Gaussian process hyper-parameter estimation using parallel asymptotically independent Markov sampling

Gaussian process emulators of computationally expensive computer codes provide fast statistical approximations to model physical processes. The training of these surrogates depends on the set of design points chosen to run the simulator. Due to computational cost, such training set is bound to be limited and quantifying the resulting uncertainty in the hyper-parameters of the emulator by uni-modal distributions is likely to induce bias. In order to quantify this uncertainty, this paper proposes a computationally efficient sampler based on an extension of Asymptotically Independent Markov Sampling, a recently developed algorithm for Bayesian inference. Structural uncertainty of the emulator is obtained as a by-product of the Bayesian treatment of the hyper-parameters. Additionally, the user can choose to perform stochastic optimisation to sample from a neighbourhood of the Maximum a Posteriori estimate, even in the presence of multimodality. Model uncertainty is also acknowledged through numerical stabilisation measures by including a nugget term in the formulation of the probability model. The efficiency of the proposed sampler is illustrated in examples where multi-modal distributions are encountered. For the purpose of reproducibility, further development, and use in other applications the code used to generate the examples is freely available for download at https://github.com/agarbuno/paims_codesComment: Computational Statistics \& Data Analysis, Volume 103, November 201

d-QPSO: A Quantum-Behaved Particle Swarm Technique for Finding D-Optimal Designs With Discrete and Continuous Factors and a Binary Response

Identifying optimal designs for generalized linear models with a binary response can be a challengingtask, especially when there are both discrete and continuous independent factors in the model. Theoreticalresults rarely exist for such models, and for the handful that do, they usually come with restrictive assumptions.In this article, we propose the d-QPSO algorithm, a modified version of quantum-behaved particleswarm optimization, to find a variety of D-optimal approximate and exact designs for experiments withdiscrete and continuous factors and a binary response. We show that the d-QPSO algorithm can efficientlyfind locally D-optimal designs even for experiments with a large number of factors and robust pseudo-Bayesian designs when nominal values for the model parameters are not available. Additionally, we investigaterobustness properties of the d-QPSO algorithm-generated designs to variousmodel assumptions andprovide real applications to design a bio-plastics odor removal experiment, an electronic static experiment,and a 10-factor car refueling experiment. Supplementary materials for the article are available online

Bayesian Updating, Model Class Selection and Robust Stochastic Predictions of Structural Response

A fundamental issue when predicting structural response by using mathematical models is how to treat both modeling and excitation uncertainty. A general framework for this is presented which uses probability as a multi-valued conditional logic for quantitative plausible reasoning in the presence of uncertainty due to incomplete information. The fundamental probability models that represent the structure’s uncertain behavior are specified by the choice of a stochastic system model class: a set of input-output probability models for the structure and a prior probability distribution over this set that quantifies the relative plausibility of each model. A model class can be constructed from a parameterized deterministic structural model by stochastic embedding utilizing Jaynes’ Principle of Maximum Information Entropy. Robust predictive analyses use the entire model class with the probabilistic predictions of each model being weighted by its prior probability, or if structural response data is available, by its posterior probability from Bayes’ Theorem for the model class. Additional robustness to modeling uncertainty comes from combining the robust predictions of each model class in a set of competing candidates weighted by the prior or posterior probability of the model class, the latter being computed from Bayes’ Theorem. This higherlevel application of Bayes’ Theorem automatically applies a quantitative Ockham razor that penalizes the data-fit of more complex model classes that extract more information from the data. Robust predictive analyses involve integrals over highdimensional spaces that usually must be evaluated numerically. Published applications have used Laplace's method of asymptotic approximation or Markov Chain Monte Carlo algorithms

Data-driven modelling of biological multi-scale processes

Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript we review mathematical modelling approaches used to describe the individual spatial scales and how they are integrated into holistic models. We discuss the relation between spatial and temporal scales and the implication of that on multi-scale modelling. Based upon this overview over state-of-the-art modelling approaches, we formulate key challenges in mathematical and computational modelling of biological multi-scale and multi-physics processes. In particular, we considered the availability of analysis tools for multi-scale models and model-based multi-scale data integration. We provide a compact review of methods for model-based data integration and model-based hypothesis testing. Furthermore, novel approaches and recent trends are discussed, including computation time reduction using reduced order and surrogate models, which contribute to the solution of inference problems. We conclude the manuscript by providing a few ideas for the development of tailored multi-scale inference methods.Comment: This manuscript will appear in the Journal of Coupled Systems and Multiscale Dynamics (American Scientific Publishers

A Metaheuristic Adaptive Cubature Based Algorithm to Find Bayesian Optimal Designs for Nonlinear Models

Finding Bayesian optimal designs for nonlinear models is a difficult task because the optimality criteriontypically requires us to evaluate complex integrals before we perform a constrained optimization. Wepropose a hybridized method where we combine an adaptive multidimensional integration algorithm anda metaheuristic algorithm called imperialist competitive algorithm to find Bayesian optimal designs. Weapply our numerical method to a few challenging design problems to demonstrate its efficiency. Theyinclude finding D-optimal designs for an item response model commonly used in education, Bayesianoptimal designs for survivalmodels, and Bayesian optimal designs for a four-parameter sigmoid Emax doseresponse model. Supplementary materials for this article are available online and they contain an R packagefor implementing the proposed algorithm and codes for reproducing all the results in this paper

The role of learning on industrial simulation design and analysis

The capability of modeling real-world system operations has turned simulation into an indispensable problemsolving methodology for business system design and analysis. Today, simulation supports decisions ranging from sourcing to operations to finance, starting at the strategic level and proceeding towards tactical and operational levels of decision-making. In such a dynamic setting, the practice of simulation goes beyond being a static problem-solving exercise and requires integration with learning. This article discusses the role of learning in simulation design and analysis motivated by the needs of industrial problems and describes how selected tools of statistical learning can be utilized for this purpose