scholarly journals Markov chain Monte Carlo inference for Markov jump processes via the linear noise approximation

2013 ◽  
Vol 371 (1984) ◽  
pp. 20110541 ◽  
Author(s):  
Vassilios Stathopoulos ◽  
Mark A. Girolami
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Jump Processes ◽  
Mcmc Methods ◽  
Computationally Efficient ◽  
Markov Jump ◽  
Riemann Manifold ◽  
Exact Inference ◽  
Markov Jump Processes

Bayesian analysis for Markov jump processes (MJPs) is a non-trivial and challenging problem. Although exact inference is theoretically possible, it is computationally demanding, thus its applicability is limited to a small class of problems. In this paper, we describe the application of Riemann manifold Markov chain Monte Carlo (MCMC) methods using an approximation to the likelihood of the MJP that is valid when the system modelled is near its thermodynamic limit. The proposed approach is both statistically and computationally efficient whereas the convergence rate and mixing of the chains allow for fast MCMC inference. The methodology is evaluated using numerical simulations on two problems from chemical kinetics and one from systems biology.

scholarly journals Mapping-Linked Quantitative Trait Loci Using Bayesian Analysis and Markov Chain Monte Carlo Algorithms

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 735-743 ◽  
Author(s):  
Pekka Uimari ◽  
Ina Hoeschele
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Allele Frequencies ◽  
Mcmc Methods ◽  
Substitution Effects ◽  
Indicator Variable ◽  
Trait Loci

A Bayesian method for mapping linked quantitative trait loci (QTL) using multiple linked genetic markers is presented. Parameter estimation and hypothesis testing was implemented via Markov chain Monte Carlo (MCMC) algorithms. Parameters included were allele frequencies and substitution effects for two biallelic QTL, map positions of the QTL and markers, allele frequencies of the markers, and polygenic and residual variances. Missing data were polygenic effects and multi-locus marker-QTL genotypes. Three different MCMC schemes for testing the presence of a single or two linked QTL on the chromosome were compared. The first approach includes a model indicator variable representing two unlinked QTL affecting the trait, one linked and one unlinked QTL, or both QTL linked with the markers. The second approach incorporates an indicator variable for each QTL into the model for phenotype, allowing or not allowing for a substitution effect of a QTL on phenotype, and the third approach is based on model determination by reversible jump MCMC. Methods were evaluated empirically by analyzing simulated granddaughter designs. All methods identified correctly a second, linked QTL and did not reject the one-QTL model when there was only a single QTL and no additional or an unlinked QTL.

scholarly journals Measuring Stellar Radial Velocity using Markov Chain Monte Carlo(MCMC) Method

2013 ◽  
Vol 9 (S298) ◽  
pp. 441-441
Author(s):  
Yihan Song ◽  
Ali Luo ◽  
Yongheng Zhao
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Probability Distribution ◽  
Radial Velocity ◽  
Mcmc Methods ◽  
Mcmc Method ◽  
Stellar Spectra ◽  
Mcmc Simulation ◽  
Template Fitting

AbstractStellar radial velocity is estimated by using template fitting and Markov Chain Monte Carlo(MCMC) methods. This method works on the LAMOST stellar spectra. The MCMC simulation generates a probability distribution of the RV. The RV error can also computed from distribution.

scholarly journals Improved Markov Chain Monte Carlo method for cryptanalysis substitution-transposition cipher

2016 ◽  
Vol 22 (4) ◽  
Author(s):  
Behrouz Fathi-Vajargah ◽  
Mohadeseh Kanafchian
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Monte Carlo Method ◽  
Mcmc Methods ◽  
Random Numbers ◽  
Simple Substitution

AbstractIn this paper we first investigate the use of Markov Chain Monte Carlo (MCMC) methods to attack classical ciphers. MCMC has previously been used to break simple substitution, transposition and substitution-transposition ciphers. Here, we improve the accuracy of obtained results by these algorithms and we show the performance of the algorithms using quasi random numbers such as Faure, Sobol and Niederreiter sequences.

Combining Particle Filters with MH Samplers

2015 ◽  
Author(s):  
Edward P. Herbst ◽  
Frank Schorfheide
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Particle Filtering ◽  
Likelihood Function ◽  
Mcmc Methods ◽  
Acceptance Probability ◽  
Likelihood Functions ◽  
Approximate Likelihood ◽  
Special Case

This chapter argues that in order to conduct Bayesian inference, the approximate likelihood function has to be embedded into a posterior sampler. It begins by combining the particle filtering methods with the MCMC methods, replacing the actual likelihood functions that appear in the formula for the acceptance probability in Algorithm 5 with particle filter approximations. The chapter refers to the resulting algorithm as PFMH algorithm. It is a special case of a larger class of algorithms called particle Markov chain Monte Carlo (PMCMC). The theoretical properties of PMCMC methods were established in Andrieu, Doucet, and Holenstein (2010). Applications of PFMH algorithms in other areas of econometrics are discussed in Flury and Shephard (2011).

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