The ill-posed nature of the MEG/EEG source localization problem requires the incorporation of prior assumptions when choosing an appropriate solution out of an infinite set of candidates. Bayesian methods are useful in this capacity because they allow these assumptions to be explicitly quantified. Recently, a number of empirical Bayesian approaches have been proposed that attempt a form of model selection by using the data to guide the search for an appropriate prior. While seemingly quite different in many respects, we apply a unifying framework based on automatic relevance determination (ARD) that elucidates various attributes of these methods and suggests directions for improvement. We also derive theoretical properties of this methodology related to convergence, local minima, and localization bias and explore connections with established algorithms.

We focus on the problem of estimating the graph structure associated with a discrete Markov random field.

Computational gene prediction using generative models has reached a plateau, with several groups converging to a generalized hidden Markov model (GHMM) incorporating phylogenetic models of nucleotide sequence evolution. Further improvements in gene calling accuracy are likely to come through new methods that incorporate additional data, both comparative and species specific. Conditional Random Fields (CRFs), which directly model the conditional probability P (y x) of a vector of hidden states conditioned on a set of observations, provide a unified framework for combining probabilistic and non-probabilistic information and have been shown to outperform HMMs on sequence labeling tasks in natural language processing. We describe the use of CRFs for comparative gene prediction. We implement a model that encapsulates both a phylogenetic-GHMM (our baseline comparative model) and additional non-probabilistic features. We tested our model on the genome sequence of the fungal human pathogen Cryptococcus neoformans.

We introduce a class of MPDs which greatly simplify Reinforcement Learning. They have discrete state spaces and continuous control spaces. The controls have the effect of rescaling the transition probabilities of an underlying Markov chain. A control cost penalizing KL divergence between controlled and uncontrolled transition probabilities makes the minimization problem convex, and allows analytical computation of the optimal controls given the optimal value function. An exponential transformation of the optimal value function makes the minimized Bellman equation linear.

Latent Dirichlet allocation (LDA) is a Bayesian network that has recently gained much popularity in applications ranging from document modeling to computer vision. Due to the large scale nature of these applications, current inference procedures like variational Bayes and Gibbs sampling have been found lacking. In this paper we propose the collapsed variational Bayesian inference algorithm for LDA, and show that it is computationally efficient, easy to implement and significantly more accurate than standard variational Bayesian inference for LDA.

We propose a nonlinear generative model for human motion data that uses an undirected model with binary latent variables and real-valued "visible" variables that represent joint angles. The latent and visible variables at each time step receive directed connections from the visible variables at the last few time-steps. Such an architecture makes online inference efficient and allows us to use a simple approximate learning procedure. After training, the model finds a single set of parameters that simultaneously capture several different kinds of motion. We demonstrate the power of our approach by synthesizing various motion sequences and by performing online filling in of data lost during motion capture.

In supervised learning there is a typical presumption that the training and test points are taken from the same distribution. In practice this assumption is commonly violated. The situations where the training and test data are from different distributions is called covariate shift. Recent work has examined techniques for dealing with covariate shift in terms of minimisation of generalisation error. As yet the literature lacks a Bayesian generative perspective on this problem. This paper tackles this issue for regression models. Recent work on covariate shift can be understood in terms of mixture regression. Using this view, we obtain a general approach to regression under covariate shift, which reproduces previous work as a special case. The main advantages of this new formulation over previous models for covariate shift are that we no longer need to presume the test and training densities are known, the regression and density estimation are combined into a single procedure, and previous methods are reproduced as special cases of this procedure, shedding light on the implicit assumptions the methods are making.

We present a new statistical framework called hidden Markov Dirichlet process (HMDP) to jointly model the genetic recombinations among possibly infinite number of founders and the coalescence-with-mutation events in the resulting genealogies. The HMDP posits that a haplotype of genetic markers is generated by a sequence of recombination events that select an ancestor for each locus from an unbounded set of founders according to a 1st-order Markov transition process. Conjoining this process with a mutation model, our method accommodates both between-lineage recombination and within-lineage sequence variations, and leads to a compact and natural interpretation of the population structure and inheritance process underlying haplotype data. We have developed an efficient sampling algorithm for HMDP based on a two-level nested Pólya urn scheme. On both simulated and real SNP haplotype data, our method performs competitively or significantly better than extant methods in uncovering the recombination hotspots along chromosomal loci; and in addition it also infers the ancestral genetic patterns and offers a highly accurate map of ancestral compositions of modern populations.

Starting with the work of Jaakkola and Haussler, a variety of approaches have been proposed for coupling domain-specific generative models with statistical learning methods. The link is established by a kernel function which provides a similarity measure based inherently on the underlying model. In computational biology, the full promise of this framework has rarely ever been exploited, as most kernels are derived from very generic models, such as sequence profiles or hidden Markov models. Here, we introduce the MTreeMix kernel, which is based on a generative model tailored to the underlying biological mechanism.

Perceptual Bistability refers to the phenomenon of spontaneously switching between two or more interpretations of an image under continuous viewing. Although switching behavior is increasingly well characterized, the origins remain elusive. We propose that perceptual switching naturally arises from the brain's search for best interpretations while performing Bayesian inference. In particular, we propose that the brain explores a posterior distribution over image interpretations at a rapid time scale via a sampling-like process and updates its interpretation when a sampled interpretation is better than the discounted value of its current interpretation. We formalize the theory, explicitly derive switching rate distributions and discuss qualitative properties of the theory including the effect of changes in the posterior distribution on switching rates. Finally, predictions of the theory are shown to be consistent with measured changes in human switching dynamics to Necker cube stimuli induced by context.