The International Monitoring System (IMS) is a global network of sensors whose purpose is to identify potential violations of the Comprehensive Nuclear-Test-Ban Treaty (CTBT), primarily through detection and localization of seismic events. We report on the first stage of a project to improve on the current automated software system with a Bayesian inference system that computes the most likely global event history given the record of local sensor data. The new system, VISA (Vertically Integrated Seismological Analysis), is based on empirically calibrated, generative models of event occurrence, signal propagation, and signal detection. VISA exhibits significantly improved precision and recall compared to the current operational system and is able to detect events that are missed even by the human analysts who post-process the IMS output.

Computing a {\em maximum a posteriori} (MAP) assignment in graphical models is a crucial inference problem for many practical applications. Several provably convergent approaches have been successfully developed using linear programming (LP) relaxation of the MAP problem. We present an alternative approach, which transforms the MAP problem into that of inference in a finite mixture of simple Bayes nets. We then derive the Expectation Maximization (EM) algorithm for this mixture that also monotonically increases a lower bound on the MAP assignment until convergence. The update equations for the EM algorithm are remarkably simple, both conceptually and computationally, and can be implemented using a graph-based message passing paradigm similar to max-product computation. We experiment on the real-world protein design dataset and show that EM's convergence rate is significantly higher than the previous LP relaxation based approach MPLP. EM achieves a solution quality within $95$\% of optimal for most instances and is often an order-of-magnitude faster than MPLP.

The Gaussian process (GP) is a popular way to specify dependencies between random variables in a probabilistic model. In the Bayesian framework the covariance structure can be specified using unknown hyperparameters. Integrating over these hyperparameters considers different possible explanations for the data when making predictions. This integration is often performed using Markov chain Monte Carlo (MCMC) sampling. However, with non-Gaussian observations standard hyperparameter sampling approaches require careful tuning and may converge slowly. In this paper we present a slice sampling approach that requires little tuning while mixing well in both strong- and weak-data regimes.

In this paper, we propose a matrix-variate normal penalty with sparse inverse covariances to couple multiple tasks. Learning multiple (parametric) models can be viewed as estimating a matrix of parameters, where rows and columns of the matrix correspond to tasks and features, respectively. Following the matrix-variate normal density, we design a penalty that decomposes the full covariance of matrix elements into the Kronecker product of row covariance and column covariance, which characterizes both task relatedness and feature representation. Several recently proposed methods are variants of the special cases of this formulation. To address the overfitting issue and select meaningful task and feature structures, we include sparse covariance selection into our matrix-normal regularization via L-1 penalties on task and feature inverse covariances. We empirically study the proposed method and compare with related models in two real-world problems: detecting landmines in multiple fields and recognizing faces between different subjects. Experimental results show that the proposed framework provides an effective and flexible way to model various different structures of multiple tasks.

Games of incomplete information, or Bayesian games, are an important game-theoretic model and have many applications in economics. We propose Bayesian action-graph games (BAGGs), a novel graphical representation for Bayesian games. BAGGs can represent arbitrary Bayesian games, and furthermore can compactly express Bayesian games exhibiting commonly encountered types of structure including symmetry, action- and type-specific utility independence, and probabilistic independence of type distributions. We provide an algorithm for computing expected utility in BAGGs, and discuss conditions under which the algorithm runs in polynomial time. Bayes-Nash equilibria of BAGGs can be computed by adapting existing algorithms for complete-information normal form games and leveraging our expected utility algorithm. We show both theoretically and empirically that our approaches improve significantly on the state of the art.

Applications of Brain-Machine-Interfaces typically estimate user intent based on biological signals that are under voluntary control. For example, we might want to estimate how a patient with a paralyzed arm wants to move based on residual muscle activity. To solve such problems it is necessary to integrate obtained information over time. To do so, state of the art approaches typically use a probabilistic model of how the state, e.g. position and velocity of the arm, evolves over time – a so-called trajectory model. We wanted to further develop this approach using two intuitive insights: (1) At any given point of time there may be a small set of likely movement targets, potentially identified by the location of objects in the workspace or by gaze information from the user. (2) The user may want to produce movements at varying speeds. We thus use a generative model with a trajectory model incorporating these insights. Approximate inference on that generative model is implemented using a mixture of extended Kalman filters. We find that the resulting algorithm allows us to decode arm movements dramatically better than when we use a trajectory model with linear dynamics.

Bayesian methods of matrix factorization (MF) have been actively explored recently as promising alternatives to classical singular value decomposition. In this paper, we show that, despite the fact that the optimization problem is non-convex, the global optimal solution of variational Bayesian (VB) MF can be computed analytically by solving a quartic equation. This is highly advantageous over a popular VBMF algorithm based on iterated conditional modes since it can only find a local optimal solution after iterations. We further show that the global optimal solution of empirical VBMF (hyperparameters are also learned from data) can also be analytically computed. We illustrate the usefulness of our results through experiments.

We define a copula process which describes the dependencies between arbitrarily many random variables independently of their marginal distributions. As an example, we develop a stochastic volatility model, Gaussian Copula Process Volatility (GCPV), to predict the latent standard deviations of a sequence of random variables. To make predictions we use Bayesian inference, with the Laplace approximation, and with Markov chain Monte Carlo as an alternative. We find our model can outperform GARCH on simulated and financial data. And unlike GARCH, GCPV can easily handle missing data, incorporate covariates other than time, and model a rich class of covariance structures.

Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of unbounded width and depth, where data can live at any node and are infinitely exchangeable. One can view our model as providing infinite mixtures where the components have a dependency structure corresponding to an evolutionary diffusion down a tree. By using a stick-breaking approach, we can apply Markov chain Monte Carlo methods based on slice sampling to perform Bayesian inference and simulate from the posterior distribution on trees. We apply our method to hierarchical clustering of images and topic modeling of text data.

To understand the relationship between genomic variations among population and complex diseases, it is essential to detect eQTLs which are associated with phenotypic effects.However, detecting eQTLs remains a challenge due to complex underlying mechanisms and the very large number of genetic loci involved compared tothe number of samples. Thus, to address the problem, it is desirable to take advantage of the structure of the data and prior information about genomic locations such as conservation scores and transcription factor binding sites. In this paper, we propose a novel regularized regression approach for detecting eQTLs which takes into account related traits simultaneously while incorporating many regulatory features. We first present a Bayesian network for a multi-task learning problem that includes priors on SNPs, making it possible to estimate the significance of each covariate adaptively. Then we find the maximum a posteriori (MAP) estimation of regression coefficients and estimate weights of covariates jointly. This optimization procedure is efficient since it can be achieved by using aprojected gradient descent and a coordinate descent procedure iteratively. Experimental results on simulated and real yeast datasets confirm that our model outperforms previous methods for finding eQTLs.