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.

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.

We present a technique for exact simulation of Gaussian Markov random fields (GMRFs), which can be interpreted as locally injecting noise to each Gaussian factor independently, followed by computing the mean/mode of the perturbed GMRF. Coupled with standard iterative techniques for the solution of symmetric positive definite systems, this yields a very efficient sampling algorithm with essentially linear complexity in terms of speed and memory requirements, well suited to extremely large scale probabilistic models. Apart from synthesizing data under a Gaussian model, the proposed technique directly leads to an efficient unbiased estimator of marginal variances. Beyond Gaussian models, the proposed algorithm is also very useful for handling highly non-Gaussian continuously-valued MRFs such as those arising in statistical image modeling or in the first layer of deep belief networks describing real-valued data, where the non-quadratic potentials coupling different sites can be represented as finite or infinite mixtures of Gaussians with the help of local or distributed latent mixture assignment variables. The Bayesian treatment of such models most naturally involves a block Gibbs sampler which alternately draws samples of the conditionally independent latent mixture assignments and the conditionally multivariate Gaussian continuous vector and we show that it can directly benefit from the proposed methods.

Functional magnetic resonance imaging (fMRI) can be applied to study the functional connectivity of the neural elements which form complex network at a whole brain level. Most analyses of functional resting state networks (RSN) have been based on the analysis of correlation between the temporal dynamics of various regions of the brain. While these models can identify coherently behaving groups in terms of correlation they give little insight into how these groups interact. In this paper we take a different view on the analysis of functional resting state networks. Starting from the definition of resting state as functional coherent groups we search for functional units of the brain that communicate with other parts of the brain in a coherent manner as measured by mutual information. We use the infinite relational model (IRM) to quantify functional coherent groups of resting state networks and demonstrate how the extracted component interactions can be used to discriminate between functional resting state activity in multiple sclerosis and normal subjects.

We introduce a new Bayesian nonparametric approach to identification of sparse dynamic linear systems. The impulse responses are modeled as Gaussian processes whose autocovariances encode the BIBO stability constraint, as defined by the recently introduced “Stable Spline kernel”. Sparse solutions are obtained by placing exponential hyperpriors on the scale factors of such kernels. Numerical experiments regarding estimation of ARMAX models show that this technique provides a definite advantage over a group LAR algorithm and state-of-the-art parametric identification techniques based on prediction error minimization.

Arithmetic circuits (ACs) exploit context-specific independence and determinism to allow exact inference even in networks with high treewidth. In this paper, we introduce the first ever approximate inference methods using ACs, for domains where exact inference remains intractable. We propose and evaluate a variety of techniques based on exact compilation, forward sampling, AC structure learning, Markov network parameter learning, variational inference, and Gibbs sampling. In experiments on eight challenging real-world domains, we find that the methods based on sampling and learning work best: one such method (AC2-F) is faster and usually more accurate than loopy belief propagation, mean field, and Gibbs sampling; another (AC2-G) has a running time similar to Gibbs sampling but is consistently more accurate than all baselines.

When software developers modify one or more files in a large code base, they must also identify and update other related files. Many file dependencies can be detected by mining the development history of the code base: in essence, groups of related files are revealed by the logs of previous workflows. From data of this form, we show how to detect dependent files by solving a problem in binary matrix completion. We explore different latent variable models (LVMs) for this problem, including Bernoulli mixture models, exponential family PCA, restricted Boltzmann machines, and fully Bayesian approaches. We evaluate these models on the development histories of three large, open-source software systems: Mozilla Firefox, Eclipse Subversive, and Gimp. In all of these applications, we find that LVMs improve the performance of related file prediction over current leading methods.

A method for computing the rarity of latent fingerprints represented by minutiae is given. It allows determining the probability of finding a match for an evidence print in a database of n known prints. The probability of random correspondence between evidence and database is determined in three procedural steps. In the registration step the latent print is aligned by finding its core point; which is done using a procedure based on a machine learning approach based on Gaussian processes. In the evidence probability evaluation step a generative model based on Bayesian networks is used to determine the probability of the evidence; it takes into account both the dependency of each minutia on nearby minutiae and the confidence of their presence in the evidence. In the specific probability of random correspondence step the evidence probability is used to determine the probability of match among n for a given tolerance; the last evaluation is similar to the birthday correspondence probability for a specific birthday. The generative model is validated using a goodness-of-fit test evaluated with a standard database of fingerprints. The probability of random correspondence for several latent fingerprints are evaluated for varying numbers of minutiae.

Layered models are a powerful way of describing natural scenes containing smooth surfaces that may overlap and occlude each other. For image motion estimation, such models have a long history but have not achieved the wide use or accuracy of non-layered methods. We present a new probabilistic model of optical flow in layers that addresses many of the shortcomings of previous approaches. In particular, we define a probabilistic graphical model that explicitly captures: 1) occlusions and disocclusions; 2) depth ordering of the layers; 3) temporal consistency of the layer segmentation. Additionally the optical flow in each layer is modeled by a combination of a parametric model and a smooth deviation based on an MRF with a robust spatial prior; the resulting model allows roughness in layers. Finally, a key contribution is the formulation of the layers using an image-dependent hidden field prior based on recent models for static scene segmentation. The method achieves state-of-the-art results on the Middlebury benchmark and produces meaningful scene segmentations as well as detected occlusion regions.