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.

Correlation between instances is often modelled via a kernel function using input attributes of the instances. Relational knowledge can further reveal additional pairwise correlations between variables of interest. In this paper, we develop a class of models which incorporates both reciprocal relational information and input attributes using Gaussian process techniques. This approach provides a novel nonparametric Bayesian framework with a data-dependent covariance function for supervised learning tasks. We also apply this framework to semi-supervised learning. Experimental results on several real world data sets verify the usefulness of this algorithm.

By adopting Gaussian process priors a fully Bayesian solution to the problem of integrating possibly heterogeneous data sets within a classification setting is presented. Approximate inference schemes employing Variational & Expectation Propagation based methods are developed and rigorously assessed. We demonstrate our approach to integrating multiple data sets on a large scale protein fold prediction problem where we infer the optimal combinations of covariance functions and achieve state-of-the-art performance without resorting to any ad hoc parameter tuning and classifier combination.

This paper proposes a new approach to model-based clustering under prior knowledge. The proposed formulation can be interpreted from two different angles: as penalized logistic regression, where the class labels are only indirectly observed (via the probability density of each class); as finite mixture learning under a grouping prior. To estimate the parameters of the proposed model, we derive a (generalized) EM algorithm with a closed-form E-step, in contrast with other recent approaches to semi-supervised probabilistic clustering which require Gibbs sampling or suboptimal shortcuts. We show that our approach is ideally suited for image segmentation: it avoids the combinatorial nature Markov random field priors, and opens the door to more sophisticated spatial priors (e.g., wavelet-based) in a simple and computationally efficient way. Finally, we extend our formulation to work in unsupervised, semi-supervised, or discriminative modes.

Data sets that characterize human activity over time through collections of timestamped events or counts are of increasing interest in application areas as humancomputer interaction, video surveillance, and Web data analysis. We propose a nonparametric Bayesian framework for modeling collections of such data. In particular, we use a Dirichlet process framework for learning a set of intensity functions corresponding to different categories, which form a basis set for representing individual time-periods (e.g., several days) depending on which categories the time-periods are assigned to. This allows the model to learn in a data-driven fashion what "factors" are generating the observations on a particular day, including (for example) weekday versus weekend effects or day-specific effects corresponding to unique (single-day) occurrences of unusual behavior, sharing information where appropriate to obtain improved estimates of the behavior associated with each category. Applications to real-world data sets of count data involving both vehicles and people are used to illustrate the technique.

Scoring structures of undirected graphical models by means of evaluating the marginal likelihood is very hard. The main reason is the presence of the partition function which is intractable to evaluate, let alone integrate over. We propose to approximate the marginal likelihood by employing two levels of approximation: we assume normality of the posterior (the Laplace approximation) and approximate all remaining intractable quantities using belief propagation and the linear response approximation.

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

We present a generalization of dynamic Bayesian networks to concisely describe complex probability distributions such as in problems with multiple interacting variable-length streams of random variables. Our framework incorporates recent graphical model constructs to account for existence uncertainty, value-specific independence, aggregation relationships, and local and global constraints, while still retaining a Bayesian network interpretation and efficient inference and learning techniques. We introduce one such general technique, which is an extension of Value Elimination, a backtracking search inference algorithm. Multi-dynamic Bayesian networks are motivated by our work on Statistical Machine Translation (MT). We present results on MT word alignment in support of our claim that MDBNs are a promising framework for the rapid prototyping of new MT systems.

We study a setting that is motivated by the problem of filtering spam messages for many users. Each user receives messages according to an individual, unknown distribution, reflected only in the unlabeled inbox. The spam filter for a user is required to perform well with respect to this distribution. Labeled messages from publicly available sources can be utilized, but they are governed by a distinct distribution, not adequately representing most inboxes. We devise a method that minimizes a loss function with respect to a user's personal distribution based on the available biased sample. A nonparametric hierarchical Bayesian model furthermore generalizes across users by learning a common prior which is imposed on new email accounts. Empirically, we observe that bias-corrected learning outperforms naive reliance on the assumption of independent and identically distributed data; Dirichlet-enhanced generalization across users outperforms a single ("one size fits all") filter as well as independent filters for all users.