The Gibbs sampler is a particularly popular Markov chain used for learning and inference problems in Graphical Models (GMs). These tasks are computationally intractable in general, and the Gibbs sampler often suffers from slow mixing. In this paper, we study the SwendsenWang dynamics which is a more sophisticated Markov chain designed to overcome bottlenecks that impede the Gibbs sampler. We pr...

For a dynamical system far from equilibrium, one has to deal with empirical probabilities defined through time–averages, and the main problem is then how to formulate an appropriate statistical thermodynamics. The common answer is that the standard functional expression of Boltzmann-Gibbs for the entropy should be used, the empirical probabilities being substituted for the Gibbs measure. Other ...

The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has the minimum total distance to the set of samples chosen from the a posteriori probability distribution of transcription factor binding-site alignments. In so doing, it garners information from the f...

This is an article I wrote for Dynamics, Games, and Science. In Dynamics, Game, and Science, one of the most important equilibrium states is a Gibbs state. The deformation of a Gibbs state becomes an important subject in these areas. An appropriate metric on the space of underlying dynamical systems is going to be very helpful in the study of deformation. The Teichmüller metric becomes a natura...

Researchers have recently introduced a promising new class of Distributed Constraint Optimization Problem (DCOP) algorithms that is based on sampling. This paradigm is very amenable to parallelization since sampling algorithms require a lot of samples to ensure convergence, and the sampling process can be designed to be executed in parallel. This paper presents GPU-based D-Gibbs (GD-Gibbs), whi...

We study the problem of continuum percolation in infinite volume Gibbs measures for particles with an attractive pair potential, with a focus on low temperatures (large β). The main results are bounds on percolation thresholds ρ±(β) in terms of the density rather than the chemical potential or activity. In addition, we prove a variational formula for a large deviations rate function for cluster...

: in this work, different levels of theory containing hf, b3lyp, and mp2 with different basis sets such as 6-31g, 6-31g*, 6-311g, 6-311+g, 6-31+g*, 6-31+g are used to predict relative acidity constants of some aniline derivatives. three different kinds of radii containing uahf, bondi, and pauling are used to study how cavity forms change acidity constants. in all cases, dpcm model is used to si...

A rich and  exible class of random probability measures, which we call stick-breaking priors, can be constructed using a sequence of independent beta random variables. Examples of random measures that have this characterization include the Dirichlet process, its two-parameter extension, the two-parameter Poisson–Dirichlet process, Ž nite dimensional Dirichlet priors, and beta two-parameter pro...