scholarly journals On the Metropolis-Hastings Acceptance Probability to Add or Drop a Quantitative Trait Locus in Markov Chain Monte Carlo-Based Bayesian Analyses

Genetics ◽  
2004 ◽  
Vol 166 (1) ◽  
pp. 641-643 ◽  
Author(s):  
Jean-Luc Jannink ◽  
Rohan L. Fernando
Keyword(s):  
Quantitative Trait Locus ◽  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Quantitative Trait ◽  
Acceptance Probability ◽  
Bayesian Analyses ◽  
Trait Locus

scholarly journals Markov chain Monte Carlo for mapping a quantitative trait locus in outbred populations

2000 ◽  
Vol 75 (2) ◽  
pp. 231-241 ◽  
Author(s):  
M. C. A. M. BINK ◽  
L. L. G. JANSS ◽  
R. L. QUAAS
Keyword(s):  
Quantitative Trait Locus ◽  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Quantitative Trait ◽  
Covariance Structure ◽  
Simulated Data ◽  
Simulated Tempering ◽  
Variance Ratios ◽  
Trait Locus

A Bayesian approach is presented for mapping a quantitative trait locus (QTL) using the ‘Fernando and Grossman’ multivariate Normal approximation to QTL inheritance. For this model, a Bayesian implementation that includes QTL position is problematic because standard Markov chain Monte Carlo (MCMC) algorithms do not mix, i.e. the QTL position gets stuck in one marker interval. This is because of the dependence of the covariance structure for the QTL effects on the adjacent markers and may be typical of the ‘Fernando and Grossman’ model. A relatively new MCMC technique, simulated tempering, allows mixing and so makes possible inferences about QTL position based on marginal posterior probabilities. The model was implemented for estimating variance ratios and QTL position using a continuous grid of allowed positions and was applied to simulated data of a standard granddaughter design. The results showed a smooth mixing of QTL position after implementation of the simulated tempering sampler. In this implementation, map distance between QTL and its flanking markers was artificially stretched to reduce the dependence of markers and covariance. The method generalizes easily to more complicated applications and can ultimately contribute to QTL mapping in complex, heterogeneous, human, animal or plant populations.

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.

Markov Chain Monte Carlo

2015 ◽  
Author(s):  
N. Thompson Hobbs ◽  
Mevin B. Hooten
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Bayesian Analysis ◽  
Posterior Distribution ◽  
Mcmc Algorithm ◽  
Bayesian Analyses ◽  
Seminal Paper ◽  
Formal Treatment ◽  
High Level

This chapter explains how to implement Bayesian analyses using the Markov chain Monte Carlo (MCMC) algorithm, a set of methods for Bayesian analysis made popular by the seminal paper of Gelfand and Smith (1990). It begins with an explanation of MCMC with a heuristic, high-level treatment of the algorithm, describing its operation in simple terms with a minimum of formalism. In this first part, the chapter explains the algorithm so that all readers can gain an intuitive understanding of how to find the posterior distribution by sampling from it. Next, the chapter offers a somewhat more formal treatment of how MCMC is implemented mathematically. Finally, this chapter discusses implementation of Bayesian models via two routes—by using software and by writing one's own algorithm.

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).

scholarly journals A comparison of approximate versus exact techniques for Bayesian parameter inference in nonlinear ordinary differential equation models

2020 ◽  
Vol 7 (3) ◽  
pp. 191315
Author(s):  
Amani A. Alahmadi ◽  
Jennifer A. Flegg ◽  
Davis G. Cochrane ◽  
Christopher C. Drovandi ◽  
Jonathan M. Keith
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Bayesian Inference ◽  
Sequential Monte Carlo ◽  
Simulated Data ◽  
Real Data ◽  
Nonlinear Ordinary Differential Equation ◽  
Unknown Parameters ◽  
Acceptance Probability

The behaviour of many processes in science and engineering can be accurately described by dynamical system models consisting of a set of ordinary differential equations (ODEs). Often these models have several unknown parameters that are difficult to estimate from experimental data, in which case Bayesian inference can be a useful tool. In principle, exact Bayesian inference using Markov chain Monte Carlo (MCMC) techniques is possible; however, in practice, such methods may suffer from slow convergence and poor mixing. To address this problem, several approaches based on approximate Bayesian computation (ABC) have been introduced, including Markov chain Monte Carlo ABC (MCMC ABC) and sequential Monte Carlo ABC (SMC ABC). While the system of ODEs describes the underlying process that generates the data, the observed measurements invariably include errors. In this paper, we argue that several popular ABC approaches fail to adequately model these errors because the acceptance probability depends on the choice of the discrepancy function and the tolerance without any consideration of the error term. We observe that the so-called posterior distributions derived from such methods do not accurately reflect the epistemic uncertainties in parameter values. Moreover, we demonstrate that these methods provide minimal computational advantages over exact Bayesian methods when applied to two ODE epidemiological models with simulated data and one with real data concerning malaria transmission in Afghanistan.

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