Transdimensional seismic inversion using the reversible jump Hamiltonian Monte Carlo algorithm

Geophysics ◽  
2017 ◽  
Vol 82 (3) ◽  
pp. R119-R134 ◽  
Author(s):  
Mrinal K. Sen ◽  
Reetam Biswas
Keyword(s):  
Monte Carlo ◽  
A Priori ◽  
Seismic Inversion ◽  
Monte Carlo Algorithm ◽  
Model Parameters ◽  
Reversible Jump ◽  
Step Method ◽  
Acceptance Probability ◽  
Hamiltonian Monte Carlo ◽  
Impedance Inversion

Prestack or angle stack gathers are inverted to estimate pseudologs at every surface location for building reservoir models. Recently, several methods have been proposed to increase the resolution of the inverted models. All of these methods, however, require that the total number of model parameters be fixed a priori. We have investigated an alternate approach in which we allow the data themselves to choose model parameterization. In other words, in addition to the layer properties, the number of layers is also treated as a variable in our formulation. Such transdimensional inverse problems are generally solved by using the reversible jump Markov chain Monte Carlo (RJMCMC) approach, which is a tool for model exploration and uncertainty quantification. This method, however, has very low acceptance. We have developed a two-step method by combining RJMCMC with a fixed-dimensional MCMC called Hamiltonian Monte Carlo, which makes use of gradient information to take large steps. Acceptance probability for such a transition is also derived. We call this new method “reversible jump Hamiltonian Monte Carlo (RJHMC).” We have applied this technique to poststack acoustic impedance inversion and to prestack (angle stack) AVA inversion for estimating acoustic and shear impedance profiles. We have determined that the marginal posteriors estimated by RJMCMC and RJHMC are in good agreement. Our results demonstrate that RJHMC converges faster than RJMCMC, and it therefore can be a practical tool for inverting seismic data when the gradient can be computed efficiently.

Seismic source inversion using Hamiltonian Monte Carlo and a 3-D Earth model in the Japanese Islands

2020 ◽  
Author(s):  
Saulė Simutė ◽  
Lion Krischer ◽  
Christian Boehm ◽  
Martin Vallée ◽  
Andreas Fichtner
Keyword(s):  
Monte Carlo ◽  
Moment Tensor ◽  
Seismic Source ◽  
Monte Carlo Algorithm ◽  
Earth Model ◽  
Model Parameters ◽  
Hamiltonian Monte Carlo ◽  
Double Couple ◽  
Full Moment Tensor ◽  
Japanese Islands

<p>We present a proof-of-concept catalogue of full-waveform seismic source solutions for the Japanese Islands area. Our method is based on the Bayesian inference of source parameters and a tomographically derived heterogeneous Earth model, used to compute Green’s strain tensors. We infer the full moment tensor, location and centroid time of the seismic events in the study area.</p><p>To compute spatial derivatives of Green’s functions, we use a previously derived regional Earth model (Simutė et al., 2016). The model is radially anisotropic, visco-elastic, and fully heterogeneous. It was constructed using full waveforms in the period band of 15–80 s.</p><p>Green’s strains are computed numerically with the spectral-element solver SES3D (Gokhberg & Fichtner, 2016). We exploit reciprocity, and by treating seismic stations as virtual sources we compute and store the wavefield across the domain. This gives us a strain database for all potential source-receiver pairs. We store the wavefield for more than 50 F-net broadband stations (www.fnet.bosai.go.jp). By assuming an impulse response as the source time function, the displacements are then promptly obtained by linear combination of the pre-computed strains scaled by the moment tensor elements.</p><p>With a feasible number of model parameters and the fast forward problem we infer the unknowns in a Bayesian framework. The fully probabilistic approach allows us to obtain uncertainty information as well as inter-parameter trade-offs. The sampling is performed with a variant of the Hamiltonian Monte Carlo algorithm, which we developed previously (Fichtner and Simutė, 2017). We apply an L2 misfit on waveform data, and we work in the period band of 15–80 s.</p><p>We jointly infer three location parameters, timing and moment tensor components. We present two sets of source solutions: 1) full moment tensor solutions, where the trace is free to vary away from zero, and 2) moment tensor solutions with the isotropic part constrained to be zero. In particular, we study events with significant non-double-couple component. Preliminary results of ~Mw 5 shallow to intermediate depth events indicate that proper incorporation of 3-D Earth structure results in solutions becoming more double-couple like. We also find that improving the Global CMT solutions in terms of waveform fit requires a very good 3-D Earth model and is not trivial.</p>

PSV-14 Using Bayesian Hamiltonian Monte Carlo and a nonlinear model for the estimation of genetic parameters for lactation curves in goats

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 305-307
Author(s):  
Andre C Araujo ◽  
Leonardo Gloria ◽  
Paulo Abreu ◽  
Fabyano Silva ◽  
Marcelo Rodrigues ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Milk Yield ◽  
Nonlinear Model ◽  
Genetic Parameters ◽  
Model Parameters ◽  
Promising Alternative ◽  
Hamiltonian Monte Carlo ◽  
Heritability Estimates ◽  
Correlated Parameters ◽  
Wood Model

Abstract Hamiltonian Monte Carlo (HMC) is an algorithm of the Markov Chain Monte Carlo (MCMC) method that uses dynamics to propose samples that follow a target distribution. This algorithm enables more effective and consistent exploration of the probability interval and is more sensitive to correlated parameters. Therefore, Bayesian-HMC is a promising alternative to estimate individual parameters of complex functions such as nonlinear models, especially when using small datasets. Our objective was to estimate genetic parameters for milk traits defined based on nonlinear model parameters predicted using the Bayesian-HMC algorithm. A total of 64,680 milk yield test-day records from 2,624 first, second, and third lactations of Saanen and Alpine goats were used. First, the Wood model was fitted to the data. Second, lactation persistency (LP), peak time (PT), peak yield (PY), and total milk yield [estimated from zero to 50 (TMY50), 100(TMY100), 150(TMY150), 200(TMY200), 250(TMY250), and 300(TMY300) days-in-milk] were predicted for each animal and parity based on the output of the first step (the individual phenotypic parameters of the Wood model). Thereafter, these predicted phenotypes were used for estimating genetic parameters for each trait. In general, the heritability estimates across lactations ranged from 0.10 to 0.20 for LP, 0.04 to 0.07 for PT, 0.26 to 0.27 for PY, and 0.21 to 0.28 for TMY (considering the different intervals). Lower heritabilities were obtained for the nonlinear function parameters (A, b and l) compared to its predicted traits (except PT), especially for the first and second lactations (range: 0.09 to 0.18). Higher heritability estimates were obtained for the third lactation traits. To our best knowledge, this study is the first attempt to use the HMC algorithm to fit a nonlinear model in animal breeding. The two-step method proposed here allowed us to estimate genetic parameters for all traits evaluated.

scholarly journals Estimation of trace gas fluxes with objectively determined basis functions using reversible-jump Markov chain Monte Carlo

2016 ◽  
Vol 9 (9) ◽  
pp. 3213-3229 ◽  
Author(s):  
Mark F. Lunt ◽  
Matt Rigby ◽  
Anita L. Ganesan ◽  
Alistair J. Manning
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Parameter Space ◽  
Spatial Domain ◽  
Monte Carlo Algorithm ◽  
Trace Gas ◽  
Reversible Jump ◽  
Pseudo Data ◽  
Atmospheric Trace Gas

Abstract. Atmospheric trace gas inversions often attempt to attribute fluxes to a high-dimensional grid using observations. To make this problem computationally feasible, and to reduce the degree of under-determination, some form of dimension reduction is usually performed. Here, we present an objective method for reducing the spatial dimension of the parameter space in atmospheric trace gas inversions. In addition to solving for a set of unknowns that govern emissions of a trace gas, we set out a framework that considers the number of unknowns to itself be an unknown. We rely on the well-established reversible-jump Markov chain Monte Carlo algorithm to use the data to determine the dimension of the parameter space. This framework provides a single-step process that solves for both the resolution of the inversion grid, as well as the magnitude of fluxes from this grid. Therefore, the uncertainty that surrounds the choice of aggregation is accounted for in the posterior parameter distribution. The posterior distribution of this transdimensional Markov chain provides a naturally smoothed solution, formed from an ensemble of coarser partitions of the spatial domain. We describe the form of the reversible-jump algorithm and how it may be applied to trace gas inversions. We build the system into a hierarchical Bayesian framework in which other unknown factors, such as the magnitude of the model uncertainty, can also be explored. A pseudo-data example is used to show the usefulness of this approach when compared to a subjectively chosen partitioning of a spatial domain. An inversion using real data is also shown to illustrate the scales at which the data allow for methane emissions over north-west Europe to be resolved.

Hamiltonian Monte Carlo algorithms for target- and interval-oriented amplitude versus angle inversions

Geophysics ◽  
2020 ◽  
Vol 85 (3) ◽  
pp. R177-R194 ◽  
Author(s):  
Mattia Aleardi ◽  
Alessandro Salusti
Keyword(s):  
Monte Carlo ◽  
A Priori ◽  
Computational Cost ◽  
Model Space ◽  
Time Interval ◽  
Long Distance ◽  
Hamiltonian Monte Carlo ◽  
Zoeppritz Equations ◽  
Monte Carlo Algorithms ◽  
Amplitude Versus

A reliable assessment of the posterior uncertainties is a crucial aspect of any amplitude versus angle (AVA) inversion due to the severe ill-conditioning of this inverse problem. To accomplish this task, numerical Markov chain Monte Carlo algorithms are usually used when the forward operator is nonlinear. The downside of these algorithms is the considerable number of samples needed to attain stable posterior estimations especially in high-dimensional spaces. To overcome this issue, we assessed the suitability of Hamiltonian Monte Carlo (HMC) algorithm for nonlinear target- and interval-oriented AVA inversions for the estimation of elastic properties and associated uncertainties from prestack seismic data. The target-oriented approach inverts the AVA responses of the target reflection by adopting the nonlinear Zoeppritz equations, whereas the interval-oriented method inverts the seismic amplitudes along a time interval using a 1D convolutional forward model still based on the Zoeppritz equations. HMC uses an artificial Hamiltonian system in which a model is viewed as a particle moving along a trajectory in an extended space. In this context, the inclusion of the derivative information of the misfit function makes possible long-distance moves with a high probability of acceptance from the current position toward a new independent model. In our application, we adopt a simple Gaussian a priori distribution that allows for an analytical inclusion of geostatistical constraints into the inversion framework, and we also develop a strategy that replaces the numerical computation of the Jacobian with a matrix operator analytically derived from a linearization of the Zoeppritz equations. Synthetic and field data inversions demonstrate that the HMC is a very promising approach for Bayesian AVA inversion that guarantees an efficient sampling of the model space and retrieves reliable estimations and accurate uncertainty quantifications with an affordable computational cost.

scholarly journals Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

2008 ◽  
Vol 363 (1512) ◽  
pp. 3955-3964 ◽  
Author(s):  
Mark Pagel ◽  
Andrew Meade
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Mixture Model ◽  
Branch Length ◽  
Monte Carlo Algorithm ◽  
Morphological Data ◽  
Reversible Jump ◽  
Rate Variation ◽  
Ancestral State

The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon—known as heterotachy—can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our ‘pattern-heterogeneity’ mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of ‘significance’ such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.

scholarly journals Unsupervised Post-Nonlinear Unmixing of Hyperspectral Images Using a Hamiltonian Monte Carlo Algorithm

2014 ◽  
Vol 23 (6) ◽  
pp. 2663-2675 ◽  
Author(s):  
Yoann Altmann ◽  
Nicolas Dobigeon ◽  
Jean-Yves Tourneret
Keyword(s):  
Monte Carlo ◽  
Hyperspectral Images ◽  
Monte Carlo Algorithm ◽  
Hamiltonian Monte Carlo

Uncertainty analysis of calibrated parameter values of an urban storm water quality model using metropolis monte carlo algorithm

1997 ◽  
Vol 36 (5) ◽  
pp. 141-148 ◽  
Author(s):  
A. Mailhot ◽  
É. Gaume ◽  
J.-P. Villeneuve
Keyword(s):  
Monte Carlo ◽  
Uncertainty Analysis ◽  
Model Calibration ◽  
Monte Carlo Algorithm ◽  
Storm Water ◽  
Model Parameters ◽  
Calibration Data ◽  
Parameter Uncertainties ◽  
Metropolis Monte Carlo ◽  
Parameter Values

The Storm Water Management Model's quality module is calibrated for a section of Québec City's sewer system using data collected during five rain events. It is shown that even for this simple model, calibration can fail: similarly a good fit between recorded data and simulation results can be obtained with quite different sets of model parameters, leading to great uncertainty on calibrated parameter values. In order to further investigate the lack of data and data uncertainty impacts on calibration, we used a new methodology based on the Metropolis Monte Carlo algorithm. This analysis shows that for a large amount of calibration data generated by the model itself, small data uncertainties are necessary to significantly decrease calibrated parameter uncertainties. This also confirms the usefulness of the Metropolis algorithm as a tool for uncertainty analysis in the context of model calibration.

scholarly journals Bayesian estimation of a phenotype network structure using reversible jump Markov chain Monte Carlo

2021 ◽  
Author(s):  
◽  
Lisa Woods
Keyword(s):  
Monte Carlo ◽  
Markov Chain ◽  
Markov Chain Monte Carlo ◽  
Network Structure ◽  
Monte Carlo Algorithm ◽  
Maximum Likelihood Estimates ◽  
Reversible Jump ◽  
Network Structures ◽  
Double Step ◽  
Phenotype Network

<p>In this thesis we aim to estimate the unknown phenotype network structure existing among multiple interacting quantitative traits, assuming the genetic architecture is known.  We begin by taking a frequentist approach and implement a score-based greedy hill-climbing search strategy using AICc to estimate an unknown phenotype network structure. This approach was inconsistent and overfitting was common, so we then propose a Bayesian approach that extends on the reversible jump Markov chain Monte Carlo algorithm. Our approach makes use of maximum likelihood estimates in the chain, so we have an efficient sampler using well-tuned proposal distributions. The common approach is to assume uniform priors over all network structures; however, we introduce a prior on the number of edges in the phenotype network structure, which prefers simple models with fewer directed edges. We determine that the relationship between the prior penalty and the joint posterior probability of the true model is not monotonic, there is some interplay between the two.  Simulation studies were carried out and our approach is also applied to a published data set. It is determined that larger trait-to-trait effects are required to recover the phenotype network structure; however, mixing is generally slow, a common occurrence with reversible jump Markov chain Monte Carlo methods. We propose the use of a double step to combine two steps that alter the phenotype network structure. This proposes larger steps than the traditional birth and death move types, possibly changing the dimension of the model by more than one. This double step helped the sampler move between different phenotype network structures in simulated data sets.</p>

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