Incorporating qualitative information into quantitative estimation via Sequentially Constrained Hamiltonian Monte Carlo sampling

Author(s):  
Daqing Yi ◽  
Shushman Choudhury ◽  
Siddhartha Srinivasa
2021 ◽  
Vol 43 (5) ◽  
pp. A3357-A3371
Author(s):  
S. Blanes ◽  
M. P. Calvo ◽  
F. Casas ◽  
J. M. Sanz-Serna

2020 ◽  
Vol 5 ◽  
pp. 53
Author(s):  
Guy Baele ◽  
Mandev S. Gill ◽  
Philippe Lemey ◽  
Marc A. Suchard

Nonparametric coalescent-based models are often employed to infer past population dynamics over time. Several of these models, such as the skyride and skygrid models, are equipped with a block-updating Markov chain Monte Carlo sampling scheme to efficiently estimate model parameters. The advent of powerful computational hardware along with the use of high-performance libraries for statistical phylogenetics has, however, made the development of alternative estimation methods feasible. We here present the implementation and performance assessment of a Hamiltonian Monte Carlo gradient-based sampler to infer the parameters of the skygrid model. The skygrid is a popular and flexible coalescent-based model for estimating population dynamics over time and is available in BEAST 1.10.5, a widely-used software package for Bayesian pylogenetic and phylodynamic analysis. Taking into account the increased computational cost of gradient evaluation, we report substantial increases in effective sample size per time unit compared to the established block-updating sampler. We expect gradient-based samplers to assume an increasingly important role for different classes of parameters typically estimated in Bayesian phylogenetic and phylodynamic analyses.


2020 ◽  
Author(s):  
Lars Gebraad ◽  
Andrea Zunino ◽  
Andreas Fichtner ◽  
Klaus Mosegaard

<div>We present a framework to solve geophysical inverse problems using the Hamiltonian Monte Carlo (HMC) method, with a focus on Bayesian tomography. Recent work in the geophysical community has shown the potential for gradient-based Monte Carlo sampling for a wide range of inverse problems across several fields.</div><div> </div><div>Many high-dimensional (non-linear) problems in geophysics have readily accessible gradient information which is unused in classical probabilistic inversions. Using HMC is a way to help improve traditional Monte Carlo sampling while increasing the scalability of inference problems, allowing access to uncertainty quantification for problems with many free parameters (>10'000). The result of HMC sampling is a collection of models representing the posterior probability density function, from which not only "best" models can be inferred, but also uncertainties and potentially different plausible scenarios, all compatible with the observed data. However, the amount of tuning parameters required by HMC, as well as the complexity of existing statistical modeling software, has limited the geophysical community in widely adopting a specific tool for performing efficient large-scale Bayesian inference.</div><div> </div><div>This work attempts to make a step towards filling that gap by providing an HMC sampler tailored for geophysical inverse problems (by e.g. supplying relevant priors and visualizations) combined with a set of different forward models, ranging from elastic and acoustic wave propagation to magnetic anomaly modeling, traveltimes, etc.. The framework is coded in the didactic but performant languages Julia and Python, with the possibility for the user to combine their own forward models, which are linked to the sampler routines by proper interfaces. In this way, we hope to illustrate the usefulness and potential of HMC in Bayesian inference. Tutorials featuring an array of physical experiments are written with the aim of both showcasing Bayesian inference and successful HMC usage. It additionally includes examples on how to speed up HMC e.g. with automated tuning techniques and GPU computations.</div>


2020 ◽  
Vol 223 (3) ◽  
pp. 1630-1643
Author(s):  
Jack B Muir ◽  
Hrvoje Tkalčić

SUMMARY Bayesian methods, powered by Markov Chain Monte Carlo estimates of posterior densities, have become a cornerstone of geophysical inverse theory. These methods have special relevance to the deep Earth, where data are sparse and uncertainties are large. We present a strategy for efficiently solving hierarchical Bayesian geophysical inverse problems for fixed parametrizations using Hamiltonian Monte Carlo sampling, and highlight an effective methodology for determining optimal parametrizations from a set of candidates by using efficient approximations to leave-one-out cross-validation for model complexity. To illustrate these methods, we use a case study of differential traveltime tomography of the lowermost mantle, using short period P-wave data carefully selected to minimize the contributions of the upper mantle and inner core. The resulting tomographic image of the lowermost mantle has a relatively weak degree 2—instead there is substantial heterogeneity at all low spherical harmonic degrees less than 15. This result further reinforces the dichotomy in the lowermost mantle between relatively simple degree 2 dominated long-period S-wave tomographic models, and more complex short-period P-wave tomographic models.


Sign in / Sign up

Export Citation Format

Share Document