Occupancy modeling focuses on inference about the distribution of organisms over space, using temporal or spatial replication to allow inference about the detection process. Inference based on spatial replication strictly requires that replicates be selected randomly and with replacement, but the importance of these design requirements is not well understood. This paper focuses on an increasing...

Markov chain Monte Carlo (MCMC) methods have been used in many fields (physics, chemistry, biology, and computer science) for simulation, inference, and optimization. The essence of these methods is to simulate a Markov chain whose state X follows a target probability X ∼ π(X). In many applications, π(X) is defined on a graph G whose vertices represent elements in the system and whose edges rep...

We develop an efficient Monte-Carlo algorithm to sample an ensemble of stochastic transition paths between stable states. In our description, paths are represented by chains of states linked by Markovian transition probabilities. Rate constants and mechanisms characterizing the transition may be determined from the path ensemble. We have previously devised several algorithms for sampling the pa...

To evaluate the performance of the empirical predictors presented in San Martino et al. (2005), we compute the cases where they are the best, “equivalent” to the best (tables 1) or poor (table2). We consider only the case of equal unknown within cluster variances. First, we consider the cases in which each of the proposed predictors has the best performance, i.e. we compute the percentage of ca...

Most medical datasets are not balanced in their class labels. Indeed in some cases it has been no ticed that the given class labels do not accurately represent characteristics of the data record. Most existing classification methods tend not to perform well on minority class examples when the dataset is extremely imbalanced. This is because they aim to optimize the overall accuracy without cons...

We present an MCMC sampler for Dirichlet process mixture models that can be parallelized to achieve significant computational gains. We combine a nonergodic, restricted Gibbs iteration with split/merge proposals in a manner that produces an ergodic Markov chain. Each cluster is augmented with two subclusters to construct likely split moves. Unlike some previous parallel samplers, the proposed s...

We look at fitting regression models using data from stratified cluster samples when the strata may depend in some way on the observed responses within clusters. One important subclass of examples is that of family studies in genetic epidemiology, where the probability of selecting a family into the study depends on the incidence of disease within the family. We develop the survey-weighted esti...

This paper presents a fully non-Gaussian version of the Hamiltonian Monte Carlo (HMC) sampling filter. The Gaussian prior assumption in the original HMC filter is relaxed. Specifically, a clustering step is introduced after the forecast phase of the filter, and the prior density function is estimated by fitting a Gaussian Mixture Model (GMM) to the prior ensemble. Using the data likelihood func...

We develop a sampling technique for Hierarchical Dirichlet process models. The parallel algorithm builds upon [1] by proposing large split and merge moves based on learned sub-clusters. The additional global split and merge moves drastically improve convergence in the experimental results. Furthermore, we discover that cross-validation techniques do not adequately determine convergence, and tha...