Learning a Gaussian Mixture Model (GMM) is hard when the number of parameters is too large given the amount of available data. As a remedy, we propose restricting the GMM to a Gaussian Markov Random Field Mixture Model (GMRF-MM), as well as a new method for estimating the latter's sparse precision (i.e., inverse covariance) matrices. When the sparsity pattern of each matrix is known, we propose an efficient optimization method for the Maximum Likelihood Estimate (MLE) of that matrix. When it is unknown, we utilize the popular Graphical LASSO (GLASSO) to estimate that pattern. However, we show that even for a single Gaussian, when GLASSO is tuned to successfully estimate the sparsity pattern, it does so at the price of a substantial bias of the values of the nonzero entries of the matrix, and we show that this problem only worsens in a mixture setting. To overcome this, we discard the non-zero values estimated by GLASSO, keep only its pattern estimate and use it within the proposed MLE method. This yields an effective two-step procedure that removes the bias. We show that our "debiasing" approach outperforms GLASSO in both the single-GMRF and the GMRF-MM cases. We also show that when learning priors for image patches, our method outperforms GLASSO even if we merely use an educated guess about the sparsity pattern, and that our GMRF-MM outperforms the baseline GMM on real and synthetic high-dimensional datasets. Our code is available at \url{https://github.com/shahaffind/GMRF-MM}.

An influence diagram is a graphical representation of sequential decision-making under uncertainty, defining a structured decision problem by conditional probability functions and additive utility functions over discrete state and action variables. The task of finding the maximum expected utility of influence diagrams is closely related to the cost-optimal probabilistic planning, stochastic programmings, or model-based reinforcement learning. In this position paper, we address the heuristic search for solving influence diagram, where we generate admissible heuristic functions from graph decomposition schemes. Then, we demonstrate how such heuristics can guide an AND/OR branch and bound search. Finally, we briefly discuss the future directions for improving the quality of heuristic functions and search strategies.

This thesis describes work on two applications of probabilistic programming: the learning of probabilistic program code given specifications, in particular program code of one-dimensional samplers; and the facilitation of sequential Monte Carlo inference with help of data-driven proposals. The latter is presented with experimental results on a linear Gaussian model and a non-parametric dependent Dirichlet process mixture of objects model for object recognition and tracking. In Chapter 1 we provide a brief introduction to probabilistic programming. In Chapter 2 we present an approach to automatic discovery of samplers in the form of probabilistic programs. We formulate a Bayesian approach to this problem by specifying a grammar-based prior over probabilistic program code. We use an approximate Bayesian computation method to learn the programs, whose executions generate samples that statistically match observed data or analytical characteristics of distributions of interest. In our experiments we leverage different probabilistic programming systems to perform Markov chain Monte Carlo sampling over the space of programs. Experimental results have demonstrated that, using the proposed methodology, we can learn approximate and even some exact samplers. Finally, we show that our results are competitive with regard to genetic programming methods. In Chapter 3, we describe a way to facilitate sequential Monte Carlo inference in probabilistic programming using data-driven proposals. In particular, we develop a distance-based proposal for the non-parametric dependent Dirichlet process mixture of objects model. We implement this approach in the probabilistic programming system Anglican, and show that for that model data-driven proposals provide significant performance improvements. We also explore the possibility of using neural networks to improve data-driven proposals.

Markov decision processes are of major interest in the planning community as well as in the model checking community. But in spite of the similarity in the considered formal models, the development of new techniques and methods happened largely independently in both communities. This work is intended as a beginning to unite the two research branches. We consider goal-reachability analysis as a common basis between both communities. The core of this paper is the translation from Jani, an overarching input language for quantitative model checkers, into the probabilistic planning domain definition language (PPDDL), and vice versa from PPDDL into Jani. These translations allow the creation of an overarching benchmark collection, including existing case studies from the model checking community, as well as benchmarks from the international probabilistic planning competitions (IPPC). We use this benchmark set as a basis for an extensive empirical comparison of various approaches from the model checking community, variants of value iteration, and MDP heuristic search algorithms developed by the AI planning community. On a per benchmark domain basis, techniques from one community can achieve state-ofthe-art performance in benchmarks of the other community. Across all benchmark domains of one community, the performance comparison is however in favor of the solvers and algorithms of that particular community. Reasons are the design of the benchmarks, as well as tool-related limitations. Our translation methods and benchmark collection foster crossfertilization between both communities, pointing out specific opportunities for widening the scope of solvers to different kinds of models, as well as for exchanging and adopting algorithms across communities.

We propose a framework called HyperVAE for encoding distributions of distributions. When a target distribution is modeled by a VAE, its neural network parameters \theta is drawn from a distribution p(\theta) which is modeled by a hyper-level VAE. We propose a variational inference using Gaussian mixture models to implicitly encode the parameters \theta into a low dimensional Gaussian distribution. Given a target distribution, we predict the posterior distribution of the latent code, then use a matrix-network decoder to generate a posterior distribution q(\theta). HyperVAE can encode the parameters \theta in full in contrast to common hyper-networks practices, which generate only the scale and bias vectors as target-network parameters. Thus HyperVAE preserves much more information about the model for each task in the latent space. We discuss HyperVAE using the minimum description length (MDL) principle and show that it helps HyperVAE to generalize. We evaluate HyperVAE in density estimation tasks, outlier detection and discovery of novel design classes, demonstrating its efficacy.

This work considers methods for imposing sparsity in Bayesian regression with applications in nonlinear system identification. We first review automatic relevance determination (ARD) and analytically demonstrate the need to additional regularization or thresholding to achieve sparse models. We then discuss two classes of methods, regularization based and thresholding based, which build on ARD to learn parsimonious solutions to linear problems. In the case of orthogonal covariates, we analytically demonstrate favorable performance with regards to learning a small set of active terms in a linear system with a sparse solution. Several example problems are presented to compare the set of proposed methods in terms of advantages and limitations to ARD in bases with hundreds of elements. The aim of this paper is to analyze and understand the assumptions that lead to several algorithms and to provide theoretical and empirical results so that the reader may gain insight and make more informed choices regarding sparse Bayesian regression.

We consider the problem of discovering the causal process that generated a collection of datasets. We assume that all these datasets were generated by unknown sparse interventions on a structural causal model (SCM) $G$, that we want to identify. Recently, Bengio et al. (2020) argued that among all SCMs, $G$ is the fastest to adapt from one dataset to another, and proposed a meta-learning criterion to identify the causal direction in a two-variable SCM. While the experiments were promising, the theoretical justification was incomplete. Our contribution is a theoretical investigation of the adaptation speed of simple two-variable SCMs. We use convergence rates from stochastic optimization to justify that a relevant proxy for adaptation speed is distance in parameter space after intervention. Using this proxy, we show that the SCM with the correct causal direction is advantaged for categorical and normal cause-effect datasets when the intervention is on the cause variable. When the intervention is on the effect variable, we provide a more nuanced picture which highlights that the fastest-to-adapt heuristic is not always valid. Code to reproduce experiments is available at https://github.com/remilepriol/causal-adaptation-speed

Traceability is a fundamental component of the modern software development process that helps to ensure properly functioning, secure programs. Due to the high cost of manually establishing trace links, researchers have developed automated approaches that draw relationships between pairs of textual software artifacts using similarity measures. However, the effectiveness of such techniques are often limited as they only utilize a single measure of artifact similarity and cannot simultaneously model (implicit and explicit) relationships across groups of diverse development artifacts. In this paper, we illustrate how these limitations can be overcome through the use of a tailored probabilistic model. To this end, we design and implement a HierarchiCal PrObabilistic Model for SoftwarE Traceability (Comet) that is able to infer candidate trace links. Comet is capable of modeling relationships between artifacts by combining the complementary observational prowess of multiple measures of textual similarity. Additionally, our model can holistically incorporate information from a diverse set of sources, including developer feedback and transitive (often implicit) relationships among groups of software artifacts, to improve inference accuracy. We conduct a comprehensive empirical evaluation of Comet that illustrates an improvement over a set of optimally configured baselines of $\approx$14% in the best case and $\approx$5% across all subjects in terms of average precision. The comparative effectiveness of Comet in practice, where optimal configuration is typically not possible, is likely to be higher. Finally, we illustrate Comets potential for practical applicability in a survey with developers from Cisco Systems who used a prototype Comet Jenkins plugin.

Solar activity It is vital to accurately predict solar activity, in order to decrease the plausible damage of electronic equipment in the event of a large high-intensity solar eruption. Recently, we have proposed BELFIS (Brain Emotional Learning-based Fuzzy Inference System) as a tool for the forecasting of chaotic systems. The structure of BELFIS is designed based on the neural structure of fear conditioning. The function of BELFIS is implemented by assigning adaptive networks to the components of the BELFIS structure. This paper especially focuses on performance evaluation of BELFIS as a predictor by forecasting solar cycles 16 to 24. The performance of BELFIS is compared with other computational models used for this purpose, and in particular with adaptive neuro-fuzzy inference system (ANFIS).

Many real data sets contain features (variables) whose distribution is far from normal (gaussian). Instead, their distribution is often skewed. In order to handle such data it is customary to preprocess the variables to make them more normal. The Box-Cox and Yeo-Johnson transformations are well-known tools for this. However, the standard maximum likelihood estimator of their transformation parameter is highly sensitive to outliers, and will often try to move outliers inward at the expense of the normality of the central part of the data. We propose an automatic preprocessing technique that is robust against such outliers, which transforms the data to central normality. It compares favorably to existing techniques in an extensive simulation study and on real data.