The R package coin implements a unified approach to permutation tests providing a huge class of independence tests for nominal, ordered, numeric, and censored data as well as multivariate data at mixed scales. Based on a rich and exible conceptual framework that embeds different permutation test procedures into a common theory, a computational framework is established in coin that likewise embeds the corresponding R functionality in a common S4 class structure with associated generic functions. As a consequence, the computational tools in coin inherit the exibility of the underlying theory and conditional inference functions for important special cases can be set up easily. Conditional versions of classical tests|such as tests for location and scale problems in two or more samples, independence in two- or three-way contingency tables, or association problems for censored, ordered categorical or multivariate data|can easily be implemented as special cases using this computational toolbox by choosing appropriate transformations of the observations. The paper gives a detailed exposition of both the internal structure of the package and the provided user interfaces along with examples on how to extend the implemented functionality. (authors' abstract)

The thesis deals with inferences and their function in text understanding. The theoretical part involve a survey of various definitions of inference, a setting of notions which are related to inferences and at last classification of inferences based on linguistic and psychological literature. The empirical part is based on analysis of cook recipes (and technical instruction partially). We have set five means of language which indicate a necessity of making inference (pronouns, ellipsis, hyponyms-hypernyms relation, pronoun vše and adjectivizated participles) - in all cases these inferences are necessary for comprehension. We confronted these inferences with classification described in the theoretical part. Another inferences we make as the text is read are infereces which are not associated with a concrete means of language: bridging inferences and instrumental inferences. Knowledge of the language, general knowledges and experiences take part in inferencing.

Attention allows us to monitor objects or regions of visual space and extract information from them to use for report or storage. Classical theories of attention assumed a single focus of selection but many everyday activities, such as playing video games, suggest otherwise. Nonetheless, the underlying mechanism which can explain the ability to divide attention has not been well established. Numerous attempts have been made in order to clarify divided attention, including analytical strategies as well as methods working with visual phenomena, even more sophisticated predictors incorporating information about past selection decisions. Virtually all the attempts approach this problem by constructing a simplified model of attention. In this study, we develop a version of the existing Bayesian framework to propose such models, and evaluate their ability to generate eye movement trajectories. For the comparison of models, we use the eye movement trajectories generated by several analytical strategies. We measure the similarity between...

Attention allows us to monitor objects or regions of visual space and extract information from them to use for report or storage. Classical theories of attention assumed a single focus of selection but many everyday activities, such as playing video games, suggest otherwise. Nonetheless, the underlying mechanism which can explain the ability to divide attention has not been well established. Numerous attempts have been made in order to clarify divided attention, including analytical strategies as well as methods working with visual phenomena, even more sophisticated predictors incorporating information about past selection decisions. Virtually all the attempts approach this problem by constructing a simplified model of attention. In this study, we develop a version of the existing Bayesian framework to propose such models, and evaluate their ability to generate eye movement trajectories. For the comparison of models, we use the eye movement trajectories generated by several analytical strategies. We measure the...

Residual-based shadings for enhancing mosaic and association plots to visualize independence models for contingency tables are extended in two directions: (a) perceptually uniform HCL colors are used and (b) the result of an associated significance test is coded by the appearance of color in the visualization. For obtaining (a), a general strategy for deriving diverging palettes in the perceptually-based HCL space is suggested. As for (b), cut offs that control the appearance of color are computed in a data-driven way based on the conditional permutation distribution of maximum-type test statistics. The shadings are first established for the case of independence in 2-way tables and then extended to more general independence models for multi-way tables, including in particular conditional independence problems. / Series: Research Report Series / Department of Statistics and Mathematics

The R package coin implements a unified approach to permutation tests providing a huge class of independence tests for nominal, ordered, numeric, and censored data as well as multivariate data at mixed scales. Based on a rich and flexible conceptual framework that embeds different permutation test procedures into a common theory, a computational framework is established in coin that likewise embeds the corresponding R functionality in a common S4 class structure with associated generic functions. As a consequence, the computational tools in coin inherit the flexibility of the underlying theory and conditional inference functions for important special cases can be set up easily. Conditional versions of classical tests - such as tests for location and scale problems in two or more samples, independence in two- or three-way contingency tables, or association problems for censored, ordered categorical or multivariate data - can be easily be implemented as special cases using this computational toolbox by choosing appropriate transformations of the observations. The paper gives a detailed exposition of both the internal structure of the package and the provided user interfaces. / Series: Research Report Series / Department of Statistics and Mathematics

<p>Dengue is an important vector-borne virus that infects on the order of 400 million individuals per year. Infection with one of the virus's four serotypes (denoted DENV-1 to 4) may be silent, result in symptomatic dengue 'breakbone' fever, or develop into the more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Extensive research has therefore focused on identifying factors that influence dengue infection outcomes. It has been well-documented through epidemiological studies that DHF is most likely to result from a secondary heterologous infection, and that individuals experiencing a DENV-2 or DENV-3 infection typically are more likely to present with more severe dengue disease than those individuals experiencing a DENV-1 or DENV-4 infection. However, a mechanistic understanding of how these risk factors affect disease outcomes, and further, how the virus's ability to evolve these mechanisms will affect disease severity patterns over time, is lacking. In the second chapter of my dissertation, I formulate mechanistic mathematical models of primary and secondary dengue infections that describe how the dengue virus interacts with the immune response and the results of this interaction on the risk of developing severe dengue disease. I show that only the innate immune response is needed to reproduce characteristic features of a primary infection whereas the adaptive immune response is needed to reproduce characteristic features of a secondary dengue infection. I then add to these models a quantitative measure of disease severity that assumes immunopathology, and analyze the effectiveness of virological indicators of disease severity. In the third chapter of my dissertation, I then statistically fit these mathematical models to viral load data of dengue patients to understand the mechanisms that drive variation in viral load. I specifically consider the roles that immune status, clinical disease manifestation, and serotype may play in explaining viral load variation observed across the patients. With this analysis, I show that there is statistical support for the theory of antibody dependent enhancement in the development of severe disease in secondary dengue infections and that there is statistical support for serotype-specific differences in viral infectivity rates, with infectivity rates of DENV-2 and DENV-3 exceeding those of DENV-1. In the fourth chapter of my dissertation, I integrate these within-host models with a vector-borne epidemiological model to understand the potential for virulence evolution in dengue. Critically, I show that dengue is expected to evolve towards intermediate virulence, and that the optimal virulence of the virus depends strongly on the number of serotypes that co-circulate. Together, these dissertation chapters show that dengue viral load dynamics provide insight into the within-host mechanisms driving differences in dengue disease patterns and that these mechanisms have important implications for dengue virulence evolution.</p> / Dissertation

No description available.

<p>Bayesian methods offer a flexible and convenient probabilistic learning framework to extract interpretable knowledge from complex and structured data. Such methods can characterize dependencies among multiple levels of hidden variables and share statistical strength across heterogeneous sources. In the first part of this dissertation, we develop two dependent variational inference methods for full posterior approximation in non-conjugate Bayesian models through hierarchical mixture- and copula-based variational proposals, respectively. The proposed methods move beyond the widely used factorized approximation to the posterior and provide generic applicability to a broad class of probabilistic models with minimal model-specific derivations. In the second part of this dissertation, we design probabilistic graphical models to accommodate multimodal data, describe dynamical behaviors and account for task heterogeneity. In particular, the sparse latent factor model is able to reveal common low-dimensional structures from high-dimensional data. We demonstrate the effectiveness of the proposed statistical learning methods on both synthetic and real-world data.</p> / Dissertation

In order for computers to interact with and understand the visual world, they must be equipped with reasoning systems that include high–level quantities such as objects, actions, and scenes. This thesis is concerned with extracting such representations of the world from visual input. The first part of this thesis describes an approach to scene understanding in which texture characteristics of the visual world are used to infer scene categories. We show that in the context of a moving camera, it is common to observe images containing very few individually salient image regions, yet overall texture structure often allows our system to derive powerful contextual cues about the environment. Our approach builds on ideas from texture recognition, and we show that our algorithm out–performs the well–known Gist descriptor on several classification tasks. In the second part of this thesis we we are interested in scene understanding in the context of multiple calibrated views of a scene, as might be obtained from a Structure–from–Motion or Simultaneous Localization and Mapping (SLAM) system. Though such systems are capable of localizing the camera robustly and efficiently, the maps produced are typically sparse point-clouds that are difficult to interpret and of little use for higher–level reasoning tasks such as scene understanding or human-machine interaction. In this thesis we begin to address this deficiency, presenting progress towards modeling scenes using semantically meaningful primitives such as floor, wall, and ceiling planes. To this end we adopt the indoor Manhattan representation, which was recently proposed for single–view reconstruction. This thesis presents the first in–depth description and analysis of this model in the literature. We describe a probabilistic model relating photometric features, stereo photo–consistencies, and 3D point clouds to Manhattan scene structure in a Bayesian framework. We then present a fast dynamic programming algorithm that solves exact MAP inference in this model in time linear in image size. We show detailed comparisons with the state–of–the art in both the single– and multiple–view contexts. Finally, we present a framework for learning within the indoor Manhattan hypothesis class. Our system is capable of extrapolating from labelled training examples to predict scene structure for unseen images. We cast learning as a structured prediction problem and show how to optimize with respect to two realistic loss functions. We present experiments in which we learn to recover scene structure from both single and multiple views — from the perspective of our learning algorithm these problems differ only by a change of feature space. This work constitutes one of the most complicated output spaces (in terms of internal constraints) yet considered within a structure prediction framework.