Multilevel hierarchical models provide an attractive framework for incorporating correlations induced in a response variable that is organized hierarchically. Model fitting is challenging, especially for a hierarchy with a large number of nodes. We provide a novel algorithm based on a multi-scale Kalman filter that is both scalable and easy to implement. For Gaussian response, we show our method provides the maximum a-posteriori (MAP) parameter estimates; for non-Gaussian response, parameter estimation is performed through a Laplace approximation. However, the Laplace approximation provides biased parameter estimates that is corrected through a parametric bootstrap procedure. We illustrate through simulation studies and analyses of real world data sets in health care and online advertising.

Bandpass filtering, orientation selectivity, and contrast gain control are prominent features of sensory coding at the level of V1 simple cells. While the effect of bandpass filtering and orientation selectivity can be assessed within a linear model, contrast gain control is an inherently nonlinear computation. Here we employ the class of $L_p$ elliptically contoured distributions to investigate the extent to which the two features---orientation selectivity and contrast gain control---are suited to model the statistics of natural images. Within this framework we find that contrast gain control can play a significant role for the removal of redundancies in natural images. Orientation selectivity, in contrast, has only a very limited potential for redundancy reduction.

Mixture of Gaussian processes models extended a single Gaussian process with ability of modeling multi-modal data and reduction of training complexity. Previous inference algorithms for these models are mostly based on Gibbs sampling, which can be very slow, particularly for large-scale data sets. We present a new generative mixture of experts model. Each expert is still a Gaussian process but is reformulated by a linear model. This breaks the dependency among training outputs and enables us to use a much faster variational Bayesian algorithm for training. Our gating network is more flexible than previous generative approaches as inputs for each expert are modeled by a Gaussian mixture model. The number of experts and number of Gaussian components for an expert are inferred automatically. A variety of tests show the advantages of our method.

Correlations between spike counts are often used to analyze neural coding. The noise is typically assumed to be Gaussian. Yet, this assumption is often inappropriate, especially for low spike counts. In this study, we present copulas as an alternative approach. With copulas it is possible to use arbitrary marginal distributions such as Poisson or negative binomial that are better suited for modeling noise distributions of spike counts. Furthermore, copulas place a wide range of dependence structures at the disposal and can be used to analyze higher order interactions. We develop a framework to analyze spike count data by means of copulas. Methods for parameter inference based on maximum likelihood estimates and for computation of Shannon entropy are provided. We apply the method to our data recorded from macaque prefrontal cortex. The data analysis leads to three significant findings: (1) copula-based distributions provide better fits than discretized multivariate normal distributions; (2) negative binomial margins fit the data better than Poisson margins; and (3) a dependence model that includes only pairwise interactions overestimates the information entropy by at least 19% compared to the model with higher order interactions.

Adaptation of visually guided reaching movements in novel visuomotor environments (e.g.wearing prism goggles) comprises not only motor adaptation but also substantial sensory adaptation, corresponding to shifts in the perceived spatial location of visual and proprioceptive cues. Previous computational modelsof the sensory component of visuomotor adaptation have assumed that it is driven purely by the discrepancy introduced between visual andproprioceptive estimates of hand position and is independent of any motor component of adaptation. We instead propose a unified model in which sensory and motor adaptation are jointly driven by optimal Bayesian estimation of the sensory and motor contributions to perceived errors. Our model is able to account for patterns of performance errors during visuomotor adaptationas well as the subsequent perceptual aftereffects. This unified model also makes the surprising prediction that force field adaptation willelicit similar perceptual shifts, even though there is never any discrepancy between visual and proprioceptive observations. We confirm this prediction with an experiment.

We show how smoother priors can preserve the benefits of these sparse priors while adding stability to the Maximum A-Posteriori (MAP) estimate that makes it more useful for prediction problems. Additionally, we show how to calculate the derivative of the MAP estimate efficiently withimplicit differentiation. One prior that can be differentiated this way is KL-regularization. We demonstrate its effectiveness on a wide variety of applications, andfind that online optimization of the parameters of the KL-regularized model can significantly improve prediction performance.

In this paper we present a novel approach to learn directed acyclic graphs (DAG) and factor models within the same framework while also allowing for model comparison between them. For this purpose, we exploit the connection between factor models and DAGs to propose Bayesian hierarchies based on spike and slab priors to promote sparsity, heavy-tailed priors to ensure identifiability and predictive densities to perform the model comparison. We require identifiability to be able to produce variable orderings leading to valid DAGs and sparsity to learn the structures. The effectiveness of our approach is demonstrated through extensive experiments on artificial and biological data showing that our approach outperform a number of state of the art methods.

Most models of categorization learn categories defined by characteristic features but some categories are described more naturally in terms of relations. We present a generative model that helps to explain how relational categories are learned and used. Our model learns abstract schemata that specify the relational similarities shared by instances of a category, and our emphasis on abstraction departs from previous theoretical proposals that focus instead on comparison of concrete instances. Ourfirst experiment suggests that abstraction can help to explain some of the findings that have previously been used to support comparison-based approaches. Oursecond experiment focuses on one-shot schema learning, a problem that raises challenges for comparison-based approaches but is handled naturally by our abstraction-based account.

In many settings, such as protein interactions and gene regulatory networks, collections ofauthor-recipient email, and social networks, the data consist of pairwise measurements, e.g., presence or absence of links between pairs of objects. Analyzing such data with probabilistic models requires nonstandard assumptions, since the usual independence or exchangeability assumptions no longer hold. In this paper, we introduce a class of latent variable models for pairwise measurements: mixedmembership stochastic blockmodels. Models in this class combine a global model of dense patches of connectivity (blockmodel) with a local model to instantiate node-specific variability in the connections (mixed membership). We develop a general variational inference algorithm for fast approximate posterior inference.We demonstrate the advantages of mixed membership stochastic blockmodel with applications to social networks and protein interaction networks.

We describe probability distributions, dubbed compressible priors, whose independent and identically distributed (iid) realizations result in compressible signals. A signal is compressible when sorted magnitudes of its coefficients exhibit a power-law decay so that the signal can be well-approximated by a sparse signal. Since compressible signals live close to sparse signals, their intrinsic information can be stably embedded via simple non-adaptive linear projections into a much lower dimensional space whose dimension grows logarithmically with the ambient signal dimension. By using order statistics, we show that N-sample iid realizations of generalized Pareto, Student’s t, log-normal, Frechet, and log-logistic distributions are compressible, i.e., they have a constant expected decay rate, which is independent of N. In contrast, we show that generalized Gaussian distribution with shape parameter q is compressible only in restricted cases since the expected decay rate of its N-sample iid realizations decreases with N as 1/[q log(N/q)]. We use compressible priors as a scaffold to build new iterative sparse signal recovery algorithms based on Bayesian inference arguments. We show how tuning of these algorithms explicitly depends on the parameters of the compressible prior of the signal, and how to learn the parameters of the signal’s compressible prior on the fly during recovery.