Search results for "Markov Chain Monte Carlo"
showing 10 items of 79 documents
Diffusion modeling of COVID-19 under lockdown
2021
Viral immune evasion by sequence variation is a significant barrier to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine design and coronavirus disease-2019 diffusion under lockdown are unpredictable with subsequent waves. Our group has developed a computational model rooted in physics to address this challenge, aiming to predict the fitness landscape of SARS-CoV-2 diffusion using a variant of the bidimensional Ising model (2DIMV) connected seasonally. The 2DIMV works in a closed system composed of limited interaction subjects and conditioned by only temperature changes. Markov chain Monte Carlo method shows that an increase in temperature implicates reduced virus diffusi…
Particle Group Metropolis Methods for Tracking the Leaf Area Index
2020
Monte Carlo (MC) algorithms are widely used for Bayesian inference in statistics, signal processing, and machine learning. In this work, we introduce an Markov Chain Monte Carlo (MCMC) technique driven by a particle filter. The resulting scheme is a generalization of the so-called Particle Metropolis-Hastings (PMH) method, where a suitable Markov chain of sets of weighted samples is generated. We also introduce a marginal version for the goal of jointly inferring dynamic and static variables. The proposed algorithms outperform the corresponding standard PMH schemes, as shown by numerical experiments.
Conditional convex orders and measurable martingale couplings
2014
Strassen's classical martingale coupling theorem states that two real-valued random variables are ordered in the convex (resp.\ increasing convex) stochastic order if and only if they admit a martingale (resp.\ submartingale) coupling. By analyzing topological properties of spaces of probability measures equipped with a Wasserstein metric and applying a measurable selection theorem, we prove a conditional version of this result for real-valued random variables conditioned on a random element taking values in a general measurable space. We also provide an analogue of the conditional martingale coupling theorem in the language of probability kernels and illustrate how this result can be appli…
Markov Chain Monte Carlo Methods for High Dimensional Inversion in Remote Sensing
2004
SummaryWe discuss the inversion of the gas profiles (ozone, NO3, NO2, aerosols and neutral density) in the upper atmosphere from the spectral occultation measurements. The data are produced by the ‘Global ozone monitoring of occultation of stars’ instrument on board the Envisat satellite that was launched in March 2002. The instrument measures the attenuation of light spectra at various horizontal paths from about 100 km down to 10–20 km. The new feature is that these data allow the inversion of the gas concentration height profiles. A short introduction is given to the present operational data management procedure with examples of the first real data inversion. Several solution options for…
A Stochastic Approach to Quantum Statistics Distributions: Theoretical Derivation and Monte Carlo Modelling
2009
Abstract. We present a method aimed at a stochastic derivation of the equilibrium distribution of a classical/quantum ideal gas in the framework of the canonical ensemble. The time evolution of these ideal systems is modelled as a series of transitions from one system microstate to another one and thermal equilibrium is reached via a random walk in the single-particle state space. We look at this dynamic process as a Markov chain satisfying the condition of detailed balance and propose a variant of the Monte Carlo Metropolis algorithm able to take into account indistinguishability of identical quantum particles. Simulations performed on different two-dimensional (2D) systems are revealed to…
Bayesian regularization for flexible baseline hazard functions in Cox survival models.
2019
Fully Bayesian methods for Cox models specify a model for the baseline hazard function. Parametric approaches generally provide monotone estimations. Semi-parametric choices allow for more flexible patterns but they can suffer from overfitting and instability. Regularization methods through prior distributions with correlated structures usually give reasonable answers to these types of situations. We discuss Bayesian regularization for Cox survival models defined via flexible baseline hazards specified by a mixture of piecewise constant functions and by a cubic B-spline function. For those "semi-parametric" proposals, different prior scenarios ranging from prior independence to particular c…
Statistical inference and Monte Carlo algorithms
1996
This review article looks at a small part of the picture of the interrelationship between statistical theory and computational algorithms, especially the Gibbs sampler and the Accept-Reject algorithm. We pay particular attention to how the methodologies affect and complement each other.
Establishing some order amongst exact approximations of MCMCs
2016
Exact approximations of Markov chain Monte Carlo (MCMC) algorithms are a general emerging class of sampling algorithms. One of the main ideas behind exact approximations consists of replacing intractable quantities required to run standard MCMC algorithms, such as the target probability density in a Metropolis-Hastings algorithm, with estimators. Perhaps surprisingly, such approximations lead to powerful algorithms which are exact in the sense that they are guaranteed to have correct limiting distributions. In this paper we discover a general framework which allows one to compare, or order, performance measures of two implementations of such algorithms. In particular, we establish an order …
Can the Adaptive Metropolis Algorithm Collapse Without the Covariance Lower Bound?
2011
The Adaptive Metropolis (AM) algorithm is based on the symmetric random-walk Metropolis algorithm. The proposal distribution has the following time-dependent covariance matrix at step $n+1$ \[ S_n = Cov(X_1,...,X_n) + \epsilon I, \] that is, the sample covariance matrix of the history of the chain plus a (small) constant $\epsilon>0$ multiple of the identity matrix $I$. The lower bound on the eigenvalues of $S_n$ induced by the factor $\epsilon I$ is theoretically convenient, but practically cumbersome, as a good value for the parameter $\epsilon$ may not always be easy to choose. This article considers variants of the AM algorithm that do not explicitly bound the eigenvalues of $S_n$ away …
Importance sampling correction versus standard averages of reversible MCMCs in terms of the asymptotic variance
2017
We establish an ordering criterion for the asymptotic variances of two consistent Markov chain Monte Carlo (MCMC) estimators: an importance sampling (IS) estimator, based on an approximate reversible chain and subsequent IS weighting, and a standard MCMC estimator, based on an exact reversible chain. Essentially, we relax the criterion of the Peskun type covariance ordering by considering two different invariant probabilities, and obtain, in place of a strict ordering of asymptotic variances, a bound of the asymptotic variance of IS by that of the direct MCMC. Simple examples show that IS can have arbitrarily better or worse asymptotic variance than Metropolis-Hastings and delayed-acceptanc…