Normalized random measures (NRMs) provide a broad class of discrete random measures that are often used as priors for Bayesian nonparametric models. Dirichlet process is a well-known example of NRMs. Most of posterior inference methods for NRM mixture models rely on MCMC methods since they are easy to implement and their convergence is well studied. However, MCMC often suffers from slow converg...

We present and study a Langevin MCMC approach for sampling nonlinear diffusion bridges. The method is based on recent theory concerning stochastic partial differential equations (SPDEs) reversible with respect to the target bridge, derived by applying the Langevin idea on the bridge pathspace. In the process, a Random-Walk Metropolis algorithm and an Independence Sampler are also obtained. The ...

Using Dynamic Bayesian Networks (DBN) to model genetic regulatory networks from gene expression data is one of the major paradigms for inferring the interactions among genes. Averaging a collection of models for predicting network is desired, rather than relying on a single high scoring model. In this paper, two kinds of model searching approaches are compared, which are Greedy hill-climbing Se...

Markov chain Monte Carlo, or MCMC, is a way to sample probability distributions that cannot be sampled practically using direct samplers. This includes a majority of probability distributions of practical interest. MCMC runs a Markov chain X1, X2, . . ., where Xk+1 is computed from Xk and some other i.i.d. random input. From a coding point of view, a direct solver is X = fSamp();, while the MCM...

Switching state-space models (SSSM) are a popular class of time series models that have found many applications in statistics, econometrics and advanced signal processing. Bayesian inference for these models typically relies on Markov chain Monte Carlo (MCMC) techniques. However, even sophisticated MCMC methods dedicated to SSSM can prove quite ine cient as they update potentially strongly corr...

Bayesian inference provides an appealing general framework for phylogenetic analysis, able to incorporate a wide variety of modeling assumptions and to provide a coherent treatment of uncertainty. Existing computational approaches to bayesian inference based on Markov chain Monte Carlo (MCMC) have not, however, kept pace with the scale of the data analysis problems in phylogenetics, and this ha...

Finely tuned process-based tree-growth models are of considerable help in understanding the variations of biomass increments measured in the dendrochronological series. Using site and species parameters, as well as daily climate variables, the MAIDEN model computes the water balance at ecosystem level and the daily increment of carbon storage in the stem through photosynthesis processes to repr...

Expected value of sample information (EVSI) involves simulating data collection, Bayesian updating, and re-examining decisions. Bayesian updating in Weibull models typically requires Markov chain Monte Carlo (MCMC). We examine five methods for calculating posterior expected net benefits: two heuristic methods (data lumping and pseudo-normal); two Bayesian approximation methods (Tierney & Kadane...

The paper illustrates how to use the MCMC procedure to fit a hierarchical, multinomial logit model for a nominal response variable with correlated responses in a Bayesian framework. In particular, the paper illustrates how to perform three important parts of Bayesian model fitting. First, to make sure appropriate prior distributions are selected, the paper shows how to simulate draws directly f...