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.

For over half a century, psychologists have been struck by how poor people are at expressing their internal sensations, impressions, and evaluations via rating scales. When individuals make judgments, they are incapable of using an absolute rating scale, and instead rely on reference points from recent experience. This relativity of judgment limits the usefulness of responses provided by individuals to surveys, questionnaires, and evaluation forms. Fortunately, the cognitive processes that transform internal states to responses are not simply noisy, but rather are influenced by recent experience in a lawful manner. We explore techniques to remove sequential dependencies, and thereby decontaminate a series of ratings to obtain more meaningful human judgments. In our formulation, decontamination is fundamentally a problem of inferring latent states (internal sensations) which, because of the relativity of judgment, have temporal dependencies. We propose a decontamination solution using a conditional random field with constraints motivated by psychological theories of relative judgment. Our exploration of decontamination models is supported by two experiments we conducted to obtain ground-truth rating data on a simple length estimation task. Our decontamination techniques yield an over 20% reduction in the error of human judgments.

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.

Spontaneous brain activity, as observed in functional neuroimaging, has been shown to display reproducible structure that expresses brain architecture and carries markers of brain pathologies. An important view of modern neuroscience is that such large-scale structure of coherent activity reflects modularity properties of brain connectivity graphs. However, to date, there has been no demonstration that the limited and noisy data available in spontaneous activity observations could be used to learn full-brain probabilistic models that generalize to new data. Learning such models entails two main challenges: i) modeling full brain connectivity is a difficult estimation problem that faces the curse of dimensionality and ii) variability between subjects, coupled with the variability of functional signals between experimental runs, makes the use of multiple datasets challenging. We describe subject-level brain functional connectivity structure as a multivariate Gaussian process and introduce a new strategy to estimate it from group data, by imposing a common structure on the graphical model in the population. We show that individual models learned from functional Magnetic Resonance Imaging (fMRI) data using this population prior generalize better to unseen data than models based on alternative regularization schemes. To our knowledge, this is the first report of a cross-validated model of spontaneous brain activity. Finally, we use the estimated graphical model to explore the large-scale characteristics of functional architecture and show for the first time that known cognitive networks appear as the integrated communities of functional connectivity graph.

Many time-series such as human movement data consist of a sequence of basic actions, e.g., forehands and backhands in tennis. Automatically extracting and characterizing such actions is an important problem for a variety of different applications. In this paper, we present a probabilistic segmentation approach in which an observed time-series is modeled as a concatenation of segments corresponding to different basic actions. Each segment is generated through a noisy transformation of one of a few hidden trajectories representing different types of movement, with possible time re-scaling. We analyze three different approximation methods for dealing with model intractability, and demonstrate how the proposed approach can successfully segment table tennis movements recorded using a robot arm as haptic input device.

Recent studies compare gene expression data across species to identify core and species specific genes in biological systems. To perform such comparisons researchers need to match genes across species. This is a challenging task since the correct matches (orthologs) are not known for most genes. Previous work in this area used deterministic matchings or reduced multidimensional expression data to binary representation. Here we develop a new method that can utilize soft matches (given as priors) to infer both, unique and similar expression patterns across species and a matching for the genes in both species. Our method uses a Dirichlet process mixture model which includes a latent data matching variable. We present learning and inference algorithms based on variational methods for this model. Applying our method to immune response data we show that it can accurately identify common and unique response patterns by improving the matchings between human and mouse genes.

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.

This paper is concerned with rank aggregation, which aims to combine multiple input rankings to get a better ranking. A popular approach to rank aggregation is based on probabilistic models on permutations, e.g., the Luce model and the Mallows model. However, these models have their limitations in either poor expressiveness or high computational complexity. To avoid these limitations, in this paper, we propose a new model, which is defined with a coset-permutation distance, and models the generation of a permutation as a stagewise process. We refer to the new model as coset-permutation distance based stagewise (CPS) model. The CPS model has rich expressiveness and can therefore be used in versatile applications, because many different permutation distances can be used to induce the coset-permutation distance. The complexity of the CPS model is low because of the stagewise decomposition of the permutation probability and the efficient computation of most coset-permutation distances. We apply the CPS model to supervised rank aggregation, derive the learning and inference algorithms, and empirically study their effectiveness and efficiency. Experiments on public datasets show that the derived algorithms based on the CPS model can achieve state-of-the-art ranking accuracy, and are much more efficient than previous algorithms.