Sequential Bayesian inference for implicit hidden Markov models and current limitations

Hidden Markov models can describe time series arising in various fields of science, by treating the data as noisy measurements of an arbitrarily complex Markov process. Sequential Monte Carlo (SMC) methods have become standard tools to estimate the hidden Markov process given the observations and a fixed parameter value. We review some of the recent developments allowing the inclusion of parameter uncertainty as well as model uncertainty. The shortcomings of the currently available methodology are emphasised from an algorithmic complexity perspective. The statistical objects of interest for time series analysis are illustrated on a toy "Lotka-Volterra" model used in population ecology. Some open challenges are discussed regarding the scalability of the reviewed methodology to longer time series, higher-dimensional state spaces and more flexible models.Comment: Review article written for ESAIM: proceedings and surveys. 25 pages, 10 figure

Free energy Sequential Monte Carlo, application to mixture modelling

We introduce a new class of Sequential Monte Carlo (SMC) methods, which we call free energy SMC. This class is inspired by free energy methods, which originate from Physics, and where one samples from a biased distribution such that a given function $\xi(\theta)$ of the state $\theta$ is forced to be uniformly distributed over a given interval. From an initial sequence of distributions $(\pi_t)$ of interest, and a particular choice of $\xi(\theta)$, a free energy SMC sampler computes sequentially a sequence of biased distributions $(\tilde{\pi}_{t})$ with the following properties: (a) the marginal distribution of $\xi(\theta)$ with respect to $\tilde{\pi}_{t}$ is approximatively uniform over a specified interval, and (b) $\tilde{\pi}_{t}$ and $\pi_{t}$ have the same conditional distribution with respect to $\xi$. We apply our methodology to mixture posterior distributions, which are highly multimodal. In the mixture context, forcing certain hyper-parameters to higher values greatly faciliates mode swapping, and makes it possible to recover a symetric output. We illustrate our approach with univariate and bivariate Gaussian mixtures and two real-world datasets.Comment: presented at "Bayesian Statistics 9" (Valencia meetings, 4-8 June 2010, Benidorm

Gains in Power from Structured Two-Sample Tests of Means on Graphs

We consider multivariate two-sample tests of means, where the location shift between the two populations is expected to be related to a known graph structure. An important application of such tests is the detection of differentially expressed genes between two patient populations, as shifts in expression levels are expected to be coherent with the structure of graphs reflecting gene properties such as biological process, molecular function, regulation, or metabolism. For a fixed graph of interest, we demonstrate that accounting for graph structure can yield more powerful tests under the assumption of smooth distribution shift on the graph. We also investigate the identification of non-homogeneous subgraphs of a given large graph, which poses both computational and multiple testing problems. The relevance and benefits of the proposed approach are illustrated on synthetic data and on breast cancer gene expression data analyzed in context of KEGG pathways