Multivariate count data are defined as the number of items of different categories issued from sampling within a population, which individuals are grouped into categories. The analysis of multivariate count data is a recurrent and crucial issue in numerous modelling problems, particularly in the fields of biology and ecology (where the data can represent, for example, children counts associated with multitype branching processes), sociology and econometrics. We focus on I) Identifying categories that appear simultaneously, or on the contrary that are mutually exclusive. This is achieved by identifying conditional independence relationships between the variables; II)Building parsimonious parametric models consistent with these relationships; III) Characterising and testing the effects of covariates on the joint distribution of the counts. To achieve these goals, we propose an approach based on graphical probabilistic models, and more specifically partially directed acyclic graphs.

We present an asymptotic analysis of Viterbi Training (VT) and contrast it with a more conventional Maximum Likelihood (ML) approach to parameter estimation in Hidden Markov Models. While ML estimator works by (locally) maximizing the likelihood of the observed data, VT seeks to maximize the probability of the most likely hidden state sequence. We develop an analytical framework based on a generating function formalism and illustrate it on an exactly solvable model of HMM with one unambiguous symbol. For this particular model the ML objective function is continuously degenerate. VT objective, in contrast, is shown to have only finite degeneracy. Furthermore, VT converges faster and results in sparser (simpler) models, thus realizing an automatic Occam's razor for HMM learning. For more general scenario VT can be worse compared to ML but still capable of correctly recovering most of the parameters.

We tackle the fundamental problem of Bayesian active learning with noise, where we need to adaptively select from a number of expensive tests in order to identify an unknown hypothesis sampled from a known prior distribution. In the case of noise-free observations, a greedy algorithm called generalized binary search (GBS) is known to perform near-optimally. We show that if the observations are noisy, perhaps surprisingly, GBS can perform very poorly. We develop EC2, a novel, greedy active learning algorithm and prove that it is competitive with the optimal policy, thus obtaining the first competitiveness guarantees for Bayesian active learning with noisy observations. Our bounds rely on a recently discovered diminishing returns property called adaptive submodularity, generalizing the classical notion of submodular set functions to adaptive policies. Our results hold even if the tests have non-uniform cost and their noise is correlated. We also propose EffECXtive, a particularly fast approximation of EC2, and evaluate it on a Bayesian experimental design problem involving human subjects, intended to tease apart competing economic theories of how people make decisions under uncertainty.

Fitting high-dimensional data involves a delicate tradeoff between faithful representation and the use of sparse models. Too often, sparsity assumptions on the fitted model are too restrictive to provide a faithful representation of the observed data. In this paper, we present a novel framework incorporating sparsity in different domains.We decompose the observed covariance matrix into a sparse Gaussian Markov model (with a sparse precision matrix) and a sparse independence model (with a sparse covariance matrix). Our framework incorporates sparse covariance and sparse precision estimation as special cases and thus introduces a richer class of high-dimensional models. We characterize sufficient conditions for identifiability of the two models, \viz Markov and independence models. We propose an efficient decomposition method based on a modification of the popular $\ell_1$-penalized maximum-likelihood estimator ($\ell_1$-MLE). We establish that our estimator is consistent in both the domains, i.e., it successfully recovers the supports of both Markov and independence models, when the number of samples $n$ scales as $n = \Omega(d^2 \log p)$, where $p$ is the number of variables and $d$ is the maximum node degree in the Markov model. Our experiments validate these results and also demonstrate that our models have better inference accuracy under simple algorithms such as loopy belief propagation.

The detection of anomalous activity in graphs is a statistical problem that arises in many applications, such as network surveillance, disease outbreak detection, and activity monitoring in social networks. Beyond its wide applicability, graph structured anomaly detection serves as a case study in the difficulty of balancing computational complexity with statistical power. In this work, we develop from first principles the generalized likelihood ratio test for determining if there is a well connected region of activation over the vertices in the graph in Gaussian noise. Because this test is computationally infeasible, we provide a relaxation, called the Lovasz extended scan statistic (LESS) that uses submodularity to approximate the intractable generalized likelihood ratio. We demonstrate a connection between LESS and maximum a-posteriori inference in Markov random fields, which provides us with a poly-time algorithm for LESS. Using electrical network theory, we are able to control type 1 error for LESS and prove conditions under which LESS is risk consistent. Finally, we consider specific graph models, the torus, k-nearest neighbor graphs, and epsilon-random graphs. We show that on these graphs our results provide near-optimal performance by matching our results to known lower bounds.

We introduce a Bayesian approach to discovering patterns in structurally complex processes. The proposed method of Bayesian Structural Inference (BSI) relies on a set of candidate unifilar HMM (uHMM) topologies for inference of process structure from a data series. We employ a recently developed exact enumeration of topological epsilon-machines. (A sequel then removes the topological restriction.) This subset of the uHMM topologies has the added benefit that inferred models are guaranteed to be epsilon-machines, irrespective of estimated transition probabilities. Properties of epsilon-machines and uHMMs allow for the derivation of analytic expressions for estimating transition probabilities, inferring start states, and comparing the posterior probability of candidate model topologies, despite process internal structure being only indirectly present in data. We demonstrate BSI's effectiveness in estimating a process's randomness, as reflected by the Shannon entropy rate, and its structure, as quantified by the statistical complexity. We also compare using the posterior distribution over candidate models and the single, maximum a posteriori model for point estimation and show that the former more accurately reflects uncertainty in estimated values. We apply BSI to in-class examples of finite- and infinite-order Markov processes, as well to an out-of-class, infinite-state hidden process.

Spectral methods have greatly advanced the estimation of latent variable models, generating a sequence of novel and efficient algorithms with strong theoretical guarantees. However, current spectral algorithms are largely restricted to mixtures of discrete or Gaussian distributions. In this paper, we propose a kernel method for learning multi-view latent variable models, allowing each mixture component to be nonparametric. The key idea of the method is to embed the joint distribution of a multi-view latent variable into a reproducing kernel Hilbert space, and then the latent parameters are recovered using a robust tensor power method. We establish that the sample complexity for the proposed method is quadratic in the number of latent components and is a low order polynomial in the other relevant parameters. Thus, our non-parametric tensor approach to learning latent variable models enjoys good sample and computational efficiencies. Moreover, the non-parametric tensor power method compares favorably to EM algorithm and other existing spectral algorithms in our experiments.

We present an exploration of the rich theoretical connections between several classes of regularized models, network flows, and recent results in submodular function theory. This work unifies key aspects of these problems under a common theory, leading to novel methods for working with several important models of interest in statistics, machine learning and computer vision. In Part 1, we review the concepts of network flows and submodular function optimization theory foundational to our results. We then examine the connections between network flows and the minimum-norm algorithm from submodular optimization, extending and improving several current results. This leads to a concise representation of the structure of a large class of pairwise regularized models important in machine learning, statistics and computer vision. In Part 2, we describe the full regularization path of a class of penalized regression problems with dependent variables that includes the graph-guided LASSO and total variation constrained models. This description also motivates a practical algorithm. This allows us to efficiently find the regularization path of the discretized version of TV penalized models. Ultimately, our new algorithms scale up to high-dimensional problems with millions of variables.

We study an economic decision problem where the actors are two firms and the Antitrust Authority whose main task is to monitor and prevent firms' potential anti-competitive behaviour and its effect on the market. The Antitrust Authority's decision process is modelled using a Bayesian network where both the relational structure and the parameters of the model are estimated from a data set provided by the Authority itself. A number of economic variables that influence this decision process are also included in the model. We analyse how monitoring by the Antitrust Authority affects firms' strategies about cooperation. Firms' strategies are modelled as a repeated prisoner's dilemma using object-oriented Bayesian networks. We show how the integration of firms' decision process and external market information can be modelled in this way. Various decision scenarios and strategies are illustrated.

Nonparametric estimation of the conditional distribution of a response given high-dimensional features is a challenging problem. It is important to allow not only the mean but also the variance and shape of the response density to change flexibly with features, which are massive-dimensional. We propose a multiscale dictionary learning model, which expresses the conditional response density as a convex combination of dictionary densities, with the densities used and their weights dependent on the path through a tree decomposition of the feature space. A fast graph partitioning algorithm is applied to obtain the tree decomposition, with Bayesian methods then used to adaptively prune and average over different sub-trees in a soft probabilistic manner. The algorithm scales efficiently to approximately one million features. State of the art predictive performance is demonstrated for toy examples and two neuroscience applications including up to a million features.