(Neal and Hinton, 1998) recast maximum likelihood estimation of any given latent variable model as the minimization of a free energy functional $F$, and the EM algorithm as coordinate descent applied to $F$. Here, we explore alternative ways to optimize the functional. In particular, we identify various gradient flows associated with $F$ and show that their limits coincide with $F$'s stationary points. By discretizing the flows, we obtain practical particle-based algorithms for maximum likelihood estimation in broad classes of latent variable models. The novel algorithms scale to high-dimensional settings and perform well in numerical experiments.

Bayesian methods are a popular choice for statistical inference in small-data regimes due to the regularization effect induced by the prior. In the context of density estimation, the standard nonparametric Bayesian approach is to target the posterior predictive of the Dirichlet process mixture model. In general, direct estimation of the posterior predictive is intractable and so methods typically resort to approximating the posterior distribution as an intermediate step. The recent development of quasi-Bayesian predictive copula updates, however, has made it possible to perform tractable predictive density estimation without the need for posterior approximation. Although these estimators are computationally appealing, they tend to struggle on non-smooth data distributions. This is due to the comparatively restrictive form of the likelihood models from which the proposed copula updates were derived. To address this shortcoming, we consider a Bayesian nonparametric model with an autoregressive likelihood decomposition and a Gaussian process prior. While the predictive update of such a model is typically intractable, we derive a quasi-Bayesian predictive update that achieves state-of-the-art results in small-data regimes.

The sole aim of this book is to give a self-contained introduction to concepts and mathematical tools in Bayesian matrix decomposition in order to seamlessly introduce matrix decomposition techniques and their applications in subsequent sections. However, we clearly realize our inability to cover all the useful and interesting results concerning Bayesian matrix decomposition and given the paucity of scope to present this discussion, e.g., the separated analysis of variational inference for conducting the optimization. We refer the reader to literature in the field of Bayesian analysis for a more detailed introduction to the related fields. This book is primarily a summary of purpose, significance of important Bayesian matrix decomposition methods, e.g., real-valued decomposition, nonnegative matrix factorization, Bayesian interpolative decomposition, and the origin and complexity of the methods which shed light on their applications. The mathematical prerequisite is a first course in statistics and linear algebra. Other than this modest background, the development is self-contained, with rigorous proof provided throughout.

In this paper, we study the problem of transferring the available Markov Decision Process (MDP) models to learn and plan efficiently in an unknown but similar MDP. We refer to it as \textit{Model Transfer Reinforcement Learning (MTRL)} problem. First, we formulate MTRL for discrete MDPs and Linear Quadratic Regulators (LQRs) with continuous state actions. Then, we propose a generic two-stage algorithm, MLEMTRL, to address the MTRL problem in discrete and continuous settings. In the first stage, MLEMTRL uses a \textit{constrained Maximum Likelihood Estimation (MLE)}-based approach to estimate the target MDP model using a set of known MDP models. In the second stage, using the estimated target MDP model, MLEMTRL deploys a model-based planning algorithm appropriate for the MDP class. Theoretically, we prove worst-case regret bounds for MLEMTRL both in realisable and non-realisable settings. We empirically demonstrate that MLEMTRL allows faster learning in new MDPs than learning from scratch and achieves near-optimal performance depending on the similarity of the available MDPs and the target MDP.

Learning the underlying Bayesian Networks (BNs), represented by directed acyclic graphs (DAGs), of the concerned events from purely-observational data is a crucial part of evidential reasoning. This task remains challenging due to the large and discrete search space. A recent flurry of developments followed NOTEARS[1] recast this combinatorial problem into a continuous optimization problem by leveraging an algebraic equality characterization of acyclicity. However, the continuous optimization methods suffer from obtaining non-spare graphs after the numerical optimization, which leads to the inflexibility to rule out the potentially cycle-inducing edges or false discovery edges with small values. To address this issue, in this paper, we develop a completely data-driven DAG structure learning method without a predefined value to post-threshold small values. We name our method NOTEARS with adaptive Lasso (NOTEARS-AL), which is achieved by applying the adaptive penalty method to ensure the sparsity of the estimated DAG. Moreover, we show that NOTEARS-AL also inherits the oracle properties under some specific conditions. Extensive experiments on both synthetic and a real-world dataset demonstrate that our method consistently outperforms NOTEARS.

The problems of selecting partial correlation and causality graphs for count data are considered. A parameter driven generalized linear model is used to describe the observed multivariate time series of counts. Partial correlation and causality graphs corresponding to this model explain the dependencies between each time series of the multivariate count data. In order to estimate these graphs with tunable sparsity, an appropriate likelihood function maximization is regularized with an l1-type constraint. A novel MCEM algorithm is proposed to iteratively solve this regularized MLE. Asymptotic convergence results are proved for the sequence generated by the proposed MCEM algorithm with l1-type regularization. The algorithm is first successfully tested on simulated data. Thereafter, it is applied to observed weekly dengue disease counts from each ward of Greater Mumbai city. The interdependence of various wards in the proliferation of the disease is characterized by the edges of the inferred partial correlation graph. On the other hand, the relative roles of various wards as sources and sinks of dengue spread is quantified by the number and weights of the directed edges originating from and incident upon each ward. From these estimated graphs, it is observed that some special wards act as epicentres of dengue spread even though their disease counts are relatively low.

Population synthesis consists of generating synthetic but realistic representations of a target population of micro-agents for the purpose of behavioral modeling and simulation. We introduce a new framework based on copulas to generate synthetic data for a target population of which only the empirical marginal distributions are known by using a sample from another population sharing similar marginal dependencies. This makes it possible to include a spatial component in the generation of population synthesis and to combine various sources of information to obtain more realistic population generators. Specifically, we normalize the data and treat them as realizations of a given copula, and train a generative model on the normalized data before injecting the information on the marginals. We compare the copulas framework to IPF and to modern probabilistic approaches such as Bayesian networks, variational auto-encoders, and generative adversarial networks. We also illustrate on American Community Survey data that the method proposed allows to study the structure of the data at different geographical levels in a way that is robust to the peculiarities of the marginal distributions.

Understanding how different classes are distributed in an unlabeled data set is an important challenge for the calibration of probabilistic classifiers and uncertainty quantification. Approaches like adjusted classify and count, black-box shift estimators, and invariant ratio estimators use an auxiliary (and potentially biased) black-box classifier trained on a different (shifted) data set to estimate the class distribution and yield asymptotic guarantees under weak assumptions. We demonstrate that all these algorithms are closely related to the inference in a particular Bayesian model, approximating the assumed ground-truth generative process. Then, we discuss an efficient Markov Chain Monte Carlo sampling scheme for the introduced model and show an asymptotic consistency guarantee in the large-data limit. We compare the introduced model against the established point estimators in a variety of scenarios, and show it is competitive, and in some cases superior, with the state of the art.

Thompson sampling (TS) is a popular heuristic for action selection, but it requires sampling from a posterior distribution. Unfortunately, this can become computationally intractable in complex environments, such as those modeled using neural networks. Approximate posterior samples can produce effective actions, but only if they reasonably approximate joint predictive distributions of outputs across inputs. Notably, accuracy of marginal predictive distributions does not suffice. Epistemic neural networks (ENNs) are designed to produce accurate joint predictive distributions. We compare a range of ENNs through computational experiments that assess their performance in approximating TS across bandit and reinforcement learning environments. The results indicate that ENNs serve this purpose well and illustrate how the quality of joint predictive distributions drives performance. Further, we demonstrate that the \textit{epinet} -- a small additive network that estimates uncertainty -- matches the performance of large ensembles at orders of magnitude lower computational cost. This enables effective application of TS with computation that scales gracefully to complex environments.

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems. Phylogenetics is an important discipline of computational biology where the goal is to identify the evolutionary history and relationships among individuals or groups of biological entities. In statistical approaches to phylogenetics, this has been formulated as an inference problem on hypotheses of shared history, i.e., phylogenetic trees, based on observed sequence data (e.g., DNA, RNA, or protein sequences) under a model of evolution.