In view of the paradigm shift that makes science ever more data-driven, in this thesis we propose a synthesis method for encoding and managing large-scale deterministic scientific hypotheses as uncertain and probabilistic data. In the form of mathematical equations, hypotheses symmetrically relate aspects of the studied phenomena. For computing predictions, however, deterministic hypotheses can be abstracted as functions. We build upon Simon's notion of structural equations in order to efficiently extract the (so-called) causal ordering between variables, implicit in a hypothesis structure (set of mathematical equations). We show how to process the hypothesis predictive structure effectively through original algorithms for encoding it into a set of functional dependencies (fd's) and then performing causal reasoning in terms of acyclic pseudo-transitive reasoning over fd's. Such reasoning reveals important causal dependencies implicit in the hypothesis predictive data and guide our synthesis of a probabilistic database. Like in the field of graphical models in AI, such a probabilistic database should be normalized so that the uncertainty arisen from competing hypotheses is decomposed into factors and propagated properly onto predictive data by recovering its joint probability distribution through a lossless join. That is motivated as a design-theoretic principle for data-driven hypothesis management and predictive analytics. The method is applicable to both quantitative and qualitative deterministic hypotheses and demonstrated in realistic use cases from computational science.

Information divergence functions play a critical role in statistics and information theory. In this paper we show that a non-parametric f-divergence measure can be used to provide improved bounds on the minimum binary classification probability of error for the case when the training and test data are drawn from the same distribution and for the case where there exists some mismatch between training and test distributions. We confirm the theoretical results by designing feature selection algorithms using the criteria from these bounds and by evaluating the algorithms on a series of pathological speech classification tasks.

A key quantity of interest in Bayesian inference are expectations of functions with respect to a posterior distribution. Markov Chain Monte Carlo is a fundamental tool to consistently compute these expectations via averaging samples drawn from an approximate posterior. However, its feasibility is being challenged in the era of so called Big Data as all data needs to be processed in every iteration. Realising that such simulation is an unnecessarily hard problem if the goal is estimation, we construct a computationally scalable methodology that allows unbiased estimation of the required expectations -- without explicit simulation from the full posterior. The scheme's variance is finite by construction and straightforward to control, leading to algorithms that are provably unbiased and naturally arrive at a desired error tolerance. This is achieved at an average computational complexity that is sub-linear in the size of the dataset and its free parameters are easy to tune. We demonstrate the utility and generality of the methodology on a range of common statistical models applied to large-scale benchmark and real-world datasets.

Inference and learning of graphical models are both well-studied problems in statistics and machine learning that have found many applications in science and engineering. However, exact inference is intractable in general graphical models, which suggests the problem of seeking the best approximation to a collection of random variables within some tractable family of graphical models. In this paper, we focus on the class of planar Ising models, for which exact inference is tractable using techniques of statistical physics. Based on these techniques and recent methods for planarity testing and planar embedding, we propose a simple greedy algorithm for learning the best planar Ising model to approximate an arbitrary collection of binary random variables (possibly from sample data). Given the set of all pairwise correlations among variables, we select a planar graph and optimal planar Ising model defined on this graph to best approximate that set of correlations. We demonstrate our method in simulations and for the application of modeling senate voting records.

Crowdsourcing provides a popular paradigm for data collection at scale. We study the problem of selecting subsets of workers from a given worker pool to maximize the accuracy under a budget constraint. One natural question is whether we should hire as many workers as the budget allows, or restrict on a small number of top-quality workers. By theoretically analyzing the error rate of a typical setting in crowdsourcing, we frame the worker selection problem into a combinatorial optimization problem and propose an algorithm to solve it efficiently. Empirical results on both simulated and real-world datasets show that our algorithm is able to select a small number of high-quality workers, and performs as good as, sometimes even better than, the much larger crowds as the budget allows.

A crucial task in system identification problems is the selection of the most appropriate model class, and is classically addressed resorting to cross-validation or using order selection criteria based on asymptotic arguments. As recently suggested in the literature, this can be addressed in a Bayesian framework, where model complexity is regulated by few hyperparameters, which can be estimated via marginal likelihood maximization. It is thus of primary importance to design effective optimization methods to solve the corresponding optimization problem. If the unknown impulse response is modeled as a Gaussian process with a suitable kernel, the maximization of the marginal likelihood leads to a challenging nonconvex optimization problem, which requires a stable and effective solution strategy. In this paper we address this problem by means of a scaled gradient projection algorithm, in which the scaling matrix and the steplength parameter play a crucial role to provide a meaningful solution in a computational time comparable with second order methods. In particular, we propose both a generalization of the split gradient approach to design the scaling matrix in the presence of box constraints, and an effective implementation of the gradient and objective function. The extensive numerical experiments carried out on several test problems show that our method is very effective in providing in few tenths of a second solutions of the problems with accuracy comparable with state-of-the-art approaches. Moreover, the flexibility of the proposed strategy makes it easily adaptable to a wider range of problems arising in different areas of machine learning, signal processing and system identification.

Falling rule lists are classification models consisting of an ordered list of if-then rules, where (i) the order of rules determines which example should be classified by each rule, and (ii) the estimated probability of success decreases monotonically down the list. These kinds of rule lists are inspired by healthcare applications where patients would be stratified into risk sets and the highest at-risk patients should be considered first. We provide a Bayesian framework for learning falling rule lists that does not rely on traditional greedy decision tree learning methods.

Determining the 3D structures of biological molecules is a key problem for both biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising technique for structure estimation which relies heavily on computational methods to reconstruct 3D structures from 2D images. This paper introduces the challenging Cryo-EM density estimation problem as a novel application for stochastic optimization techniques. Structure discovery is formulated as MAP estimation in a probabilistic latent-variable model, resulting in an optimization problem to which an array of seven stochastic optimization methods are applied. The methods are tested on both real and synthetic data, with some methods recovering reasonable structures in less than one epoch from a random initialization. Complex quasi-Newton methods are found to converge more slowly than simple gradient-based methods, but all stochastic methods are found to converge to similar optima. This method represents a major improvement over existing methods as it is significantly faster and is able to converge from a random initialization.

We present the Bayesian Echo Chamber, a new Bayesian generative model for social interaction data. By modeling the evolution of people's language usage over time, this model discovers latent influence relationships between them. Unlike previous work on inferring influence, which has primarily focused on simple temporal dynamics evidenced via turn-taking behavior, our model captures more nuanced influence relationships, evidenced via linguistic accommodation patterns in interaction content. The model, which is based on a discrete analog of the multivariate Hawkes process, permits a fully Bayesian inference algorithm. We validate our model's ability to discover latent influence patterns using transcripts of arguments heard by the US Supreme Court and the movie "12 Angry Men."

We introduce a probabilistic approach to the LMS filter. By means of an efficient approximation, this approach provides an adaptable step-size LMS algorithm together with a measure of uncertainty about the estimation. In addition, the proposed approximation preserves the linear complexity of the standard LMS. Numerical results show the improved performance of the algorithm with respect to standard LMS and state-of-the-art algorithms with similar complexity. The goal of this work, therefore, is to open the door to bring some more Bayesian machine learning techniques to adaptive filtering.