Bayesian methods for segmentation of objects from multimodal and complex shape densities using statistical shape priors

In many image segmentation problems involving limited and low-quality data, employing statistical prior information about the shapes of the objects to be segmented can significantly improve the segmentation result. However, defining probability densities in the space of shapes is an open and challenging problem, especially if the object to be segmented comes from a shape density involving multiple modes (classes). In the literature, there are some techniques that exploit nonparametric shape priors to learn multimodal prior densities from a training set. These methods solve the problem of segmenting objects of limited and low-quality to some extent by performing maximum a posteriori (MAP) estimation. However, these methods assume that the boundaries found by using the observed data can provide at least a good initialization for MAP estimation so that convergence to a desired mode of the posterior density is achieved. There are two major problems with this assumption that we focus in this thesis. First, as the data provide less information, these approaches can get stuck at a local optimum which may not be the desired solution. Second, even though a good initialization directs the segmenting curve to a local optimum solution that looks like the desired segmentation, it does not provide a picture of other probable solutions, potentially from different modes of the posterior density, based on the data and the priors. In this thesis, we propose methods for segmentation of objects that come from multimodal posterior densities and suffer from severe noise, occlusion and missing data. The first framework that we propose represents the segmentation problem in terms of the joint posterior density of shapes and features. We incorporate the learned joint shape and feature prior distribution into a maximum a posteri- ori estimation framework for segmentation. In our second proposed framework, we approach the segmentation problem from the approximate Bayesian inference perspective. We propose two different Markov chain Monte Carlo (MCMC) sampling based image segmentation approaches that generates samples from the posterior density. As a final contribution of this thesis, we propose a new shape model that learns binary shape distributions by exploiting local shape priors and the Boltzmann machine. Although the proposed generative shape model has not been used in the context of object segmentation in this thesis, it has great potential to be used for this purpose. The source code of the methods introduced in this thesis will be available in https://github.com/eerdil

Bayesian astrostatistics: a backward look to the future

This perspective chapter briefly surveys: (1) past growth in the use of Bayesian methods in astrophysics; (2) current misconceptions about both frequentist and Bayesian statistical inference that hinder wider adoption of Bayesian methods by astronomers; and (3) multilevel (hierarchical) Bayesian modeling as a major future direction for research in Bayesian astrostatistics, exemplified in part by presentations at the first ISI invited session on astrostatistics, commemorated in this volume. It closes with an intentionally provocative recommendation for astronomical survey data reporting, motivated by the multilevel Bayesian perspective on modeling cosmic populations: that astronomers cease producing catalogs of estimated fluxes and other source properties from surveys. Instead, summaries of likelihood functions (or marginal likelihood functions) for source properties should be reported (not posterior probability density functions), including nontrivial summaries (not simply upper limits) for candidate objects that do not pass traditional detection thresholds.Comment: 27 pp, 4 figures. A lightly revised version of a chapter in "Astrostatistical Challenges for the New Astronomy" (Joseph M. Hilbe, ed., Springer, New York, forthcoming in 2012), the inaugural volume for the Springer Series in Astrostatistics. Version 2 has minor clarifications and an additional referenc

Bayesian inference for structured additive regression models for large-scale problems with applications to medical imaging

In der angewandten Statistik können Regressionsmodelle mit hochdimensionalen Koeffizienten auftreten, die sich nicht mit gewöhnlichen Computersystemen schätzen lassen. Dies betrifft unter anderem die Analyse digitaler Bilder unter Berücksichtigung räumlich-zeitlicher Abhängigkeiten, wie sie innerhalb der medizinisch-biologischen Forschung häufig vorkommen. In der vorliegenden Arbeit wird ein Verfahren formuliert, das in der Lage ist, Regressionsmodelle mit hochdimensionalen Koeffizienten und nicht-normalverteilten Zielgrößen unter moderaten Anforderungen an die benötigte Hardware zu schätzen. Hierzu wird zunächst im Rahmen strukturiert additiver Regressionsmodelle aufgezeigt, worin die Limitationen aktueller Inferenzansätze bei der Anwendung auf hochdimensionale Problemstellungen liegen, sowie Möglichkeiten diskutiert, diese zu umgehen. Darauf basierend wird ein Algorithmus formuliert, dessen Stärken und Schwächen anhand von Simulationsstudien analysiert werden. Darüber hinaus findet das Verfahren Anwendung in drei verschiedenen Bereichen der medizinisch-biologischen Bildgebung und zeigt dadurch, dass es ein vielversprechender Kandidat für die Beantwortung hochdimensionaler Fragestellungen ist.In applied statistics regression models with high-dimensional coefficients can occur which cannot be estimated using ordinary computers. Amongst others, this applies to the analysis of digital images taking spatio-temporal dependencies into account as they commonly occur within bio-medical research. In this thesis a procedure is formulated which allows to fit regression models with high-dimensional coefficients and non-normal response values requiring only moderate computational equipment. To this end, limitations of different inference strategies for structured additive regression models are demonstrated when applied to high-dimensional problems and possible solutions are discussed. Based thereon an algorithm is formulated whose strengths and weaknesses are subsequently analyzed using simulation studies. Furthermore, the procedure is applied to three different fields of bio-medical imaging from which can be concluded that the algorithm is a promising candidate for answering high-dimensional problems

Recent advances in directional statistics

Mainstream statistical methodology is generally applicable to data observed in Euclidean space. There are, however, numerous contexts of considerable scientific interest in which the natural supports for the data under consideration are Riemannian manifolds like the unit circle, torus, sphere and their extensions. Typically, such data can be represented using one or more directions, and directional statistics is the branch of statistics that deals with their analysis. In this paper we provide a review of the many recent developments in the field since the publication of Mardia and Jupp (1999), still the most comprehensive text on directional statistics. Many of those developments have been stimulated by interesting applications in fields as diverse as astronomy, medicine, genetics, neurology, aeronautics, acoustics, image analysis, text mining, environmetrics, and machine learning. We begin by considering developments for the exploratory analysis of directional data before progressing to distributional models, general approaches to inference, hypothesis testing, regression, nonparametric curve estimation, methods for dimension reduction, classification and clustering, and the modelling of time series, spatial and spatio-temporal data. An overview of currently available software for analysing directional data is also provided, and potential future developments discussed.Comment: 61 page

Task adapted reconstruction for inverse problems

The paper considers the problem of performing a task defined on a model parameter that is only observed indirectly through noisy data in an ill-posed inverse problem. A key aspect is to formalize the steps of reconstruction and task as appropriate estimators (non-randomized decision rules) in statistical estimation problems. The implementation makes use of (deep) neural networks to provide a differentiable parametrization of the family of estimators for both steps. These networks are combined and jointly trained against suitable supervised training data in order to minimize a joint differentiable loss function, resulting in an end-to-end task adapted reconstruction method. The suggested framework is generic, yet adaptable, with a plug-and-play structure for adjusting both the inverse problem and the task at hand. More precisely, the data model (forward operator and statistical model of the noise) associated with the inverse problem is exchangeable, e.g., by using neural network architecture given by a learned iterative method. Furthermore, any task that is encodable as a trainable neural network can be used. The approach is demonstrated on joint tomographic image reconstruction, classification and joint tomographic image reconstruction segmentation

Graphical models for visual object recognition and tracking

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 277-301).We develop statistical methods which allow effective visual detection, categorization, and tracking of objects in complex scenes. Such computer vision systems must be robust to wide variations in object appearance, the often small size of training databases, and ambiguities induced by articulated or partially occluded objects. Graphical models provide a powerful framework for encoding the statistical structure of visual scenes, and developing corresponding learning and inference algorithms. In this thesis, we describe several models which integrate graphical representations with nonparametric statistical methods. This approach leads to inference algorithms which tractably recover high-dimensional, continuous object pose variations, and learning procedures which transfer knowledge among related recognition tasks. Motivated by visual tracking problems, we first develop a nonparametric extension of the belief propagation (BP) algorithm. Using Monte Carlo methods, we provide general procedures for recursively updating particle-based approximations of continuous sufficient statistics. Efficient multiscale sampling methods then allow this nonparametric BP algorithm to be flexibly adapted to many different applications.(cont.) As a particular example, we consider a graphical model describing the hand's three-dimensional (3D) structure, kinematics, and dynamics. This graph encodes global hand pose via the 3D position and orientation of several rigid components, and thus exposes local structure in a high-dimensional articulated model. Applying nonparametric BP, we recover a hand tracking algorithm which is robust to outliers and local visual ambiguities. Via a set of latent occupancy masks, we also extend our approach to consistently infer occlusion events in a distributed fashion. In the second half of this thesis, we develop methods for learning hierarchical models of objects, the parts composing them, and the scenes surrounding them. Our approach couples topic models originally developed for text analysis with spatial transformations, and thus consistently accounts for geometric constraints. By building integrated scene models, we may discover contextual relationships, and better exploit partially labeled training images. We first consider images of isolated objects, and show that sharing parts among object categories improves accuracy when learning from few examples.(cont.) Turning to multiple object scenes, we propose nonparametric models which use Dirichlet processes to automatically learn the number of parts underlying each object category, and objects composing each scene. Adapting these transformed Dirichlet processes to images taken with a binocular stereo camera, we learn integrated, 3D models of object geometry and appearance. This leads to a Monte Carlo algorithm which automatically infers 3D scene structure from the predictable geometry of known object categories.by Erik B. Sudderth.Ph.D

Filter-Based Probabilistic Markov Random Field Image Priors: Learning, Evaluation, and Image Analysis

Markov random fields (MRF) based on linear filter responses are one of the most popular forms for modeling image priors due to their rigorous probabilistic interpretations and versatility in various applications. In this dissertation, we propose an application-independent method to quantitatively evaluate MRF image priors using model samples. To this end, we developed an efficient auxiliary-variable Gibbs samplers for a general class of MRFs with flexible potentials. We found that the popular pairwise and high-order MRF priors capture image statistics quite roughly and exhibit poor generative properties. We further developed new learning strategies and obtained high-order MRFs that well capture the statistics of the inbuilt features, thus being real maximum-entropy models, and other important statistical properties of natural images, outlining the capabilities of MRFs. We suggest a multi-modal extension of MRF potentials which not only allows to train more expressive priors, but also helps to reveal more insights of MRF variants, based on which we are able to train compact, fully-convolutional restricted Boltzmann machines (RBM) that can model visual repetitive textures even better than more complex and deep models. The learned high-order MRFs allow us to develop new methods for various real-world image analysis problems. For denoising of natural images and deconvolution of microscopy images, the MRF priors are employed in a pure generative setting. We propose efficient sampling-based methods to infer Bayesian minimum mean squared error (MMSE) estimates, which substantially outperform maximum a-posteriori (MAP) estimates and can compete with state-of-the-art discriminative methods. For non-rigid registration of live cell nuclei in time-lapse microscopy images, we propose a global optical flow-based method. The statistics of noise in fluorescence microscopy images are studied to derive an adaptive weighting scheme for increasing model robustness. High-order MRFs are also employed to train image filters for extracting important features of cell nuclei and the deformation of nuclei are then estimated in the learned feature spaces. The developed method outperforms previous approaches in terms of both registration accuracy and computational efficiency