Header logo is


2017


no image
Improving performance of linear field generation with multi-coil setup by optimizing coils position

Aghaeifar, A., Loktyushin, A., Eschelbach, M., Scheffler, K.

Magnetic Resonance Materials in Physics, Biology and Medicine, 30(Supplement 1):S259, 34th Annual Scientific Meeting of the European Society for Magnetic Resonance in Medicine and Biology (ESMRMB), October 2017 (poster)

ei

link (url) DOI [BibTex]

2017


link (url) DOI [BibTex]


Human Shape Estimation using Statistical Body Models
Human Shape Estimation using Statistical Body Models

Loper, M. M.

University of Tübingen, May 2017 (thesis)

Abstract
Human body estimation methods transform real-world observations into predictions about human body state. These estimation methods benefit a variety of health, entertainment, clothing, and ergonomics applications. State may include pose, overall body shape, and appearance. Body state estimation is underconstrained by observations; ambiguity presents itself both in the form of missing data within observations, and also in the form of unknown correspondences between observations. We address this challenge with the use of a statistical body model: a data-driven virtual human. This helps resolve ambiguity in two ways. First, it fills in missing data, meaning that incomplete observations still result in complete shape estimates. Second, the model provides a statistically-motivated penalty for unlikely states, which enables more plausible body shape estimates. Body state inference requires more than a body model; we therefore build obser- vation models whose output is compared with real observations. In this thesis, body state is estimated from three types of observations: 3D motion capture markers, depth and color images, and high-resolution 3D scans. In each case, a forward process is proposed which simulates observations. By comparing observations to the results of the forward process, state can be adjusted to minimize the difference between simulated and observed data. We use gradient-based methods because they are critical to the precise estimation of state with a large number of parameters. The contributions of this work include three parts. First, we propose a method for the estimation of body shape, nonrigid deformation, and pose from 3D markers. Second, we present a concise approach to differentiating through the rendering process, with application to body shape estimation. And finally, we present a statistical body model trained from human body scans, with state-of-the-art fidelity, good runtime performance, and compatibility with existing animation packages.

ps

Official Version [BibTex]


no image
Estimating B0 inhomogeneities with projection FID navigator readouts

Loktyushin, A., Ehses, P., Schölkopf, B., Scheffler, K.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


no image
Image Quality Improvement by Applying Retrospective Motion Correction on Quantitative Susceptibility Mapping and R2*

Feng, X., Loktyushin, A., Deistung, A., Reichenbach, J.

25th Annual Meeting and Exhibition of the International Society for Magnetic Resonance in Medicine (ISMRM), April 2017 (poster)

ei

link (url) [BibTex]

link (url) [BibTex]


Learning Inference Models for Computer Vision
Learning Inference Models for Computer Vision

Jampani, V.

MPI for Intelligent Systems and University of Tübingen, 2017 (phdthesis)

Abstract
Computer vision can be understood as the ability to perform 'inference' on image data. Breakthroughs in computer vision technology are often marked by advances in inference techniques, as even the model design is often dictated by the complexity of inference in them. This thesis proposes learning based inference schemes and demonstrates applications in computer vision. We propose techniques for inference in both generative and discriminative computer vision models. Despite their intuitive appeal, the use of generative models in vision is hampered by the difficulty of posterior inference, which is often too complex or too slow to be practical. We propose techniques for improving inference in two widely used techniques: Markov Chain Monte Carlo (MCMC) sampling and message-passing inference. Our inference strategy is to learn separate discriminative models that assist Bayesian inference in a generative model. Experiments on a range of generative vision models show that the proposed techniques accelerate the inference process and/or converge to better solutions. A main complication in the design of discriminative models is the inclusion of prior knowledge in a principled way. For better inference in discriminative models, we propose techniques that modify the original model itself, as inference is simple evaluation of the model. We concentrate on convolutional neural network (CNN) models and propose a generalization of standard spatial convolutions, which are the basic building blocks of CNN architectures, to bilateral convolutions. First, we generalize the existing use of bilateral filters and then propose new neural network architectures with learnable bilateral filters, which we call `Bilateral Neural Networks'. We show how the bilateral filtering modules can be used for modifying existing CNN architectures for better image segmentation and propose a neural network approach for temporal information propagation in videos. Experiments demonstrate the potential of the proposed bilateral networks on a wide range of vision tasks and datasets. In summary, we propose learning based techniques for better inference in several computer vision models ranging from inverse graphics to freely parameterized neural networks. In generative vision models, our inference techniques alleviate some of the crucial hurdles in Bayesian posterior inference, paving new ways for the use of model based machine learning in vision. In discriminative CNN models, the proposed filter generalizations aid in the design of new neural network architectures that can handle sparse high-dimensional data as well as provide a way for incorporating prior knowledge into CNNs.

ps

pdf [BibTex]

pdf [BibTex]


no image
Development and Evaluation of a Portable BCI System for Remote Data Acquisition

Emde, T.

Graduate School of Neural Information Processing, Eberhard Karls Universität Tübingen, Germany, 2017 (mastersthesis)

ei

[BibTex]

[BibTex]


no image
Brain-Computer Interfaces for patients with Amyotrophic Lateral Sclerosis

Fomina, T.

Eberhard Karls Universität Tübingen, Germany, 2017 (phdthesis)

ei

[BibTex]

[BibTex]


no image
Generalized phase locking analysis of electrophysiology data

Safavi, S., Panagiotaropoulos, T., Kapoor, V., Logothetis, N. K., Besserve, M.

ESI Systems Neuroscience Conference (ESI-SyNC 2017): Principles of Structural and Functional Connectivity, 2017 (poster)

ei

[BibTex]

[BibTex]


no image
Causal models for decision making via integrative inference

Geiger, P.

University of Stuttgart, Germany, 2017 (phdthesis)

ei

[BibTex]

[BibTex]


Capturing Hand-Object Interaction and Reconstruction of Manipulated Objects
Capturing Hand-Object Interaction and Reconstruction of Manipulated Objects

Tzionas, D.

University of Bonn, 2017 (phdthesis)

Abstract
Hand motion capture with an RGB-D sensor gained recently a lot of research attention, however, even most recent approaches focus on the case of a single isolated hand. We focus instead on hands that interact with other hands or with a rigid or articulated object. Our framework successfully captures motion in such scenarios by combining a generative model with discriminatively trained salient points, collision detection and physics simulation to achieve a low tracking error with physically plausible poses. All components are unified in a single objective function that can be optimized with standard optimization techniques. We initially assume a-priori knowledge of the object's shape and skeleton. In case of unknown object shape there are existing 3d reconstruction methods that capitalize on distinctive geometric or texture features. These methods though fail for textureless and highly symmetric objects like household articles, mechanical parts or toys. We show that extracting 3d hand motion for in-hand scanning effectively facilitates the reconstruction of such objects and we fuse the rich additional information of hands into a 3d reconstruction pipeline. Finally, although shape reconstruction is enough for rigid objects, there is a lack of tools that build rigged models of articulated objects that deform realistically using RGB-D data. We propose a method that creates a fully rigged model consisting of a watertight mesh, embedded skeleton and skinning weights by employing a combination of deformable mesh tracking, motion segmentation based on spectral clustering and skeletonization based on mean curvature flow.

ps

Thesis link (url) Project Page [BibTex]


Evaluation of the passive dynamics of compliant legs with inertia
Evaluation of the passive dynamics of compliant legs with inertia

Györfi, B.

University of Applied Science Pforzheim, Germany, 2017 (mastersthesis)

dlg

[BibTex]

[BibTex]


no image
Learning Optimal Configurations for Modeling Frowning by Transcranial Electrical Stimulation

Sücker, K.

Graduate School of Neural Information Processing, Eberhard Karls Universität Tübingen, Germany, 2017 (mastersthesis)

ei

[BibTex]

[BibTex]


no image
Understanding FORC using synthetic micro-structured systems with variable coupling- and coercivefield distributions

Groß, Felix

Universität Stuttgart, Stuttgart, 2017 (mastersthesis)

mms

[BibTex]


no image
Adsorption von Wasserstoffmolekülen in nanoporösen Gerüststrukturen

Kotzur, Nadine

Universität Stuttgart, Stuttgart, 2017 (mastersthesis)

mms

[BibTex]

[BibTex]

2014


no image
Pole Balancing with Apollo

Holger Kaden

Eberhard Karls Universität Tübingen, December 2014 (mastersthesis)

am

[BibTex]

2014


[BibTex]


no image
Modeling the polygenic architecture of complex traits

Rakitsch, Barbara

Eberhard Karls Universität Tübingen, November 2014 (phdthesis)

ei

[BibTex]

[BibTex]


no image
Learning Coupling Terms for Obstacle Avoidance

Rai, A.

École polytechnique fédérale de Lausanne, August 2014 (mastersthesis)

am

Project Page [BibTex]

Project Page [BibTex]


no image
Object Tracking in Depth Images Using Sigma Point Kalman Filters

Issac, J.

Karlsruhe Institute of Technology, July 2014 (mastersthesis)

am

Project Page [BibTex]

Project Page [BibTex]


Modeling the Human Body in 3D: Data Registration and Human Shape Representation
Modeling the Human Body in 3D: Data Registration and Human Shape Representation

Tsoli, A.

Brown University, Department of Computer Science, May 2014 (phdthesis)

ps

pdf [BibTex]

pdf [BibTex]


no image
Dynamical source analysis of hippocampal sharp-wave ripple episodes

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

Bernstein Conference, 2014 (poster)

ei

DOI [BibTex]

DOI [BibTex]


no image
A Novel Causal Inference Method for Time Series

Shajarisales, N.

Eberhard Karls Universität Tübingen, Germany, Eberhard Karls Universität Tübingen, Germany, 2014 (mastersthesis)

ei

PDF [BibTex]

PDF [BibTex]


no image
FID-guided retrospective motion correction based on autofocusing

Babayeva, M., Loktyushin, A., Kober, T., Granziera, C., Nickisch, H., Gruetter, R., Krueger, G.

Joint Annual Meeting ISMRM-ESMRMB, Milano, Italy, 2014 (poster)

ei

[BibTex]

[BibTex]


no image
Cluster analysis of sharp-wave ripple field potential signatures in the macaque hippocampus

Ramirez-Villegas, J. F., Logothetis, N. K., Besserve, M.

Computational and Systems Neuroscience Meeting (COSYNE), 2014 (poster)

ei

[BibTex]

[BibTex]


no image
A global analysis of extreme events and consequences for the terrestrial carbon cycle

Zscheischler, J.

Diss. No. 22043, ETH Zurich, Switzerland, ETH Zurich, Switzerland, 2014 (phdthesis)

ei

[BibTex]

[BibTex]


no image
Learning objective functions for autonomous motion generation

Kalakrishnan, M.

University of Southern California, University of Southern California, Los Angeles, CA, 2014 (phdthesis)

am

Project Page Project Page [BibTex]

Project Page Project Page [BibTex]


no image
Development of advanced methods for improving astronomical images

Schmeißer, N.

Eberhard Karls Universität Tübingen, Germany, Eberhard Karls Universität Tübingen, Germany, 2014 (diplomathesis)

ei

[BibTex]

[BibTex]


no image
The Feasibility of Causal Discovery in Complex Systems: An Examination of Climate Change Attribution and Detection

Lacosse, E.

Graduate Training Centre of Neuroscience, University of Tübingen, Germany, Graduate Training Centre of Neuroscience, University of Tübingen, Germany, 2014 (mastersthesis)

ei

[BibTex]

[BibTex]


no image
Causal Discovery in the Presence of Time-Dependent Relations or Small Sample Size

Huang, B.

Graduate Training Centre of Neuroscience, University of Tübingen, Germany, Graduate Training Centre of Neuroscience, University of Tübingen, Germany, 2014 (mastersthesis)

ei

[BibTex]

[BibTex]


Deep apprenticeship learning for playing video games
Deep apprenticeship learning for playing video games

Bogdanovic, M.

University of Oxford, 2014 (mastersthesis)

[BibTex]


no image
Analysis of Distance Functions in Graphs

Alamgir, M.

University of Hamburg, Germany, University of Hamburg, Germany, 2014 (phdthesis)

ei

[BibTex]

[BibTex]


no image
Data-driven autonomous manipulation

Pastor, P.

University of Southern California, University of Southern California, Los Angeles, CA, 2014 (phdthesis)

am

Project Page Project Page [BibTex]

Project Page Project Page [BibTex]


no image
Schalten der Polarität magnetischer Vortexkerne durch eine Zwei-Frequenzen Anregung und mittels direkter Einkopplung eines Stroms

Sproll, M.

Universität Stuttgart, Stuttgart (und Cuvillier Verlag, Göttingen), Stuttgart, 2014 (phdthesis)

mms

[BibTex]

[BibTex]


no image
Vortex-Kern-Korrelation in gekoppelten Systemen

Jüllig, P.

Universität Stuttgart, Stuttgart, 2014 (phdthesis)

mms

link (url) [BibTex]

link (url) [BibTex]


no image
Realization of a new Magnetic Scanning X-ray Microscope and Investigation of Landau Structures under Pulsed Field Excitation

Weigand, M.

Universität Stuttgart, Stuttgart (und Cuvillier Verlag, Göttingen), 2014 (phdthesis)

mms

[BibTex]

[BibTex]


no image
Nanoporous Materials for Hydrogen Storage and H2/D2 Isotope Separation

Oh, H.

Universität Stuttgart, Stuttgart, 2014 (phdthesis)

mms

link (url) [BibTex]

link (url) [BibTex]

2010


no image
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)

ei

PDF Web [BibTex]

2010


PDF Web [BibTex]


no image
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.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
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.

ei

Web [BibTex]

Web [BibTex]


no image
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)

ei

[BibTex]

[BibTex]


no image
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)

ei

Web [BibTex]

Web [BibTex]


no image
Probabilistic Assignment of Chemical Shift Data for Semi-Automatic Amino Acid Recognition

Hooge, J.

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.

ei

PDF [BibTex]

PDF [BibTex]


no image
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.

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
Bayesian Inference and Experimental Design for Large Generalised Linear Models

Nickisch, H.

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

ei

PDF Web [BibTex]

PDF Web [BibTex]


no image
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.

ei

Web [BibTex]

Web [BibTex]