Sequential multiple-point statistics simulations conditioned on arithmetic averages

Bayesian model updating provides a rigorous framework to account for uncertainty induced by lack of knowledge about engineering systems in their respective mathematical models through updates of the joint probability density function (PDF), the so-called posterior PDF, of the unknown model parameters. The Markov chain Monte Carlo (MCMC) methods are currently the most popular approaches for generating samples from the posterior PDF. However, these methods often found wanting when sampling from difficult distributions (e.g., high-dimensional PDFs, PDFs with flat manifolds, multimodal PDFs, and very peaked PDFs). This paper introduces a new multi-level sampling approach for Bayesian model updating, called Sequential Gauss-Newton algorithm, which is inspired by the Transitional Markov chain Monte Carlo (TMCMC) algorithm. The Sequential Gauss-Newton algorithm improves two aspects of TMCMC to make an efficient and effective MCMC algorithm for drawing samples from difficult posterior PDFs. First, the statistical efficiency of the algorithm is enhanced by use of the systematic resampling scheme. Second, a new MCMC algorithm, called Gauss-Newton MCMC algorithm, is proposed which is essentially an M-H algorithm with a Gaussian proposal PDF tailored to the posterior PDF using the gradient and Hessian information of the negative log posterior. The effectiveness of the proposed algorithm for solving the Bayesian model updating problem is illustrated using three examples with irregularly shaped posterior PDFs.

Multiple point statistics (MPS) provides a systematic approach for pattern-based simulation of geologic objects from a conceptual training image (TI). The TI encodes the higher-order spatial statistics of the expected connectivity structures through stationary patterns representing the underlying geologic features. The pattern-imitating nature of MPS simulation implies that the simulated facies inherit the spatial structure of the general features in the TI. This property makes the MPS approach very sensitive to uncertainty in the prior TI. Since TIs are constructed using uncertain data and imperfect assumptions, multiple TIs may be necessary to account for the uncertainty and full range of structural variability in facies descriptions. We present a Bayesian mixture modeling approach for adaptively sampling conditional facies from multiple uncertain TIs using a probability conditioning method (PCM). Using the PCM, we invert the flow data to obtain a facies probability map for drawing conditional facies realizations from each TI. The number of samples drawn from each TI is proportional to the weight assigned to them. The TI weights are assigned based on the predictive performance of its corresponding conditional facies realizations. We demonstrate the suitability of the proposed method using numerical experiments in fluvial formations.

Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topologies. MCMC algorithms using such moves tend to get trapped in tree space, making them slow in finding the globally most probable trees (known as “convergence”) and in estimating the correct proportions of the different types of them (known as “mixing”). Here, we introduce a new class of moves, which propose trees based on their parsimony scores. The proposal distribution derived from the parsimony scores is a quickly computable albeit rough approximation of the conditional posterior distribution over candidate trees. We demonstrate with simulations that parsimony-guided moves correctly sample the uniform distribution of topologies from the prior. We then evaluate their performance against standard moves using six challenging empirical data sets, for which we were able to obtain accurate reference estimates of the posterior using long MCMC runs, a mix of topology proposals, and Metropolis coupling. On these data sets, ranging in size from 357 to 934 taxa and from 1740 to 5681 sites, we find that single chains using parsimony-guided moves usually converge an order of magnitude faster than chains using standard moves. They also exhibit better mixing, that is, they cover the most probable trees more quickly. Our results show that tree moves based on quick and dirty estimates of the posterior probability can significantly outperform standard moves. Future research will have to show to what extent the performance of such moves can be improved further by finding better ways of approximating the posterior probability, taking the trade-off between accuracy and speed into account. [Bayesian phylogenetic inference; MCMC; parsimony; tree proposal.]

Abstract. This study introduces a novel workflow to model the heterogeneity of complex aquifers using the multiple-point statistics algorithm DeeSse. We illustrate the approach by modeling the Continental Pliocene layer of the Roussillon aquifer in the region of Perpignan (southern France). When few direct observations are available, statistical inference from field data is difficult if not impossible and traditional geostatistical approaches cannot be applied directly. By contrast, multiple-point statistics simulations can rely on one or several alternative conceptual geological models provided using training images (TIs). But since the spatial arrangement of geological structures is often non-stationary and complex, there is a need for methods that allow to describe and account for the non-stationarity in a simple but efficient manner. The main aim of this paper is therefore to propose a workflow, based on the direct sampling algorithm DeeSse, for these situations. The conceptual model is provided by the geologist as a 2D non-stationary training image in map view displaying the possible organization of the geological structures and their spatial evolution. To control the non-stationarity, a 3D trend map is obtained by solving numerically the diffusivity equation as a proxy to describe the spatial evolution of the sedimentary patterns, from the sources of the sediments to the outlet of the system. A 3D continuous rotation map is estimated from inferred paleo-orientations of the fluvial system. Both trend and orientation maps are derived from geological insights gathered from outcrops and general knowledge of processes occurring in these types of sedimentary environments. Finally, the 3D model is obtained by stacking 2D simulations following the paleo-topography of the aquifer. The vertical facies transition between successive 2D simulations is controlled partly by the borehole data used for conditioning and by a sampling strategy. This strategy accounts for vertical probability of transitions, which are derived from the borehole observations, and works by simulating a set of conditional data points from one layer to the next. This process allows us to bypass the creation of a 3D training image, which may be cumbersome, while honoring the observed vertical continuity.

One of the most common types of models that helps us to understand neuron behavior is based on the Hodgkin–Huxley ion channel formulation (HH model). A major challenge with inferring parameters in HH models is non-uniqueness: many different sets of ion channel parameter values produce similar outputs for the same input stimulus. Such phenomena result in an objective function that exhibits multiple modes (i.e., multiple local minima). This non-uniqueness of local optimality poses challenges for parameter estimation with many algorithmic optimization techniques. HH models additionally have severe non-linearities resulting in further challenges for inferring parameters in an algorithmic fashion. To address these challenges with a tractable method in high-dimensional parameter spaces, we propose using a particular Markov chain Monte Carlo (MCMC) algorithm, which has the advantage of inferring parameters in a Bayesian framework. The Bayesian approach is designed to be suitable for multimodal solutions to inverse problems. We introduce and demonstrate the method using a three-channel HH model. We then focus on the inference of nine parameters in an eight-channel HH model, which we analyze in detail. We explore how the MCMC algorithm can uncover complex relationships between inferred parameters using five injected current levels. The MCMC method provides as a result a nine-dimensional posterior distribution, which we analyze visually with solution maps or landscapes of the possible parameter sets. The visualized solution maps show new complex structures of the multimodal posteriors, and they allow for selection of locally and globally optimal value sets, and they visually expose parameter sensitivities and regions of higher model robustness. We envision these solution maps as enabling experimentalists to improve the design of future experiments, increase scientific productivity and improve on model structure and ideation when the MCMC algorithm is applied to experimental data.

Resource estimation of mineral deposits requires spatial modelling of orebody boundaries based on a set of exploration borehole data. Given lateritic bauxite deposits, the spacing between the boreholes is often determined based on the grade continuity. As a result, the selected drill spacing might not capture the underlying (true) lateral variability apparent in the orebody boundaries. The purpose of this study is to investigate and address the limitations imposed by such problems in lateritic metal deposits through multiple-point statistics (MPS) framework. Rather than relying on a semivariogram model, we obtain the required structural information from the footwall topographies exposed after previous mining operations. The investigation utilising the MPS was carried out using the Direct Sampling (DS) MPS algorithm. Two historical mine areas along with their mined-out surfaces and ground penetrating radar surveys were incorporated as a bivariate training image to perform the MPS simulations. In addition, geostatistical simulations using the Turning Bands method were also performed to make the comparison against the MPS results. The performances were assessed using several statistical indicators including higher-order spatial cumulants. The results have shown that the DS can satisfactorily simulate the orebody boundaries by using prior information from the previously mined-out areas.

For strongly non-linear and high-dimensional inverse problems, Markov chain Monte Carlo (MCMC) methods may fail to properly explore the posterior probability density function (PDF) given a realistic computational budget and are generally poorly amenable to parallelization. Particle methods approximate the posterior PDF using the states and weights of a population of evolving particles and they are very well suited to parallelization. We focus on adaptive sequential Monte Carlo (ASMC), an extension of annealed importance sampling (AIS). In AIS and ASMC, importance sampling is performed over a sequence of intermediate distributions, known as power posteriors, linking the prior to the posterior PDF. The AIS and ASMC algorithms also provide estimates of the evidence (marginal likelihood) as needed for Bayesian model selection, at basically no additional cost. ASMC performs better than AIS as it adaptively tunes the tempering schedule and performs resampling of particles when the variance of the particle weights becomes too large. We consider a challenging synthetic groundwater transport inverse problem with a categorical channelized 2D hydraulic conductivity field defined such that the posterior facies distribution includes two distinct modes. The model proposals are obtained by iteratively re-simulating a fraction of the current model using conditional multiple-point statistics (MPS) simulations. We examine how ASMC explores the posterior PDF and compare with results obtained with parallel tempering (PT), a state-of-the-art MCMC inversion approach that runs multiple interacting chains targeting different power posteriors. For a similar computational budget, ASMC outperforms PT as the ASMC-derived models fit the data better and recover the reference likelihood. Moreover, we show that ASMC partly retrieves both posterior modes, while none of them is recovered by PT. Lastly, we demonstrate how the power posteriors obtained by ASMC can be used to assess the influence of the assumed data errors on the posterior means and variances, as well as on the evidence. We suggest that ASMC can advantageously replace MCMC for solving many challenging inverse problems arising in the field of water resources.

Recent progress using geometry in the design of efficient Markov chain Monte Carlo (MCMC) algorithms have shown the effectiveness of the Fisher Riemannian structure. Furthermore, the theory of the underlying geometry of spaces of statistical models has made an important breakthrough by extending the classical theory on exponential families to their closures, the so-called extended exponential families. This paper looks at the underlying geometry of the Fisher information, in particular its limiting behaviour near boundaries, which illuminates the excellent behaviour of the corresponding geometric MCMC algorithms. Further, the paper shows how Fisher geodesics in extended exponential families smoothly attach the boundaries of extended exponential families to their relative interior. We conjecture that this behaviour could be exploited for trans-dimensional MCMC algorithms.

Markov Chain Monte Carlo (MCMC) is widely applied to fit complex, practical models in various disciplines, such as engineering, physics, agriculture, etc. Indeed, when the target density $f$ is not available in closed form, a Markov chain is constructed with stationary density $f$ for forming Monte Carlo estimators of means with respect to $f$. Although a Harris ergodic Markov chain will converge to the target distribution as the Monte Carlo sample size tends to infinity, and the population means can be consistently estimated by the corresponding MCMC estimators, in practice, it is important to estimate the standard errors associated with these Monte Carlo estimates due to the availability of only a finite sample. Therefore, the geometric ergodicity of a Markov Chain is highly desired as it is the most standard method for guaranteeing a central limit theorem (CLT) for MCMC estimators and finding its standard errors. Among the different MCMC algorithms, Metropolis-Hastings (MH) algorithms are predominant. This thesis establishes conditions under which MH algorithms with a position-dependent proposal covariance matrix will or will not have the geometric convergence rate. Indeed, we provide these results for MH algorithms where the normal proposal density has a general mean function $c(x)$ and a covariance matrix $G(x)$ depending on the current position $x$ of the Markov chain. For modern variants of the popular Metropolis adjusted Langevin algorithms (MALA), like the manifold MALA (MMALA) that adapt to the geometry of the target distributions, the proposal covariance matrix changes in every iteration. Thus, we provide conditions for the geometric ergodicity of different variations of the Langevin algorithms, e.g., MMALA, position-dependent MALA (PMALA), and the pre-conditioned MALA (PCMALA). We also provide conditions guaranteeing geometric ergodicity of the pre-conditioned unadjusted Langevin algorithms (PCULA). Generalized linear mixed models (GLMMs), where the response variable is allowed to follow a non-Gaussian distribution, are popular statistical models, although their likelihood functions are not available in closed form. GLMMs can handle the over-dispersion often present in real-world data, and MCMC methods are generally used to fit frequentist and Bayesian GLMMs. Since the likelihood function for GLMMs is not available in closed form, Monte Carlo EM or Monte Carlo maximum likelihood methods are often used for making inferences from GLMMs. Simulation from the conditional (on the data) distribution of the random effects is, in turn, needed for implementing the Monte Carlo EM or Monte Carlo maximum likelihood methods. In this thesis, our general conditions for geometric ergodicity of variants of Langevin algorithms are also verified in the context of conditional simulation from the two most popular GLMMs, namely the binomial GLMM with the logit link and the Poisson GLMM with the log link. These results have important practical implications as users can now confidently fit these models by attaching asymptotically valid standard errors with their Markov chain-based Monte Carlo estimates. Spatial generalized linear mixed models (SGLMMs) are GLMMs where the random effects form a spatial process and are useful for modeling spatially correlated data. We compare the performance of different variants of MALA mentioned above as well as other popular MH algorithms like Random Walk Metropolis in the context of conditional simulation from SGLMMs. Next, we consider MCMC algorithms for full Bayesian analysis of GLMMs. Blocking and reparameterization are techniques used to improve the efficiency and convergence properties of MCMC algorithms. We combine these strategies with pre-conditioning to develop efficient Langevin algorithms for Bayesian GLMMs and SGLMMs. We illustrate our algorithms using extensive real and simulated data analyses.

In this paper, we derive a Markov chain Monte Carlo (MCMC) algorithm supported by a neural network. In particular, we use the neural network to substitute derivative calculations made during a Metropolis adjusted Langevin algorithm (MALA) step with inexpensive neural network evaluations. Using a complex, high-dimensional blood coagulation model and a set of measurements, we define a likelihood function on which we evaluate the new MCMC algorithm. The blood coagulation model is a dynamic model, where derivative calculations are expensive and hence limit the efficiency of derivative-based MCMC algorithms. The MALA adaptation greatly reduces the time per iteration, while only slightly affecting the sample quality. We also test the new algorithm on a 2-dimensional example with a non-convex shape, a case where the MALA algorithm has a clear advantage over other state of the art MCMC algorithms. To assess the impact of the new algorithm, we compare the results to previously generated results of the MALA and the random walk Metropolis Hastings (RWMH).

We describe the importance and widespread use of Markov chain Monte Carlo (MCMC) algorithms, with an emphasis on the ways in which theoretical analysis can help with their practical implementation. In particular, we discuss how to achieve rigorous quantitative bounds on convergence to stationarity using the coupling method together with drift and minorisation conditions. We also discuss recent advances in the field of adaptive MCMC, where the computer iteratively selects from among many different MCMC algorithms. Such adaptive MCMC algorithms may fail to converge if implemented naively, but they will converge correctly if certain conditions such as Diminishing Adaptation are satisfied.

There is an increasing use of Markov chain Monte Carlo (MCMC) algorithms for fitting statistical models in psychometrics, especially in situations where the traditional estimation techniques are very difficult to apply. One of the disadvantages of using an MCMC algorithm is that it is not straightforward to determine the convergence of the algorithm. Using the output of an MCMC algorithm that has not converged may lead to incorrect inferences on the problem at hand. The convergence is not one to a point, but that of the distribution of a sequence of generated values to another distribution, and hence is not easy to assess; there is no guaranteed diagnostic tool to determine convergence of an MCMC algorithm in general. This article examines the convergence of MCMC algorithms using a number of convergence diagnostics for two real data examples from psychometrics. Findings from this research have the potential to be useful to researchers using the algorithms. For both the examples, the number of iterations required (suggested by the diagnostics) to be reasonably confident that the MCMC algorithm has converged may be larger than what many practitioners consider to be safe.

Multiple-point statistics are widely used for the simulation of categorical variables because the method allows for integrating a conceptual model via a training image and then simulating complex heterogeneous fields. The multiple-point statistics inferred from the training image can be stored in several ways. The tree structure used in classical implementations has the advantage of being efficient in terms of CPU time, but is very RAM demanding and then implies limitations on the size of the template, which serves to make a proper reproduction of complex structures difficult. Another technique consists in storing the multiple-point statistics in lists. This alternative requires much less memory and allows for a straightforward parallel algorithm. Nevertheless, the list structure does not benefit from the shortcuts given by the branches of the tree for retrieving the multiple-point statistics. Hence, a serial algorithm based on list structure is generally slower than a tree-based algorithm. In this paper, a new approach using both list and tree structures is proposed. The idea is to index the lists by trees of reduced size: the leaves of the tree correspond to distinct sublists that constitute a partition of the entire list. The size of the indexing tree can be controlled, and then the resulting algorithm keeps memory requirements low while efficiency in terms of CPU time is significantly improved. Moreover, this new method benefits from the parallelization of the list approach.

Markov Chain Monte Carlo (MCMC) algorithms are employed for accurate uncertainty assessments in non-linear geophysical inverse problems. However, one of their main drawbacks is the considerable number of sampled models needed to attain stable posterior estimations, especially in high-dimensional parameter spaces. We use the Discrete Cosine Transform (DCT) to reparametrize a Bayesian Electrical Resistivity Tomography (ERT) inversion solved through an MCMC sampling. In this framework, the unknown parameters become the series of coefficients associated with the retained DCT base functions. We employ the Differential Evolution Markov Chain (DEMC) algorithm that guarantees a more accurate and rapid sampling of the posterior density than more standard MCMC algorithms (such as the random walk Metropolis). To draw essential conclusions about the reliability of the implemented algorithm, we focus on inversions of a synthetic subsurface block model. We assess the benefits provided by the DCT compression of the model space by comparing the outcomes of the implemented inversion approach with those provided by a DEMC algorithm running in the full, un-reduced model space. Although preliminary, our results are promising and prove that the implemented inversion approach guarantees rapid convergence toward the stationary regime, thereby preserving an accurate sampling of the posterior model.

Left-censored linear regression models are quite popular models and have been deeply considered in the last three decades. In this paper, we consider a completely Bayesian approach for making a new Markov chain Monte Carlo (MCMC) algorithm with tractable full posteriors. Simulated consequences and real data analyses depict that the new Markov chain Monte Carlo algorithm has excellent mixing property and carry out very well than the present methods based on prediction accuracy.