scholarly journals Performance of Hamiltonian Monte Carlo and No-U-Turn Sampler for estimating genetic parameters and breeding values

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Motohide Nishio ◽  
Aisaku Arakawa
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Gibbs Sampling ◽  
Genetic Parameters ◽  
Simulated Data ◽  
Animal Breeding ◽  
Posterior Distributions ◽  
Breeding Values ◽  
Hamiltonian Monte Carlo

Abstract Background Hamiltonian Monte Carlo is one of the algorithms of the Markov chain Monte Carlo method that uses Hamiltonian dynamics to propose samples that follow a target distribution. The method can avoid the random walk behavior to achieve a more effective and consistent exploration of the probability space and sensitivity to correlated parameters, which are shortcomings that plague many Markov chain Monte Carlo methods. However, the performance of Hamiltonian Monte Carlo is highly sensitive to two hyperparameters. The No-U-Turn Sampler, an extension of Hamiltonian Monte Carlo, was recently introduced to automate the tuning of these hyperparameters. Thus, this study compared the performances of Gibbs sampling, Hamiltonian Monte Carlo, and the No-U-Turn Sampler for estimating genetic parameters and breeding values as well as sampling qualities in both simulated and real pig data. For all datasets, we used a pedigree-based univariate linear mixed model. Results For all datasets, the No-U-Turn Sampler and Gibbs sampling performed comparably regarding the estimation of heritabilities and accuracies of breeding values. Compared with Gibbs sampling, the estimates of effective sample sizes for simulated and pig data with the No-U-Turn Sampler were 3.2 to 22.6 and 3.5 to 5.9 times larger, respectively. Autocorrelations decreased more quickly with the No-U-Turn Sampler than with Gibbs sampling. When true heritability was low in the simulated data, the skewness of the marginal posterior distributions with the No-U-Turn Sampler was smaller than that with Gibbs sampling. The performance of Hamiltonian Monte Carlo for sampling quality was inferior to that of No-U-Turn Sampler in the simulated data. Moreover, Hamiltonian Monte Carlo could not estimate genetic parameters because of difficulties with the hyperparameter settings with pig data. Conclusions The No-U-Turn Sampler is a promising sampling method for animal breeding because of its good sampling qualities: large effective sample sizes, low autocorrelations, and low skewness of marginal posterior distributions, particularly when heritability is low. Meanwhile, Hamiltonian Monte Carlo failed to converge with a simple univariate model for pig data. Thus, it might be difficult to use Hamiltonian Monte Carlo for usual complex models in animal breeding.

scholarly journals Parallel Markov chain Monte Carlo for non-Gaussian posterior distributions

Stat ◽  
2015 ◽  
Vol 4 (1) ◽  
pp. 304-319 ◽  
Author(s):  
Alexey Miroshnikov ◽  
Zheng Wei ◽  
Erin Marie Conlon
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Posterior Distributions ◽  
Non Gaussian

scholarly journals Bayesian calibration of terrestrial ecosystem models: a study of advanced Markov chain Monte Carlo methods

2017 ◽  
Vol 14 (18) ◽  
pp. 4295-4314 ◽  
Author(s):  
Dan Lu ◽  
Daniel Ricciuto ◽  
Anthony Walker ◽  
Cosmin Safta ◽  
William Munger
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Likelihood Function ◽  
Terrestrial Ecosystem ◽  
Error Model ◽  
Model Parameters ◽  
Posterior Distributions ◽  
Ecosystem Models ◽  
Bayesian Calibration

Abstract. Calibration of terrestrial ecosystem models is important but challenging. Bayesian inference implemented by Markov chain Monte Carlo (MCMC) sampling provides a comprehensive framework to estimate model parameters and associated uncertainties using their posterior distributions. The effectiveness and efficiency of the method strongly depend on the MCMC algorithm used. In this work, a differential evolution adaptive Metropolis (DREAM) algorithm is used to estimate posterior distributions of 21 parameters for the data assimilation linked ecosystem carbon (DALEC) model using 14 years of daily net ecosystem exchange data collected at the Harvard Forest Environmental Measurement Site eddy-flux tower. The calibration of DREAM results in a better model fit and predictive performance compared to the popular adaptive Metropolis (AM) scheme. Moreover, DREAM indicates that two parameters controlling autumn phenology have multiple modes in their posterior distributions while AM only identifies one mode. The application suggests that DREAM is very suitable to calibrate complex terrestrial ecosystem models, where the uncertain parameter size is usually large and existence of local optima is always a concern. In addition, this effort justifies the assumptions of the error model used in Bayesian calibration according to the residual analysis. The result indicates that a heteroscedastic, correlated, Gaussian error model is appropriate for the problem, and the consequent constructed likelihood function can alleviate the underestimation of parameter uncertainty that is usually caused by using uncorrelated error models.

scholarly journals A sequential Bayesian approach for the estimation of the age–depth relationship of Dome Fuji ice core

2015 ◽  
Vol 2 (3) ◽  
pp. 939-968
Author(s):  
S. Nakano ◽  
K. Suzuki ◽  
K. Kawamura ◽  
F. Parrenin ◽  
T. Higuchi
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Sequential Monte Carlo ◽  
Ice Core ◽  
Posterior Distributions ◽  
Metropolis Method ◽  
Depth Relationship ◽  
Relationship Of ◽  
Thinning Process

Abstract. A technique for estimating the age–depth relationship in an ice core and evaluating its uncertainty is presented. The age–depth relationship is mainly determined by the accumulation of snow at the site of the ice core and the thinning process due to the horizontal stretching and vertical compression of ice layers. However, since neither the accumulation process nor the thinning process are fully understood, it is essential to incorporate observational information into a model that describes the accumulation and thinning processes. In the proposed technique, the age as a function of depth is estimated from age markers and δ18O data. The estimation is achieved using the particle Markov chain Monte Carlo (PMCMC) method, in which the sequential Monte Carlo (SMC) method is combined with the Markov chain Monte Carlo method. In this hybrid method, the posterior distributions for the parameters in the models for the accumulation and thinning processes are computed using the Metropolis method, in which the likelihood is obtained with the SMC method. Meanwhile, the posterior distribution for the age as a function of depth is obtained by collecting the samples generated by the SMC method with Metropolis iterations. The use of this PMCMC method enables us to estimate the age–depth relationship without assuming either linearity or Gaussianity. The performance of the proposed technique is demonstrated by applying it to ice core data from Dome Fuji in Antarctica.

scholarly journals Joint Estimation of Pedigrees and Effective Population Size Using Markov Chain Monte Carlo

2018 ◽  
Author(s):  
Amy Ko ◽  
Rasmus Nielsen
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Population Size ◽  
Effective Population Size ◽  
Simulated Data ◽  
Composite Likelihood ◽  
Joint Estimation ◽  
Pedigree Information ◽  
Effective Population

Pedigrees provide a fine resolution of the genealogical relationships among individuals and serve an important function in many areas of genetic studies. One such use of pedigree information is in the estimation of short-term effective population size (Ne), which is of great relevance in fields such as conservation genetics. Despite the usefulness of pedigrees, however, they are often an unknown parameter and must be inferred from genetic data. In this study, we present a Bayesian method to jointly estimate pedigrees and Ne from genetic markers using Markov Chain Monte Carlo. Our method supports analysis of a large number of markers and individuals with the use of composite likelihood, which significantly increases computational efficiency. We show on simulated data that our method is able to jointly estimate relationships up to first cousins and Ne with high accuracy. We also apply the method on a real dataset of house sparrows to reconstruct their previously unreported pedigree.

scholarly journals PENDUGAAN ANGKA KEMISKINAN DI KABUPATEN PADANG PARIAMAN MENGGUNAKAN SMALL AREA ESTIMATION DENGAN PENDEKATAN HIERARCHICAL BAYESIAN (HB) LOGLOGISTIK

2019 ◽  
Vol 8 (2) ◽  
pp. 76
Author(s):  
Jusri Repi Basri Yuliani ◽  
Maiyastri Maiyastri ◽  
Rita Diana
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Gibbs Sampling ◽  
Standard Error ◽  
Small Area ◽  
Small Area Estimation ◽  
Hierarchical Bayesian ◽  
Area Estimation ◽  
Level Model

Penelitian ini mengkaji tentang pendekatan Hierarchical Bayesian (HB) Loglogistik yang diaplikasikan pada Small Area Estimation (SAE) dengan tujuan mengestimasi tingkat kemiskinan di Kabupaten Padang Pariaman. Metode pendugaan area kecil yang digunakan pada penelitian ini adalah model level area dasar (basic area level model ) dengan bantuan variabel penyerta yang tersedia pada level kecamatan. Variabel penyerta yang digunakan pada penelitian ini yaitu rasio SLTA/Sederajat (X1), persentase keluarga pertanian (X2), rasio industri mikro kecil (X3), persentase buruh tani dalam setiap anggota keluarga (X4), kepadatan penduduk (X5), dan persentase penduduk pelanggan listrik PLN (X6). Bentuk integrasi yang kompleks dari sebaran peluang bersyarat pada model diselesaikan menggunakan Markov Chain Monte Carlo (MCMC) dengan menerapkan algortima Gibbs Sampling dan bantuan software WinBugs 1.4.3. Hasil estimasi menggunkan model HB yang diperoleh dibandingkan dengan hasil estimasi pendugaan langsung dengan memperhatikan nilai standard error sebagai tolok ukurnya. Hasil pendugaan tingkat kemiskinan untuk level kecamatan di Kabupaten Padang Pariaman dengan model HB menunjukkan nilai standard error yang kecil.Kata Kunci: Tingkat kemiskinan, Small Area Estimation, Hierarchical Bayesian

A two-stage Markov chain Monte Carlo method for seismic inversion and uncertainty quantification

Geophysics ◽  
2019 ◽  
Vol 84 (6) ◽  
pp. R1003-R1020 ◽  
Author(s):  
Georgia K. Stuart ◽  
Susan E. Minkoff ◽  
Felipe Pereira
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Uncertainty Quantification ◽  
Bayesian Methods ◽  
Posterior Distributions ◽  
Mcmc Algorithm ◽  
Two Stage ◽  
Fine Grid ◽  
Highest Posterior Density

Bayesian methods for full-waveform inversion allow quantification of uncertainty in the solution, including determination of interval estimates and posterior distributions of the model unknowns. Markov chain Monte Carlo (MCMC) methods produce posterior distributions subject to fewer assumptions, such as normality, than deterministic Bayesian methods. However, MCMC is computationally a very expensive process that requires repeated solution of the wave equation for different velocity samples. Ultimately, a large proportion of these samples (often 40%–90%) is rejected. We have evaluated a two-stage MCMC algorithm that uses a coarse-grid filter to quickly reject unacceptable velocity proposals, thereby reducing the computational expense of solving the velocity inversion problem and quantifying uncertainty. Our filter stage uses operator upscaling, which provides near-perfect speedup in parallel with essentially no communication between processes and produces data that are highly correlated with those obtained from the full fine-grid solution. Four numerical experiments demonstrate the efficiency and accuracy of the method. The two-stage MCMC algorithm produce the same results (i.e., posterior distributions and uncertainty information, such as medians and highest posterior density intervals) as the Metropolis-Hastings MCMC. Thus, no information needed for uncertainty quantification is compromised when replacing the one-stage MCMC with the more computationally efficient two-stage MCMC. In four representative experiments, the two-stage method reduces the time spent on rejected models by one-third to one-half, which is important because most of models tried during the course of the MCMC algorithm are rejected. Furthermore, the two-stage MCMC algorithm substantially reduced the overall time-per-trial by as much as 40%, while increasing the acceptance rate from 9% to 90%.

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