Bayesian two-sample tests

In this paper, we present two classes of Bayesian approaches to the two-sample problem. Our first class of methods extends the Bayesian t-test to include all parametric models in the exponential family and their conjugate priors. Our second class of methods uses Dirichlet process mixtures (DPM) of such conjugate-exponential distributions as flexible nonparametric priors over the unknown distributions.

Nonparametric Bayesian sparse factor models with application to gene expression modeling

A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data $\mathbf{Y}$ is modeled as a linear superposition, $\mathbf{G}$, of a potentially infinite number of hidden factors, $\mathbf{X}$. The Indian Buffet Process (IBP) is used as a prior on $\mathbf{G}$ to incorporate sparsity and to allow the number of latent features to be inferred. The model's utility for modeling gene expression data is investigated using randomly generated data sets based on a known sparse connectivity matrix for E. Coli, and on three biological data sets of increasing complexity.

Bayesian and L1 Approaches to Sparse Unsupervised Learning

The use of L1 regularisation for sparse learning has generated immense research interest, with successful application in such diverse areas as signal acquisition, image coding, genomics and collaborative filtering. While existing work highlights the many advantages of L1 methods, in this paper we find that L1 regularisation often dramatically underperforms in terms of predictive performance when compared with other methods for inferring sparsity. We focus on unsupervised latent variable models, and develop L1 minimising factor models, Bayesian variants of "L1", and Bayesian models with a stronger L0-like sparsity induced through spike-and-slab distributions. These spike-and-slab Bayesian factor models encourage sparsity while accounting for uncertainty in a principled manner and avoiding unnecessary shrinkage of non-zero values. We demonstrate on a number of data sets that in practice spike-and-slab Bayesian methods outperform L1 minimisation, even on a computational budget. We thus highlight the need to re-assess the wide use of L1 methods in sparsity-reliant applications, particularly when we care about generalising to previously unseen data, and provide an alternative that, over many varying conditions, provides improved generalisation performance.

Pitman-Yor Diffusion Trees

We introduce the Pitman Yor Diffusion Tree (PYDT) for hierarchical clustering, a generalization of the Dirichlet Diffusion Tree (Neal, 2001) which removes the restriction to binary branching structure. The generative process is described and shown to result in an exchangeable distribution over data points. We prove some theoretical properties of the model and then present two inference methods: a collapsed MCMC sampler which allows us to model uncertainty over tree structures, and a computationally efficient greedy Bayesian EM search algorithm. Both algorithms use message passing on the tree structure. The utility of the model and algorithms is demonstrated on synthetic and real world data, both continuous and binary.

Bayesian approach to signal modelling

In this paper, an introduction to Bayesian methods in signal processing will be given. The paper starts by considering the important issues of model selection and parameter estimation and derives analytic expressions for the model probabilities of two simple models. The idea of marginal estimation of certain model parameter is then introduced and expressions are derived for the marginal probability densities for frequencies in white Gaussian noise and a Bayesian approach to general changepoint analysis is given. Numerical integration methods are introduced based on Markov chain Monte Carlo techniques and the Gibbs sampler in particular.

The Bayesian Approach to Signal Modelling

In this paper, an introduction to Bayesian methods in signal processing will be given. The paper starts by considering the important issues of model selection and parameter estimation and derives analytic expressions for the model probabilities of two simple models. The idea of marginal estimation of certain model parameter is then introduced and expressions are derived for the marginal probabilitiy densities for frequencies in white Gaussian noise and a Bayesian approach to general changepoint analysis is given. Numerical integration methods are introduced based on Markov chain Monte Carlo techniques and the Gibbs sampler in particular.