Suppose that a graph is realized from a stochastic block model where one of the blocks is of interest, but many or all of the vertices' block labels are unobserved. The task is to order the vertices with unobserved block labels into a ``nomination list'' such that, with high probability, vertices from the interesting block are concentrated near the list's beginning. We propose several vertex nomination schemes. Our basic - but principled - setting and development yields a best nomination scheme (which is a Bayes-Optimal analogue), and also a likelihood maximization nomination scheme that is practical to implement when there are a thousand vertices, and which is empirically near-optimal when the number of vertices is small enough to allow comparison to the best nomination scheme. We then illustrate the robustness of the likelihood maximization nomination scheme to the modeling challenges inherent in real data, using examples which include a social network involving human trafficking, the Enron Graph, a worm brain connectome and a political blog network.

Capacity control, the bias/variance dilemma, and learning unknown functions from data, are all concerned with identifying effective and consistent fits of unknown geometric loci to random data points. A geometric locus is a curve or surface formed by points, all of which possess some uniform property. A geometric locus of an algebraic equation is the set of points whose coordinates are solutions of the equation. Any given curve or surface must pass through each point on a specified locus. This paper argues that it is impossible to fit random data points to algebraic equations of partially configured geometric loci that reference arbitrary Cartesian coordinate systems. It also argues that the fundamental curve of a linear decision boundary is actually a principal eigenaxis. It is shown that learning principal eigenaxes of linear decision boundaries involves finding a point of statistical equilibrium for which eigenenergies of principal eigenaxis components are symmetrically balanced with each other. It is demonstrated that learning linear decision boundaries involves strong duality relationships between a statistical eigenlocus of principal eigenaxis components and its algebraic forms, in primal and dual, correlated Hilbert spaces. Locus equations are introduced and developed that describe principal eigen-coordinate systems for lines, planes, and hyperplanes. These equations are used to introduce and develop primal and dual statistical eigenlocus equations of principal eigenaxes of linear decision boundaries. Important generalizations for linear decision boundaries are shown to be encoded within a dual statistical eigenlocus of principal eigenaxis components. Principal eigenaxes of linear decision boundaries are shown to encode Bayes' likelihood ratio for common covariance data and a robust likelihood ratio for all other data.

We present a convex approach to probabilistic segmentation and modeling of time series data. Our approach builds upon recent advances in multivariate total variation regularization, and seeks to learn a separate set of parameters for the distribution over the observations at each time point, but with an additional penalty that encourages the parameters to remain constant over time. We propose efficient optimization methods for solving the resulting (large) optimization problems, and a two-stage procedure for estimating recurring clusters under such models, based upon kernel density estimation. Finally, we show on a number of real-world segmentation tasks, the resulting methods often perform as well or better than existing latent variable models, while being substantially easier to train.

In dynamic topic modeling, the proportional contribution of a topic to a document depends on the temporal dynamics of that topic's overall prevalence in the corpus. We extend the Dynamic Topic Model of Blei and Lafferty (2006) by explicitly modeling document level topic proportions with covariates and dynamic structure that includes polynomial trends and periodicity. A Markov Chain Monte Carlo (MCMC) algorithm that utilizes Polya-Gamma data augmentation is developed for posterior inference. Conditional independencies in the model and sampling are made explicit, and our MCMC algorithm is parallelized where possible to allow for inference in large corpora. To address computational bottlenecks associated with Polya-Gamma sampling, we appeal to the Central Limit Theorem to develop a Gaussian approximation to the Polya-Gamma random variable. This approximation is fast and reliable for parameter values relevant in the text mining domain. Our model and inference algorithm are validated with multiple simulation examples, and we consider the application of modeling trends in PubMed abstracts. We demonstrate that sharing information across documents is critical for accurately estimating document-specific topic proportions. We also show that explicitly modeling polynomial and periodic behavior improves our ability to predict topic prevalence at future time points.

Latent factor models are the canonical statistical tool for exploratory analyses of low-dimensional linear structure for an observation matrix with p features across n samples. We develop a structured Bayesian group factor analysis model that extends the factor model to multiple coupled observation matrices; in the case of two observations, this reduces to a Bayesian model of canonical correlation analysis. The main contribution of this work is to carefully define a structured Bayesian prior that encourages both element-wise and column-wise shrinkage and leads to desirable behavior on high-dimensional data. In particular, our model puts a structured prior on the joint factor loading matrix, regularizing at three levels, which enables element-wise sparsity and unsupervised recovery of latent factors corresponding to structured variance across arbitrary subsets of the observations. In addition, our structured prior allows for both dense and sparse latent factors so that covariation among either all features or only a subset of features can both be recovered. We use fast parameter-expanded expectation-maximization for parameter estimation in this model. We validate our method on both simulated data with substantial structure and real data, comparing against a number of state-of-the-art approaches. These results illustrate useful properties of our model, including i) recovering sparse signal in the presence of dense effects; ii) the ability to scale naturally to large numbers of observations; iii) flexible observation- and factor-specific regularization to recover factors with a wide variety of sparsity levels and percentage of variance explained; and iv) tractable inference that scales to modern genomic and document data sizes.

We present a semi-supervised learning algorithm for learning discrete factor analysis models with arbitrary structure on the latent variables. Our algorithm assumes that every latent variable has an "anchor", an observed variable with only that latent variable as its parent. Given such anchors, we show that it is possible to consistently recover moments of the latent variables and use these moments to learn complete models. We also introduce a new technique for improving the robustness of method-of-moment algorithms by optimizing over the marginal polytope or its relaxations. We evaluate our algorithm using two real-world tasks, tag prediction on questions from the Stack Overflow website and medical diagnosis in an emergency department.

One approach for constructing copula functions is by multiplication. Given that products of cumulative distribution functions (CDFs) are also CDFs, an adjustment to this multiplication will result in a copula model, as discussed by Liebscher (J Mult Analysis, 2008). Parameterizing models via products of CDFs has some advantages, both from the copula perspective (e.g., it is well-defined for any dimensionality) and from general multivariate analysis (e.g., it provides models where small dimensional marginal distributions can be easily read-off from the parameters). Independently, Huang and Frey (J Mach Learn Res, 2011) showed the connection between certain sparse graphical models and products of CDFs, as well as message-passing (dynamic programming) schemes for computing the likelihood function of such models. Such schemes allows models to be estimated with likelihood-based methods. We discuss and demonstrate MCMC approaches for estimating such models in a Bayesian context, their application in copula modeling, and how message-passing can be strongly simplified. Importantly, our view of message-passing opens up possibilities to scaling up such methods, given that even dynamic programming is not a scalable solution for calculating likelihood functions in many models.

This paper is devoted to the bipartite ranking problem, a classical statistical learning task, in a high dimensional setting. We propose a scoring and ranking strategy based on the PAC-Bayesian approach. We consider nonlinear additive scoring functions, and we derive non-asymptotic risk bounds under a sparsity assumption. In particular, oracle inequalities in probability holding under a margin condition assess the performance of our procedure, and prove its minimax optimality. An MCMC-flavored algorithm is proposed to implement our method, along with its behavior on synthetic and real-life datasets.

Computing the marginal likelihood (ML) of a model requires marginalizing out all of the parameters and latent variables, a difficult high-dimensional summation or integration problem. To make matters worse, it is often hard to measure the accuracy of one's ML estimates. We present bidirectional Monte Carlo, a technique for obtaining accurate log-ML estimates on data simulated from a model. This method obtains stochastic lower bounds on the log-ML using annealed importance sampling or sequential Monte Carlo, and obtains stochastic upper bounds by running these same algorithms in reverse starting from an exact posterior sample. The true value can be sandwiched between these two stochastic bounds with high probability. Using the ground truth log-ML estimates obtained from our method, we quantitatively evaluate a wide variety of existing ML estimators on several latent variable models: clustering, a low rank approximation, and a binary attributes model. These experiments yield insights into how to accurately estimate marginal likelihoods.

We consider the problem of Bayesian parameter estimation for deep neural networks, which is important in problem settings where we may have little data, and/ or where we need accurate posterior predictive densities, e.g., for applications involving bandits or active learning. One simple approach to this is to use online Monte Carlo methods, such as SGLD (stochastic gradient Langevin dynamics). Unfortunately, such a method needs to store many copies of the parameters (which wastes memory), and needs to make predictions using many versions of the model (which wastes time). We describe a method for "distilling" a Monte Carlo approximation to the posterior predictive density into a more compact form, namely a single deep neural network. We compare to two very recent approaches to Bayesian neural networks, namely an approach based on expectation propagation [Hernandez-Lobato and Adams, 2015] and an approach based on variational Bayes [Blundell et al., 2015]. Our method performs better than both of these, is much simpler to implement, and uses less computation at test time.