<p>Graphs are a natural choice for understanding the associations between variables, and assuming a probabilistic embedding for the graph structure leads to a variety of graphical models that enable us to understand these associations even further. In the realm of high-dimensional data, where the number of associations between interacting variables is far greater than the available number of data points, the goal is to infer a sparse graph. In this thesis, we make contributions in the domain of Bayesian graphical models, where our prior belief on the graph structure, encoded via uncertainty on the model parameters, enables the estimation of sparse graphs.</p> <p><br></p> <p>We begin with the Gaussian Graphical Model (GGM) in Chapter 2, one of the simplest and most famous graphical models, where the joint distribution of interacting variables is assumed to be Gaussian. In GGMs, the conditional independence among variables is encoded in the inverse of the covariance matrix, also known as the precision matrix. Under a Bayesian framework, we propose a novel prior--penalty dual called the `graphical horseshoe-like' prior and penalty, to estimate precision matrix. We also establish the posterior convergence of the precision matrix estimate and the frequentist consistency of the maximum a posteriori (MAP) estimator.</p> <p><br></p> <p>In Chapter 3, we develop a general framework based on local linear approximation for MAP estimation of the precision matrix in GGMs. This general framework holds true for any graphical prior, where the element-wise priors can be written as a Laplace scale mixture. As an application of the framework, we perform MAP estimation of the precision matrix under the graphical horseshoe penalty.</p> <p><br></p> <p>In Chapter 4, we focus on graphical models where the joint distribution of interacting variables cannot be assumed Gaussian. Motivated by the quantile graphical models, where the Gaussian likelihood assumption is relaxed, we draw inspiration from the domain of precision medicine, where personalized inference is crucial to tailor individual-specific treatment plans. With an aim to infer Directed Acyclic Graphs (DAGs), we propose a novel quantile DAG learning framework, where the DAGs depend on individual-specific covariates, making personalized inference possible. We demonstrate the potential of this framework in the regime of precision medicine by applying it to infer protein-protein interaction networks in Lung adenocarcinoma and Lung squamous cell carcinoma.</p> <p><br></p> <p>Finally, we conclude this thesis in Chapter 5, by developing a novel framework to compute the marginal likelihood in a GGM, addressing a longstanding open problem. Under this framework, we can compute the marginal likelihood for a broad class of priors on the precision matrix, where the element-wise priors on the diagonal entries can be written as gamma or scale mixtures of gamma random variables and those on the off-diagonal terms can be represented as normal or scale mixtures of normal. This result paves new roads for model selection using Bayes factors and tuning of prior hyper-parameters.</p>

<p dir="ltr">The primary purpose of this thesis is to propose and demonstrate BioGRNsemble, a modular and flexible approach for inferencing gene regulatory networks from RNA-Seq data. Integrating the GENIE3 and GRNBoost2 algorithms, this ensembles-of-ensembles method attempts to balance the outputs of both models through averaging, before providing a trimmed-down gene regulatory network consisting of transcription and target genes. Using a Drosophila Eye Dataset, we were able to successfully test this novel methodology, and our validation analysis using an online database determined over 3500 gene links correctly detected, albeit out of almost 530,000 predictions, leaving plenty of room for improvement in the future.</p>

The thesis concentrates on the issue of sexual abuse in childhood. The work is divided into four main chapters. The first and second chapter characterizes the development of a role of child from past to the present, particularly in legal terms. The author's focus is dedicated to the term definition of sexual child abuse, data and incidence of sexual abuse in context with other countries. Supported by viewpoint of other authors, a description of different views on sexual abuse of children is presented with specific forms of abuse (contact and non-contact). The third chapter deals with specific risk factors, related to children, the perpetrators (aggressors) and families. Autor´s focus is on the offender (deviant and non-deviant) and their degree of threat. The data is supported by research results published in the Czech Republic and statistical data from OSPOD MLSA. The last, fourth chapter is considered by the author to be of a great importance as it discusses the implications derived from sexual abuse in childhood. This traumatic experience may have crucial impact on further development and quality of life of the victim. The work is concluded with offers of preventative methods and the role of social worker in the process of uncovering a case of sexual abuse of a child.

<p dir="ltr">The generalization error of a classifier is related to the complexity of the set of functions among which the classifier is chosen. We study a family of low-complexity classifiers consisting of thresholding a random one-dimensional feature. The feature is obtained by projecting the data on a random line after embedding it into a higher-dimensional space parametrized by monomials of order up to k. More specifically, the extended data is projected n-times and the best classifier among those n, based on its performance on training data, is chosen. </p><p dir="ltr">We show that this type of classifier is extremely flexible, as it is likely to approximate, to an arbitrary precision, any continuous function on a compact set as well as any Boolean function on a compact set that splits the support into measurable subsets. In particular, given full knowledge of the class conditional densities, the error of these low-complexity classifiers would converge to the optimal (Bayes) error as k and n go to infinity. On the other hand, if only a training dataset is given, we show that the classifiers will perfectly classify all the training points as k and n go to infinity. </p><p dir="ltr">We also bound the generalization error of our random classifiers. In general, our bounds are better than those for any classifier with VC dimension greater than O(ln(n)). In particular, our bounds imply that, unless the number of projections n is extremely large, there is a significant advantageous gap between the generalization error of the random projection approach and that of a linear classifier in the extended space. Asymptotically, as the number of samples approaches infinity, the gap persists for any such n. Thus, there is a potentially large gain in generalization properties by selecting parameters at random, rather than optimization. </p><p dir="ltr">Given a classification problem and a family of classifiers, the Rashomon ratio measures the proportion of classifiers that yield less than a given loss. Previous work has explored the advantage of a large Rashomon ratio in the case of a finite family of classifiers. Here we consider the more general case of an infinite family. We show that a large Rashomon ratio guarantees that choosing the classifier with the best empirical accuracy among a random subset of the family, which is likely to improve generalizability, will not increase the empirical loss too much. </p><p dir="ltr">We quantify the Rashomon ratio in two examples involving infinite classifier families in order to illustrate situations in which it is large. In the first example, we estimate the Rashomon ratio of the classification of normally distributed classes using an affine classifier. In the second, we obtain a lower bound for the Rashomon ratio of a classification problem with a modified Gram matrix when the classifier family consists of two-layer ReLU neural networks. In general, we show that the Rashomon ratio can be estimated using a training dataset along with random samples from the classifier family and we provide guarantees that such an estimation is close to the true value of the Rashomon ratio.</p>