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2015


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easyGWAS: An Integrated Computational Framework for Advanced Genome-Wide Association Studies

Grimm, Dominik

Eberhard Karls Universität Tübingen, November 2015 (phdthesis)

[BibTex]

2015

[BibTex]


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Causal Discovery Beyond Conditional Independences

Sgouritsa, E.

Eberhard Karls Universität Tübingen, Germany, October 2015 (phdthesis)

link (url) [BibTex]

link (url) [BibTex]


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Causal Inference for Empirical Time Series Based on the Postulate of Independence of Cause and Mechanism

Besserve, M.

53rd Annual Allerton Conference on Communication, Control, and Computing, September 2015 (talk)

[BibTex]

[BibTex]


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From Points to Probability Measures: A Statistical Learning on Distributions with Kernel Mean Embedding

Muandet, K.

University of Tübingen, Germany, University of Tübingen, Germany, September 2015 (phdthesis)

[BibTex]

[BibTex]


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Machine Learning Approaches to Image Deconvolution

Schuler, C.

University of Tübingen, Germany, University of Tübingen, Germany, September 2015 (phdthesis)

[BibTex]

[BibTex]


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Kernel methods in medical imaging

Charpiat, G., Hofmann, M., Schölkopf, B.

In Handbook of Biomedical Imaging, pages: 63-81, 4, (Editors: Paragios, N., Duncan, J. and Ayache, N.), Springer, Berlin, Germany, June 2015 (inbook)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Blind Retrospective Motion Correction of MR Images

Loktyushin, A.

University of Tübingen, Germany, May 2015 (phdthesis)

[BibTex]

[BibTex]


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Independence of cause and mechanism in brain networks

Besserve, M.

DALI workshop on Networks: Processes and Causality, April 2015 (talk)

[BibTex]

[BibTex]


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Information-Theoretic Implications of Classical and Quantum Causal Structures

Chaves, R., Majenz, C., Luft, L., Maciel, T., Janzing, D., Schölkopf, B., Gross, D.

18th Conference on Quantum Information Processing (QIP), 2015 (talk)

Web link (url) [BibTex]

Web link (url) [BibTex]


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Assessment of brain tissue damage in the Sub-Acute Stroke Region by Multiparametric Imaging using [89-Zr]-Desferal-EPO-PET/MRI

Castaneda, S. G., Katiyar, P., Russo, F., Disselhorst, J. A., Calaminus, C., Poli, S., Maurer, A., Ziemann, U., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

[BibTex]

[BibTex]


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Statistical and Machine Learning Methods for Neuroimaging: Examples, Challenges, and Extensions to Diffusion Imaging Data

O’Donnell, L. J., Schultz, T.

In Visualization and Processing of Higher Order Descriptors for Multi-Valued Data, pages: 299-319, (Editors: Hotz, I. and Schultz, T.), Springer, 2015 (inbook)

[BibTex]

[BibTex]


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A Cognitive Brain-Computer Interface for Patients with Amyotrophic Lateral Sclerosis

Hohmann, M.

Graduate Training Centre of Neuroscience, University of Tübingen, Germany, 2015 (mastersthesis)

[BibTex]

[BibTex]


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Early time point in vivo PET/MR is a promising biomarker for determining efficacy of a novel Db(\alphaEGFR)-scTRAIL fusion protein therapy in a colon cancer model

Divine, M. R., Harant, M., Katiyar, P., Disselhorst, J. A., Bukala, D., Aidone, S., Siegemund, M., Pfizenmaier, K., Kontermann, R., Pichler, B. J.

World Molecular Imaging Conference, 2015 (talk)

[BibTex]

[BibTex]


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Cosmology from Cosmic Shear with DES Science Verification Data

Abbott, T., Abdalla, F. B., Allam, S., Amara, A., Annis, J., Armstrong, R., Bacon, D., Banerji, M., Bauer, A. H., Baxter, E., others,

arXiv preprint arXiv:1507.05552, 2015 (techreport)

link (url) [BibTex]

link (url) [BibTex]


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The DES Science Verification Weak Lensing Shear Catalogs

Jarvis, M., Sheldon, E., Zuntz, J., Kacprzak, T., Bridle, S. L., Amara, A., Armstrong, R., Becker, M. R., Bernstein, G. M., Bonnett, C., others,

arXiv preprint arXiv:1507.05603, 2015 (techreport)

link (url) [BibTex]

link (url) [BibTex]


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Sequential Image Deconvolution Using Probabilistic Linear Algebra

Gao, M.

Technical University of Munich, Germany, 2015 (mastersthesis)

[BibTex]

[BibTex]


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Causal Inference in Neuroimaging

Casarsa de Azevedo, L.

Graduate Training Centre of Neuroscience, University of Tübingen, Germany, 2015 (mastersthesis)

[BibTex]

[BibTex]


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The effect of frowning on attention

Ibarra Chaoul, A.

Graduate Training Centre of Neuroscience, University of Tübingen, Germany, 2015 (mastersthesis)

[BibTex]

[BibTex]


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Justifying Information-Geometric Causal Inference

Janzing, D., Steudel, B., Shajarisales, N., Schölkopf, B.

In Measures of Complexity: Festschrift for Alexey Chervonenkis, pages: 253-265, 18, (Editors: Vovk, V., Papadopoulos, H. and Gammerman, A.), Springer, 2015 (inbook)

DOI [BibTex]

DOI [BibTex]


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The search for single exoplanet transits in the Kepler light curves

Foreman-Mackey, D., Hogg, D. W., Schölkopf, B.

IAU General Assembly, 22, pages: 2258352, 2015 (talk)

link (url) [BibTex]

link (url) [BibTex]

2013


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Camera-specific Image Denoising

Schober, M.

Eberhard Karls Universität Tübingen, Germany, October 2013 (diplomathesis)

PDF [BibTex]

2013

PDF [BibTex]


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Studying large-scale brain networks: electrical stimulation and neural-event-triggered fMRI

Logothetis, N., Eschenko, O., Murayama, Y., Augath, M., Steudel, T., Evrard, H., Besserve, M., Oeltermann, A.

Twenty-Second Annual Computational Neuroscience Meeting (CNS*2013), July 2013, journal = {BMC Neuroscience}, year = {2013}, month = {7}, volume = {14}, number = {Supplement 1}, pages = {A1}, (talk)

Web [BibTex]

Web [BibTex]


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A Review of Performance Variations in SMR-Based Brain–Computer Interfaces (BCIs)

Grosse-Wentrup, M., Schölkopf, B.

In Brain-Computer Interface Research, pages: 39-51, 4, SpringerBriefs in Electrical and Computer Engineering, (Editors: Guger, C., Allison, B. Z. and Edlinger, G.), Springer, 2013 (inbook)

PDF DOI [BibTex]

PDF DOI [BibTex]


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Semi-supervised learning in causal and anticausal settings

Schölkopf, B., Janzing, D., Peters, J., Sgouritsa, E., Zhang, K., Mooij, J.

In Empirical Inference, pages: 129-141, 13, Festschrift in Honor of Vladimir Vapnik, (Editors: Schölkopf, B., Luo, Z. and Vovk, V.), Springer, 2013 (inbook)

DOI [BibTex]

DOI [BibTex]


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Tractable large-scale optimization in machine learning

Sra, S.

In Tractability: Practical Approaches to Hard Problems, pages: 202-230, 7, (Editors: Bordeaux, L., Hamadi , Y., Kohli, P. and Mateescu, R. ), Cambridge University Press , 2013 (inbook)

[BibTex]

[BibTex]


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Modelling and Learning Approaches to Image Denoising

Burger, HC.

Eberhard Karls Universität Tübingen, Germany, 2013 (phdthesis)

[BibTex]

[BibTex]


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Animating Samples from Gaussian Distributions

Hennig, P.

(8), Max Planck Institute for Intelligent Systems, Tübingen, Germany, 2013 (techreport)

PDF [BibTex]

PDF [BibTex]


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Domain Generalization via Invariant Feature Representation

Muandet, K.

30th International Conference on Machine Learning (ICML2013), 2013 (talk)

PDF [BibTex]

PDF [BibTex]


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Linear mixed models for genome-wide association studies

Lippert, C.

University of Tübingen, Germany, 2013 (phdthesis)

[BibTex]

[BibTex]


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Maximizing Kepler science return per telemetered pixel: Detailed models of the focal plane in the two-wheel era

Hogg, D. W., Angus, R., Barclay, T., Dawson, R., Fergus, R., Foreman-Mackey, D., Harmeling, S., Hirsch, M., Lang, D., Montet, B. T., Schiminovich, D., Schölkopf, B.

arXiv:1309.0653, 2013 (techreport)

link (url) [BibTex]

link (url) [BibTex]


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Maximizing Kepler science return per telemetered pixel: Searching the habitable zones of the brightest stars

Montet, B. T., Angus, R., Barclay, T., Dawson, R., Fergus, R., Foreman-Mackey, D., Harmeling, S., Hirsch, M., Hogg, D. W., Lang, D., Schiminovich, D., Schölkopf, B.

arXiv:1309.0654, 2013 (techreport)

link (url) [BibTex]

link (url) [BibTex]


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On the Relations and Differences between Popper Dimension, Exclusion Dimension and VC-Dimension

Seldin, Y., Schölkopf, B.

In Empirical Inference - Festschrift in Honor of Vladimir N. Vapnik, pages: 53-57, 6, (Editors: Schölkopf, B., Luo, Z. and Vovk, V.), Springer, 2013 (inbook)

[BibTex]

[BibTex]


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Modeling and Learning Complex Motor Tasks: A case study on Robot Table Tennis

Mülling, K.

Technical University Darmstadt, Germany, 2013 (phdthesis)

[BibTex]

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.

PDF [BibTex]

2010

PDF [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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Markerless tracking of Dynamic 3D Scans of Faces

Walder, C., Breidt, M., Bülthoff, H., Schölkopf, B., Curio, C.

In Dynamic Faces: Insights from Experiments and Computation, pages: 255-276, (Editors: Curio, C., Bülthoff, H. H. and Giese, M. A.), MIT Press, Cambridge, MA, USA, December 2010 (inbook)

Web [BibTex]

Web [BibTex]


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Policy Gradient Methods

Peters, J., Bagnell, J.

In Encyclopedia of Machine Learning, pages: 774-776, (Editors: Sammut, C. and Webb, G. I.), Springer, Berlin, Germany, December 2010 (inbook)

PDF Web DOI [BibTex]

PDF Web DOI [BibTex]


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Approximate Inference in Graphical Models

Hennig, P.

University of Cambridge, November 2010 (phdthesis)

Web [BibTex]

Web [BibTex]


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Comparative Quantitative Evaluation of MR-Based Attenuation Correction Methods in Combined Brain PET/MR

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

2010(M08-4), 2010 Nuclear Science Symposium and Medical Imaging Conference (NSS-MIC), November 2010 (talk)

Abstract
Combined PET/MR provides at the same time molecular and functional imaging as well as excellent soft tissue contrast. It does not allow one to directly measure the attenuation properties of scanned tissues, despite the fact that accurate attenuation maps are necessary for quantitative PET imaging. Several methods have therefore been proposed for MR-based attenuation correction (MR-AC). So far, they have only been evaluated on data acquired from separate MR and PET scanners. We evaluated several MR-AC methods on data from 10 patients acquired on a combined BrainPET/MR scanner. This allowed the consideration of specific PET/MR issues, such as the RF coil that attenuates and scatters 511 keV gammas. We evaluated simple MR thresholding methods as well as atlas and machine learning-based MR-AC. CT-based AC served as gold standard reference. To comprehensively evaluate the MR-AC accuracy, we used RoIs from 2 anatomic brain atlases with different levels of detail. Visual inspection of the PET images indicated that even the basic FLASH threshold MR-AC may be sufficient for several applications. Using a UTE sequence for bone prediction in MR-based thresholding occasionally led to false prediction of bone tissue inside the brain, causing a significant overestimation of PET activity. Although it yielded a lower mean underestimation of activity, it exhibited the highest variance of all methods. The atlas averaging approach had a smaller mean error, but showed high maximum overestimation on the RoIs of the more detailed atlas. The Nave Bayes and Atlas-Patch MR-AC yielded the smallest variance, and the Atlas-Patch also showed the smallest mean error. In conclusion, Atlas-based AC using only MR information on the BrainPET/MR yields a high level of accuracy that is sufficient for clinical quantitative imaging requirements. The Atlas-Patch approach was superior to alternative atlas-based methods, yielding a quantification error below 10% for all RoIs except very small ones.

[BibTex]

[BibTex]


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Bayesian Inference and Experimental Design for Large Generalised Linear Models

Nickisch, H.

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

PDF Web [BibTex]

PDF Web [BibTex]


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A PAC-Bayesian Analysis of Graph Clustering and Pairwise Clustering

Seldin, Y.

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.

PDF Web [BibTex]

PDF Web [BibTex]


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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.

PDF [BibTex]

PDF [BibTex]


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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.

PDF [BibTex]

PDF [BibTex]


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Statistical image analysis and percolation theory

Davies, P., Langovoy, M., Wittich, O.

73rd Annual Meeting of the Institute of Mathematical Statistics (IMS), August 2010 (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 objects of unknown shapes in the case of nonparametric noise. The noise density is unknown and can be heavy-tailed. We view the object detection problem as hypothesis testing for discrete statistical inverse problems. We present an algorithm that allows to detect objects of various shapes in noisy images. We prove results on consistency and algorithmic complexity of our procedures.

Web [BibTex]

Web [BibTex]


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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.

Web [BibTex]


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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.

Web [BibTex]

Web [BibTex]


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Inferring High-Dimensional Causal Relations using Free Probability Theory

Zscheischler, J.

Humboldt Universität Berlin, Germany, August 2010 (diplomathesis)

PDF [BibTex]

PDF [BibTex]