The bipartite record linkage task consists of merging two disparate datafiles containing information on two overlapping sets of entities. This is non-trivial in the absence of unique identifiers and it is important for a wide variety of applications given that it needs to be solved whenever we have to combine information from different sources. Most statistical techniques currently used for record linkage are derived from a seminal paper by Fellegi and Sunter (1969). These techniques usually assume independence in the matching statuses of record pairs to derive estimation procedures and optimal point estimators. We argue that this independence assumption is unreasonable and instead target a bipartite matching between the two datafiles as our parameter of interest. Bayesian implementations allow us to quantify uncertainty on the matching decisions and derive a variety of point estimators using different loss functions. We propose partial Bayes estimates that allow uncertain parts of the bipartite matching to be left unresolved. We evaluate our approach to record linkage using a variety of challenging scenarios and show that it outperforms the traditional methodology. We illustrate the advantages of our methods merging two datafiles on casualties from the civil war of El Salvador.

Continuous time Bayesian networks are investigated with a special focus on their ability to express causality. A framework is presented for doing inference in these networks. The central contributions are a representation of the intensity matrices for the networks and the introduction of a causality measure. A new model for high-frequency financial data is presented. It is calibrated to market data and by the new causality measure it performs better than older models.

We study the problem of recovering a hidden community of cardinality $K$ from an $n \times n$ symmetric data matrix $A$, where for distinct indices $i,j$, $A_{ij} \sim P$ if $i, j$ both belong to the community and $A_{ij} \sim Q$ otherwise, for two known probability distributions $P$ and $Q$ depending on $n$. If $P={\rm Bern}(p)$ and $Q={\rm Bern}(q)$ with $p>q$, it reduces to the problem of finding a densely-connected $K$-subgraph planted in a large Erd\"os-R\'enyi graph; if $P=\mathcal{N}(\mu,1)$ and $Q=\mathcal{N}(0,1)$ with $\mu>0$, it corresponds to the problem of locating a $K \times K$ principal submatrix of elevated means in a large Gaussian random matrix. We focus on two types of asymptotic recovery guarantees as $n \to \infty$: (1) weak recovery: expected number of classification errors is $o(K)$; (2) exact recovery: probability of classifying all indices correctly converges to one. Under mild assumptions on $P$ and $Q$, and allowing the community size to scale sublinearly with $n$, we derive a set of sufficient conditions and a set of necessary conditions for recovery, which are asymptotically tight with sharp constants. The results hold in particular for the Gaussian case, and for the case of bounded log likelihood ratio, including the Bernoulli case whenever $\frac{p}{q}$ and $\frac{1-p}{1-q}$ are bounded away from zero and infinity. An important algorithmic implication is that, whenever exact recovery is information theoretically possible, any algorithm that provides weak recovery when the community size is concentrated near $K$ can be upgraded to achieve exact recovery in linear additional time by a simple voting procedure.

For many complex diseases, there is a wide variety of ways in which an individual can manifest the disease. The challenge of personalized medicine is to develop tools that can accurately predict the trajectory of an individual's disease, which can in turn enable clinicians to optimize treatments. We represent an individual's disease trajectory as a continuous-valued continuous-time function describing the severity of the disease over time. We propose a hierarchical latent variable model that individualizes predictions of disease trajectories. This model shares statistical strength across observations at different resolutions--the population, subpopulation and the individual level. We describe an algorithm for learning population and subpopulation parameters offline, and an online procedure for dynamically learning individual-specific parameters. Finally, we validate our model on the task of predicting the course of interstitial lung disease, a leading cause of death among patients with the autoimmune disease scleroderma. We compare our approach against state-of-the-art and demonstrate significant improvements in predictive accuracy.

In recent years there has been an increased interest in statistical analysis of data with multiple types of relations among a set of entities. Such multi-relational data can be represented as multi-layer graphs where the set of vertices represents the entities and multiple types of edges represent the different relations among them. For community detection in multi-layer graphs, we consider two random graph models, the multi-layer stochastic blockmodel (MLSBM) and a model with a restricted parameter space, the restricted multi-layer stochastic blockmodel (RMLSBM). We derive consistency results for community assignments of the maximum likelihood estimators (MLEs) in both models where MLSBM is assumed to be the true model, and either the number of nodes or the number of types of edges or both grow. We compare MLEs in the two models with other baseline approaches, such as separate modeling of layers, aggregating the layers and majority voting. RMLSBM is shown to have advantage over MLSBM when either the growth rate of the number of communities is high or the growth rate of the average degree of the component graphs in the multi-graph is low. We also derive minimax rates of error and sharp thresholds for achieving consistency of community detection in both models, which are then used to compare the multi-layer models with a baseline model, the aggregate stochastic block model. The simulation studies and real data applications confirm the superior performance of the multi-layer approaches in comparison to the baseline procedures.

Models for which the likelihood function can be evaluated only up to a parameter-dependent unknown normalising constant, such as Markov random field models, are used widely in computer science, statistical physics, spatial statistics, and network analysis. However, Bayesian analysis of these models using standard Monte Carlo methods is not possible due to the intractability of their likelihood functions. Several methods that permit exact, or close to exact, simulation from the posterior distribution have recently been developed. However, estimating the evidence and Bayes' factors (BFs) for these models remains challenging in general. This paper describes new random weight importance sampling and sequential Monte Carlo methods for estimating BFs that use simulation to circumvent the evaluation of the intractable likelihood, and compares them to existing methods. In some cases we observe an advantage in the use of biased weight estimates. An initial investigation into the theoretical and empirical properties of this class of methods is presented. Some support for the use of biased estimates is presented, but we advocate caution in the use of such estimates.

Convolutional neural networks (CNNs) work well on large datasets. But labelled data is hard to collect, and in some applications larger amounts of data are not available. The problem then is how to use CNNs with small data -- as CNNs overfit quickly. We present an efficient Bayesian CNN, offering better robustness to over-fitting on small data than traditional approaches. This is by placing a probability distribution over the CNN's kernels. We approximate our model's intractable posterior with Bernoulli variational distributions, requiring no additional model parameters. On the theoretical side, we cast dropout network training as approximate inference in Bayesian neural networks. This allows us to implement our model using existing tools in deep learning with no increase in time complexity, while highlighting a negative result in the field. We show a considerable improvement in classification accuracy compared to standard techniques and improve on published state-of-the-art results for CIFAR-10.

Dyadic Data Prediction (DDP) is an important problem in many research areas. This paper develops a novel fully Bayesian nonparametric framework which integrates two popular and complementary approaches, discrete mixed membership modeling and continuous latent factor modeling into a unified Heterogeneous Matrix Factorization~(HeMF) model, which can predict the unobserved dyadics accurately. The HeMF can determine the number of communities automatically and exploit the latent linear structure for each bicluster efficiently. We propose a Variational Bayesian method to estimate the parameters and missing data. We further develop a novel online learning approach for Variational inference and use it for the online learning of HeMF, which can efficiently cope with the important large-scale DDP problem. We evaluate the performance of our method on the EachMoive, MovieLens and Netflix Prize collaborative filtering datasets. The experiment shows that, our model outperforms state-of-the-art methods on all benchmarks. Compared with Stochastic Gradient Method (SGD), our online learning approach achieves significant improvement on the estimation accuracy and robustness.

Conjugate pairs of distributions over infinite dimensional spaces are prominent in statistical learning theory, particularly due to the widespread adoption of Bayesian nonparametric methodologies for a host of models and applications. Much of the existing literature in the learning community focuses on processes possessing some form of computationally tractable conjugacy as is the case for the beta and gamma processes (and, via normalization, the Dirichlet process). For these processes, proofs of conjugacy and requisite derivation of explicit computational formulae for posterior density parameters are idiosyncratic to the stochastic process in question. As such, Bayesian Nonparametric models are currently available for a limited number of conjugate pairs, e.g. the Dirichlet-multinomial and beta-Bernoulli process pairs. In each of these above cases the likelihood process belongs to the class of discrete exponential family distributions. The exclusion of continuous likelihood distributions from the known cases of Bayesian Nonparametric Conjugate models stands as a disparity in the researcher's toolbox. In this paper we first address the problem of obtaining a general construction of prior distributions over infinite dimensional spaces possessing distributional properties amenable to conjugacy. Second, we bridge the divide between the discrete and continuous likelihoods by illustrating a canonical construction for stochastic processes whose Levy measure densities are from positive exponential families, and then demonstrate that these processes in fact form the prior, likelihood, and posterior in a conjugate family. Our canonical construction subsumes known computational formulae for posterior density parameters in the cases where the likelihood is from a discrete distribution belonging to an exponential family.

The problem of developing binary classifiers from positive and unlabeled data is often encountered in machine learning. A common requirement in this setting is to approximate posterior probabilities of positive and negative classes for a previously unseen data point. This problem can be decomposed into two steps: (i) the development of accurate predictors that discriminate between positive and unlabeled data, and (ii) the accurate estimation of the prior probabilities of positive and negative examples. In this work we primarily focus on the latter subproblem. We study nonparametric class prior estimation and formulate this problem as an estimation of mixing proportions in two-component mixture models, given a sample from one of the components and another sample from the mixture itself. We show that estimation of mixing proportions is generally ill-defined and propose a canonical form to obtain identifiability while maintaining the flexibility to model any distribution. We use insights from this theory to elucidate the optimization surface of the class priors and propose an algorithm for estimating them. To address the problems of high-dimensional density estimation, we provide practical transformations to low-dimensional spaces that preserve class priors. Finally, we demonstrate the efficacy of our method on univariate and multivariate data.