. Using different entropy measures, different model spaces for p and different approximation criteria for the data constraints yields a family of discriminative supervised learning methods (e.g., logistic regression, conditional random fields, least squares and boosting). This framework is known as the generalized maximum entropy framework. Semi-supervised learning (SSL) has emerged in the last decade as a promising field that combines unlabeled data along with labeled data so as to increase the accuracy and robustness of inference algorithms. However, most SSL algorithms to date have had trade-offs, e.g., in terms of scalability or applicability to multi-categorical data. We extend the generalized MaxEnt framework to develop a family of novel SSL algorithms. Extensive empirical evaluation on benchmark data sets that are widely used in the literature demonstrates the validity and competitiveness of the proposed algorithms.

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Erkan, A., Altun, Y. A Maximum Entropy Approach to Semi-supervised Learning 30th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (MaxEnt 2010), 30, pages: 80, July 2010 (poster)

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The effect of positioning aids on PET quantification following MR-based attenuation correction (AC) in PET/MR imaging

Mantlik, F., Hofmann, M., Kupferschläger, J., Werner, M., Pichler, B., Beyer, T.

Journal of Nuclear Medicine, 51(Supplement 2):1418 , June 2010 (poster)

Abstract

Objectives: We study the quantitative effect of not accounting for the attenuation of patient positioning aids in combined PET/MR imaging. Methods: Positioning aids cannot be detected with conventional MR sequences. We mimic this effect using PET/CT data (Biograph HiRez16) with the foams removed from CT images prior to using them for CT-AC. PET/CT data were acquired using standard parameters (phantoms/patients): 120/140 kVp, 30/250 mAs, 5 mm slices, OSEM (4i, 8s, 5 mm filter) following CT-AC. First, a uniform 68Ge-cylinder was positioned centrally in the PET/CT and fixed with a vacuum mattress (10 cm thick). Second, the same cylinder was placed in 3 positioning aids from the PET/MR (BrainPET-3T). Third, 5 head/neck patients who were fixed in a vacuum mattress were selected. In all 3 studies PET recon post CT-AC based on measured CT images was used as the reference (mCT-AC). The PET/MR set-up was mimicked by segmenting the foam inserts from the measured CT images and setting their voxel values to -1000 HU (air). PET images were reconstructed using CT-AC with the segmented CT images (sCT-AC). PET images with mCT- and sCT-AC were compared. Results: sCT-AC underestimated PET voxel values in the phantom by 6.7% on average compared to mCT-AC with the vacuum mattress in place. 5% of the PET voxels were underestimated by >=10%. Not accounting for MR positioning aids during AC led to an underestimation of 2.8% following sCT-AC, with 5% of the PET voxels being underestimated by >=7% wrt mCT-AC. Preliminary evaluation of the patient data indicates a slightly higher bias from not accounting for patient positioning aids (mean: -9.1%, 5% percentile: -11.2%). Conclusions: A considerable and regionally variable underestimation of the PET activity following AC is observed when positioning aids are not accounted for. This bias may become relevant in neurological activation or dementia studies with PET/MR

Mantlik, F., Hofmann, M., Kupferschläger, J., Werner, M., Pichler, B., Beyer, T. The effect of positioning aids on PET quantification following MR-based attenuation correction (AC) in PET/MR imaging Journal of Nuclear Medicine, 51(Supplement 2):1418 , June 2010 (poster)

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Multi-task Learning for Zero Training Brain-Computer Interfaces

Alamgir, M., Grosse-Wentrup, M., Altun, Y.

4th International BCI Meeting, June 2010 (poster)

Abstract

Brain-computer interfaces (BCIs) are limited in their applicability in everyday settings by the current necessity to record subject-specific calibration data prior to actual use of the BCI for communication. In this work, we utilize the framework of multitask learning to construct a BCI that can be used without any subject-specific calibration process, i.e., with zero training data. In BCIs based on EEG or MEG, the predictive function of a subject's intention is commonly modeled as a linear combination of some features derived from spatial and spectral recordings. The coefficients of this combination correspond to the importance of the features for predicting the intention of the subject. These coefficients are usually learned separately for each subject due to inter-subject variability. Principle feature characteristics, however, are known to remain invariant across subject. For example, it is well known that in motor imagery paradigms spectral power in the mu- and beta frequency ranges (roughly 8-14 Hz and 20-30 Hz, respectively) over sensorimotor areas provides most information on a subject's intention. Based on this assumption, we define the intention prediction function as a combination of subject-invariant and subject-specific models, and propose a machine learning method that infers these models jointly using data from multiple subjects. This framework leads to an out-of-the-box intention predictor, where the subject-invariant model can be employed immediately for a subject with no prior data. We present a computationally efficient method to further improve this BCI to incorporate subject-specific variations as such data becomes available. To overcome the problem of high dimensional feature spaces in this context, we further present a new method for finding the relevance of different recording channels according to actions performed by subjects. Usually, the BCI feature representation is a concatenation of spectral features extracted from different channels. This representation, however, is redundant, as recording channels at different spatial locations typically measure overlapping sources within the brain due to volume conduction. We address this problem by assuming that the relevance of different spectral bands is invariant across channels, while learning different weights for each recording electrode. This framework allows us to significantly reduce the feature space dimensionality without discarding potentially useful information. Furthermore, the resulting out-of-the-box BCI can be adapted to different experimental setups, for example EEG caps with different numbers of channels, as long as there exists a mapping across channels in different setups. We demonstrate the feasibility of our approach on a set of experimental EEG data recorded during a standard two-class motor imagery paradigm from a total of ten healthy subjects. Specifically, we show that satisfactory classification results can be achieved with zero training data, and that combining prior recordings with subject-specific calibration data substantially outperforms using subject-specific data only.

Alamgir, M., Grosse-Wentrup, M., Altun, Y. Multi-task Learning for Zero Training Brain-Computer Interfaces 4th International BCI Meeting, June 2010 (poster)

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Causal Influence of Gamma Oscillations on Performance in Brain-Computer Interfaces

Grosse-Wentrup, M., Hill, J., Schölkopf, B.

4th International BCI Meeting0, June 2010 (poster)

Abstract

Background and Objective: While machine learning approaches have led to tremendous advances in brain-computer interfaces (BCIs) in recent years (cf. [1]), there still exists a large variation in performance across subjects. Furthermore, a significant proportion of subjects appears incapable of achieving above chance-level classification accuracy [2], which to date includes all subjects in a completely locked-in state that have been trained in BCI control. Understanding the reasons for this variation in performance arguably constitutes one of the most fundamental open questions in research on BCIs. Methods & Results Using a machine learning approach, we derive a trial-wise measure of how well EEG recordings can be classified as either left- or right-hand motor imagery. Specifically, we train a support vector machine (SVM) on log-bandpower features (7-40 Hz) derived from EEG channels after spatial filtering with a surface Laplacian, and then compute the trial-wise distance of the output of the SVM from the separating hyperplane using a cross-validation procedure. We then correlate this trial-wise performance measure, computed on EEG recordings of ten healthy subjects, with log-bandpower in the gamma frequency range (55-85 Hz), and demonstrate that it is positively correlated with frontal- and occipital gamma-power and negatively correlated with centro-parietal gamma-power. This correlation is shown to be highly significant on the group level as well as in six out of ten subjects on the single-subject level. We then utilize the framework for causal inference developed by Pearl, Spirtes and others [3,4] to present evidence that gamma-power is not only correlated with BCI performance but does indeed exert a causal influence on it. Discussion and Conclusions Our results indicate that successful execution of motor imagery, and hence reliable communication by means of a BCI based on motor imagery, requires a volitional shift of gamma-power from centro-parietal to frontal and occipital regions. As such, our results provide the first non-trivial explanation for the variation in BCI performance across and within subjects. As this topographical alteration in gamma-power is likely to correspond to a specific attentional shift, we propose to provide subjects with feedback on their topographical distribution of gamma-power in order to establish the attentional state required for successful execution of motor imagery.

Grosse-Wentrup, M., Hill, J., Schölkopf, B. Causal Influence of Gamma Oscillations on Performance in Brain-Computer Interfaces 4th International BCI Meeting0, June 2010 (poster)

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Solving large-scale nonnegative least-squares

16th Conference of the International Linear Algebra Society (ILAS 2010), 16, pages: 19, June 2010, based on Joint work with Dongmin Kim and Inderjit Dhillon (poster)

Abstract

We study the fundamental problem of nonnegative least squares. This problem was apparently introduced by Lawson and Hanson [1] under the name NNLS. As is evident from its name, NNLS seeks least-squares solutions that are also nonnegative. Owing to its wide-applicability numerous algorithms have been derived for NNLS, beginning from the active-set approach of Lawson and Hanson [1] leading up to the sophisticated interior-point method of Bellavia et al. [2]. We present a new algorithm for NNLS that combines projected subgradients with the non-monotonic gradient descent idea of Barzilai and Borwein [3]. Our resulting algorithm is called BBSG, and we guarantee its convergence by exploiting properties of NNLS in conjunction with projected subgradients. BBSG is surprisingly simple and scales well to large problems. We substantiate our claims by empirically evaluating BBSG and comparing it with established convex solvers and specialized NNLS algorithms. The numerical results suggest that BBSG is a practical method for solving large-scale NNLS problems.

PDF Web [BibTex]

Sra, S. Solving large-scale nonnegative least-squares 16th Conference of the International Linear Algebra Society (ILAS 2010), 16, pages: 19, June 2010, based on Joint work with Dongmin Kim and Inderjit Dhillon (poster)

PDF Web [BibTex]

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Simultaneous PET/MRI for the evaluation of hemato-oncological diseases with lower extremity manifestations

Sauter, A., Horger, M., Boss, A., Kolb, A., Mantlik, F., Kanz, L., Pfannenberg, C., Stegger, L., Claussen, C., Pichler, B.

Journal of Nuclear Medicine, 51(Supplement 2):1001 , June 2010 (poster)

Abstract

Objectives: The study purpose is the evaluation of patients, suffering from hemato-oncological disease with complications at the lower extremities, using simultaneous PET/MRI. Methods: Until now two patients (chronic active graft-versus-host-disease [GvHD], B-non Hodgkin lymphoma [B-NHL]) before and after therapy were examined in a 3-Tesla-BrainPET/MRI hybrid system following F-18-FDG-PET/CT. Simultaneous static PET (1200 sec.) and MRI scans (T1WI, T2WI, post-CA) were acquired. Results: Initial results show the feasibility of using hybrid PET/MRI-technology for musculoskeletal imaging of the lower extremities. Simultaneous PET and MRI could be acquired in diagnostic quality. Before treatment our patient with GvHD had a high fascia and muscle FDG uptake, possibly due to muscle encasement. T2WI and post gadolinium T1WI revealed a fascial thickening and signs of inflammation. After therapy with steroids followed by imatinib the patients symptoms improved while, the muscular FDG uptake droped whereas the MRI signal remained unchanged. We assume that fascial elasticity improved during therapy despite persistance of fascial thickening. The examination of the second patient with B-NHL manifestation in the tibia showed a significant signal and uptake decrease in the bone marrow and surrounding lesions in both, MRI and PET after therapy with rituximab. The lack of residual FDG-uptake proved superior to MRI information alone helping for exclusion of vital tumor. Conclusions: Combined PET/MRI is a powerful tool to monitor diseases requiring high soft tissue contrast along with molecular information from the FDG uptake.

Sauter, A., Horger, M., Boss, A., Kolb, A., Mantlik, F., Kanz, L., Pfannenberg, C., Stegger, L., Claussen, C., Pichler, B. Simultaneous PET/MRI for the evaluation of hemato-oncological diseases with lower extremity manifestations Journal of Nuclear Medicine, 51(Supplement 2):1001 , June 2010 (poster)

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Gaussian Mixture Modeling with Gaussian Process Latent Variable Models

Nickisch, H., Rasmussen, C.

Max Planck Institute for Biological Cybernetics, June 2010 (techreport)

Abstract

Density modeling is notoriously difficult for high dimensional data. One approach to the problem is to search for a lower dimensional manifold which captures the main characteristics of the data. Recently, the Gaussian Process Latent Variable Model (GPLVM) has successfully been used to find low dimensional manifolds in a variety of complex data. The GPLVM consists of a set of points in a low dimensional latent space, and a stochastic map to the observed space. We show how it can be interpreted as a density model in the observed space. However, the GPLVM is not trained as a density model and therefore yields bad density estimates. We propose a new training strategy and obtain improved generalisation performance and better density estimates in comparative evaluations on several benchmark data sets.

Nickisch, H., Rasmussen, C. Gaussian Mixture Modeling with Gaussian Process Latent Variable Models Max Planck Institute for Biological Cybernetics, June 2010 (techreport)

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Generalized Proximity and Projection with Norms and Mixed-norms

(192), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, May 2010 (techreport)

Abstract

We discuss generalized proximity operators (GPO) and their associated generalized projection problems. On inputs of size n, we show how to efficiently apply GPOs and generalized projections for separable norms and distance-like functions to accuracy e in O(n log(1/e)) time. We also derive projection algorithms that run theoretically in O(n log n log(1/e)) time but can for suitable parameter ranges empirically outperform the O(n log(1/e)) projection method. The proximity and projection tasks are either separable, and solved directly, or are reduced to a single root-finding step. We highlight that as a byproduct, our analysis also yields an O(n log(1/e)) (weakly linear-time) procedure for Euclidean projections onto the l1;1-norm ball; previously only an O(n log n) method was known. We provide empirical evaluation to illustrate the performance of our methods, noting that for the l1;1-norm projection, our implementation is more than two orders of magnitude faster than the previously known method.

Sra, S. Generalized Proximity and Projection with Norms and Mixed-norms (192), Max Planck Institute for Biological Cybernetics, Tübingen, Germany, May 2010 (techreport)

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Solving large-scale nonnegative least squares using an adaptive non-monotonic method

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

24th European Conference on Operational Research (EURO 2010), 24, pages: 223, April 2010 (poster)

Abstract

We present an efficient algorithm for large-scale non-negative least-squares (NNLS). We solve NNLS by extending the unconstrained quadratic optimization method of Barzilai and Borwein (BB) to handle nonnegativity constraints. Our approach is simple yet efficient. It differs from other constrained BB variants as: (i) it uses a specific subset of variables for computing BB steps; and (ii) it scales these steps adaptively to ensure convergence. We compare our method with both established convex solvers and specialized NNLS methods, and observe highly competitive empirical performance.

Sra, S., Kim, D., Dhillon, I. Solving large-scale nonnegative least squares using an adaptive non-monotonic method 24th European Conference on Operational Research (EURO 2010), 24, pages: 223, April 2010 (poster)

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Sparse regression via a trust-region proximal method

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

24th European Conference on Operational Research (EURO 2010), 24, pages: 278, April 2010 (poster)

Abstract

We present a method for sparse regression problems. Our method is based on the nonsmooth trust-region framework that minimizes a sum of smooth convex functions and a nonsmooth convex regularizer. By employing a separable quadratic approximation to the smooth part, the method enables the use of proximity operators, which in turn allow tackling the nonsmooth part efficiently. We illustrate our method by implementing it for three important sparse regression problems. In experiments with synthetic and real-world large-scale data, our method is seen to be competitive, robust, and scalable.

Kim, D., Sra, S., Dhillon, I. Sparse regression via a trust-region proximal method 24th European Conference on Operational Research (EURO 2010), 24, pages: 278, April 2010 (poster)

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Cooperative Cuts: Graph Cuts with Submodular Edge Weights

Jegelka, S., Bilmes, J.

(189), Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, March 2010 (techreport)

Abstract

We introduce a problem we call Cooperative cut, where the goal is to find a minimum-cost graph cut but where a submodular function is used to define the cost of a subsets of edges. That means, the cost of an edge that is added to the current cut set C depends on the edges in C. This generalization of the cost in the standard min-cut problem to a submodular cost function immediately makes the problem harder. Not only do we prove NP hardness even for nonnegative submodular costs, but also show a lower bound of Omega(|V|^(1/3)) on the approximation factor for the problem. On the positive side, we propose and compare four approximation algorithms with an overall approximation factor of min { |V|/2, |C*|, O( sqrt(|E|) log |V|), |P_max|}, where C* is the optimal solution, and P_max is the longest s, t path across the cut between given s, t. We also introduce additional heuristics for the problem which have attractive properties from the perspective of practical applications and implementations in that existing fast min-cut libraries may be used as subroutines. Both our approximation algorithms, and our heuristics, appear to do well in practice.

Jegelka, S., Bilmes, J. Cooperative Cuts: Graph Cuts with Submodular Edge Weights (189), Max Planck Institute for Biological Cybernetics, Tuebingen, Germany, March 2010 (techreport)

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Quantitative Evaluation of MR-based Attenuation Correction for Positron Emission Tomography (PET)

Biologische Kybernetik, Universität Mannheim, Germany, March 2010 (diplomathesis)

Mantlik, F. Quantitative Evaluation of MR-based Attenuation Correction for Positron Emission Tomography (PET) Biologische Kybernetik, Universität Mannheim, Germany, March 2010 (diplomathesis)

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PAC-Bayesian Bounds for Discrete Density Estimation and Co-clustering Analysis

Seldin, Y., Tishby, N.

Workshop "Foundations and New Trends of PAC Bayesian Learning", 2010, March 2010 (poster)

Abstract

We applied PAC-Bayesian framework to derive gen- eralization bounds for co-clustering1. The analysis yielded regularization terms that were absent in the preceding formulations of this task. The bounds sug- gested that co-clustering should optimize a trade-off between its empirical performance and the mutual in- formation that the cluster variables preserve on row and column indices. Proper regularization enabled us to achieve state-of-the-art results in prediction of the missing ratings in the MovieLens collaborative filtering dataset. In addition a PAC-Bayesian bound for discrete den- sity estimation was derived. We have shown that the PAC-Bayesian bound for classification is a spe- cial case of the PAC-Bayesian bound for discrete den- sity estimation. We further introduced combinatorial priors to PAC-Bayesian analysis. The combinatorial priors are more appropriate for discrete domains, as opposed to Gaussian priors, the latter of which are suitable for continuous domains. It was shown that combinatorial priors lead to regularization terms in the form of mutual information.

PDF Web [BibTex]

Seldin, Y., Tishby, N. PAC-Bayesian Bounds for Discrete Density Estimation and Co-clustering Analysis Workshop "Foundations and New Trends of PAC Bayesian Learning", 2010, March 2010 (poster)

PDF Web [BibTex]

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Finding Gene-Gene Interactions using Support Vector Machines

Rakitsch, B.

Eberhard Karls Universität Tübingen, Germany, 2010 (diplomathesis)

Rakitsch, B. Finding Gene-Gene Interactions using Support Vector Machines Eberhard Karls Universität Tübingen, Germany, 2010 (diplomathesis)

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Accurate Prediction of Protein-Coding Genes with Discriminative Learning Techniques

Technische Universität Berlin, Germany, 2010 (phdthesis)

Schweikert, G. Accurate Prediction of Protein-Coding Genes with Discriminative Learning Techniques Technische Universität Berlin, Germany, 2010 (phdthesis)

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Quantitative Positron Emission Tomography with a Combined PET/MR System

University of Oxford, UK, 2010 (phdthesis)

Hofmann, M. Quantitative Positron Emission Tomography with a Combined PET/MR System University of Oxford, UK, 2010 (phdthesis)

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Structural and Relational Data Mining for Systems Biology Applications

Eberhard Karls Universität Tübingen, Germany , 2010 (phdthesis)

Georgii, E. Structural and Relational Data Mining for Systems Biology Applications Eberhard Karls Universität Tübingen, Germany , 2010 (phdthesis)

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Learning the Reward Model of Dialogue POMDPs

Boularias, A., Chinaei, H., Chaib-Draa, B.

NIPS Workshop on Machine Learning for Assistive Technology (MLAT-2010), 2010 (poster)

Boularias, A., Chinaei, H., Chaib-Draa, B. Learning the Reward Model of Dialogue POMDPs NIPS Workshop on Machine Learning for Assistive Technology (MLAT-2010), 2010 (poster)

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Population Coding in the Visual System: Statistical Methods and Theory

Macke, J.

Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

Macke, J. Population Coding in the Visual System: Statistical Methods and Theory Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

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Bayesian Methods for Neural Data Analysis

Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

Gerwinn, S. Bayesian Methods for Neural Data Analysis Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

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Clustering with Neighborhood Graphs

Universität des Saarlandes, Saarbrücken, Germany, 2010 (phdthesis)

Maier, M. Clustering with Neighborhood Graphs Universität des Saarlandes, Saarbrücken, Germany, 2010 (phdthesis)

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Information-theoretic inference of common ancestors

Steudel, B., Ay, N.

Computing Research Repository (CoRR), abs/1010.5720, pages: 18, 2010 (techreport)

Steudel, B., Ay, N. Information-theoretic inference of common ancestors Computing Research Repository (CoRR), abs/1010.5720, pages: 18, 2010 (techreport)

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Erste Erfahrungen bei der Beurteilung hämato-onkologischer Krankheitsmanifestationen an den Extremitäten mit einem PET/MRT-Hybridsystem.

Sauter, A., Boss, A., Kolb, A., Mantlik, F., Bethge, W., Kanz, L., Pfannenberg, C., Stegger, L., Pichler, B., Claussen, C., Horger, M.

Thieme Verlag, Stuttgart, Germany, 91. Deutscher R{\"o}ntgenkongress, 2010 (poster)

Web DOI [BibTex]

Sauter, A., Boss, A., Kolb, A., Mantlik, F., Bethge, W., Kanz, L., Pfannenberg, C., Stegger, L., Pichler, B., Claussen, C., Horger, M. Erste Erfahrungen bei der Beurteilung hämato-onkologischer Krankheitsmanifestationen an den Extremitäten mit einem PET/MRT-Hybridsystem. Thieme Verlag, Stuttgart, Germany, 91. Deutscher R{\"o}ntgenkongress, 2010 (poster)

Web DOI [BibTex]

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Detecting and modeling time shifts in microarray time series data applying Gaussian processes

Zwießele, M.

Eberhard Karls Universität Tübingen, Germany, 2010 (thesis)

Zwießele, M. Detecting and modeling time shifts in microarray time series data applying Gaussian processes Eberhard Karls Universität Tübingen, Germany, 2010 (thesis)

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Detecting the mincut in sparse random graphs

Eberhard Karls Universität Tübingen, Germany, 2010 (diplomathesis)

Köhler, R. Detecting the mincut in sparse random graphs Eberhard Karls Universität Tübingen, Germany, 2010 (diplomathesis)

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A wider view on encoding and decoding in the visual brain-computer interface speller system

Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

Martens, S. A wider view on encoding and decoding in the visual brain-computer interface speller system Eberhard Karls Universität Tübingen, Germany, 2010 (phdthesis)

2009

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Learning an Interactive Segmentation System

Nickisch, H., Kohli, P., Rother, C.

Max Planck Institute for Biological Cybernetics, December 2009 (techreport)

Abstract

Many successful applications of computer vision to image or video manipulation are interactive by nature. However, parameters of such systems are often trained neglecting the user. Traditionally, interactive systems have been treated in the same manner as their fully automatic counterparts. Their performance is evaluated by computing the accuracy of their solutions under some fixed set of user interactions. This paper proposes a new evaluation and learning method which brings the user in the loop. It is based on the use of an active robot user - a simulated model of a human user. We show how this approach can be used to evaluate and learn parameters of state-of-the-art interactive segmentation systems. We also show how simulated user models can be integrated into the popular max-margin method for parameter learning and propose an algorithm to solve the resulting optimisation problem.

2009

Nickisch, H., Kohli, P., Rother, C. Learning an Interactive Segmentation System Max Planck Institute for Biological Cybernetics, December 2009 (techreport)

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Learning Probabilistic Models via Bayesian Inverse Planning

Boularias, A., Chaib-Draa, B.

NIPS Workshop on Probabilistic Approaches for Robotics and Control, December 2009 (poster)

PDF Web [BibTex]

Boularias, A., Chaib-Draa, B. Learning Probabilistic Models via Bayesian Inverse Planning NIPS Workshop on Probabilistic Approaches for Robotics and Control, December 2009 (poster)

PDF Web [BibTex]

Our goal is to understand the principles of Perception, Action and Learning in autonomous systems that successfully interact with complex environments and to use this understanding to design future systems

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