A Review of Bayesian Optimal Experimental Design on Different Models

Surrogate-based sequential Bayesian experimental design using non-stationary Gaussian Processes

Bayesian optimal experimental design for constitutive model calibration

Summary When Shannon entropy is used as a criterion in the optimal design of experiments, advantage can be taken of the classical identity representing the joint entropy of parameters and observations as the sum of the marginal entropy of the observations and the preposterior conditional entropy of the parameters. Following previous work in which this idea was used in spatial sampling, the method is applied to standard parameterized Bayesian optimal experimental design. Under suitable conditions, which include non-linear as well as linear regression models, it is shown in a few steps that maximizing the marginal entropy of the sample is equivalent to minimizing the preposterior entropy, the usual Bayesian criterion, thus avoiding the use of conditional distributions. It is shown using this marginal formulation that under normality assumptions every standard model which has a two-point prior distribution on the parameters gives an optimal design supported on a single point. Other results include a new asymptotic formula which applies as the error variance is large and bounds on support size.

Bayesian experimental design (BED) is a framework that uses statistical models and decision making under uncertainty to optimise the cost and performance of a scientific experiment. Sequential BED, as opposed to static BED, considers the scenario where we can sequentially update our beliefs about the model parameters through data gathered in the experiment. A class of models of particular interest for the natural and medical sciences are implicit models, where the data generating distribution is intractable, but sampling from it is possible. Even though there has been a lot of work on static BED for implicit models in the past few years, the notoriously difficult problem of sequential BED for implicit models has barely been touched upon. We address this gap in the literature by devising a novel sequential design framework for parameter estimation that uses the Mutual Information (MI) between model parameters and simulated data as a utility function to find optimal experimental designs, which has not been done before for implicit models. Our approach uses likelihood-free inference by ratio estimation to simultaneously estimate posterior distributions and the MI. During the sequential BED procedure we utilise Bayesian optimisation to help us optimise the MI utility. We find that our framework is efficient for the various implicit models tested, yielding accurate parameter estimates after only a few iterations.

We are honored to be guest editors for this special issue of Applied Stochastic Models in Business and Industry, dedicated to Kathryn Chaloner's life and achievements. Contributions from her colleagues and friends in this volume are devoted to Kathryn's early research interest in Bayesian optimal design. She was a pioneer in this field and had a broad impact on the subsequent literature on experimental design. Kathryn was internationally known for her research in Bayesian Statistics, which included design of experiments, outlier detection, prior elicitation, and clinical trials, and for her advancements in the study of HIV/AIDS. She was an accomplished researcher, teacher, and mentor. She actively encouraged women and under-represented minority students to join the field of biostatistics and provided mentorship, support, and encouragement. The special issue contains seven papers. The first three papers present some of the recent work in Bayesian optimal designs for nonlinear models, binary responses, and experiments with adversarial components. This is followed by two articles on Bayesian designs in clinical trials. The last two articles of the special issue involve engineering design problems. The paper by Giovagnoli considers the binary response models of Chaloner and Larntz (1989, Journal of Statistical Planning and Inference, 21:191–208) and develops an adaptive version of A-optimal Bayesian designs that are revised as additional data become available during the experiment. Adaptive Bayesian compound designs is also discussed as another extension. Konstantinou and Dette develop approximate Bayesian D-optimal designs for nonlinear regression models that involve covariates that cannot be observed directly. Applications to specific nonlinear models including the exponential regression model are considered and characterizations of the D-optimal saturated designs are presented. Optimal sample size selection for experiments is considered by De Santis and Gubbiotti in an adversarial setting where the decision makers have different prior opinions while having common utility functions and data. Using a Bayesian decision approach with a quadratic loss function, the authors present results for the one-parameter exponential family and investigate effect of the priors on the optimal sample size. Müller, Xu, and Thall discuss advantages and limitations of Bayesian decision theoretic approach in design of clinical trials. In doing so, the authors present a specific case study and point out the limitations such as the computational difficulties involved in solving sequential problems as well as selection of utility functions capturing different stakeholder interests. The article by Ventz, Parmigiani, and Trippa also consider limitations of the Bayesian framework in design of clinical trials and propose a strategy to alleviate these. The proposed strategy involves combining Bayesian designs with frequentist metrics such as error rates, confidence intervals, etc. that are commonly used by medical community and regulatory agencies. The authors show that this can be achieved by an inclusion of frequentist constraints into the Bayesian formulation. The constrained decision theoretic framework is illustrated via several applications and computational algorithms are presented for implementing the proposed approach. Nakamura, Seepaul, Kadane, and Reeja-Jayan discuss design of experiments in materials science. The authors consider use of a batch-sequential experiment and a regression model to determine optimal levels of input variables for synthesis of ceramic materials. It is illustrated that the optimal settings produce more reliable results than other experiments. The final article by Polson and Soyer considers Bayesian design of accelerated life tests for reliability assessment. An augmented probability simulation (APS) approach using Lindley's (1976, Annals of Statistics, 4:1–10) conjugate utility functions is proposed to compute optimal designs in an efficient manner. The proposed approach is illustrated using single and multiple point designs. Use of particle based methods for APS is also discussed as an alternative to Markov chain Monte Carlo methods.

Optimal experimental design is an important methodology for most efficiently allocating resources in an experiment to best achieve some goal. Bayesian experimental design considers the potential impact that various choices of the controllable variables has on the posterior distribution of the unknowns. Optimal Bayesian design involves optimising an expected utility function, which is an analytically intractable integral over the prior predictive distribution. These integrals are typically estimated via standard Monte Carlo methods. In this paper, we demonstrate that the use of randomised quasi-Monte Carlo can bring significant reductions to the variance of the estimated expected utility. This variance reduction will then lead to a more efficient optimisation algorithm for maximising the expected utility.

The sequential optimal experimental design formulated as an information-theoretic sensitivity analysis is applied to the ignition delay problem using real experimental. The optimal design is obtained by maximizing the statistical dependence between the model parameters and observables, which is quantified in this study using mutual information. This is naturally posed in the Bayesian framework. The study shows that by monitoring the information gain after each measurement update, one can design a stopping criteria for the experimental process which gives a minimal set of experiments to efficiently learn the Arrhenius parameters.

The Bayesian optimal experimental design (OED) problem seeks to identify data, sensor configurations, or experiments which can optimally reduce uncertainty. The goal of OED is to find an experiment that maximizes the expected information gain (EIG) about quantities of interest given prior knowledge about expected data. Therefore, within the context of seismic monitoring, we can use Bayesian OED to configure sensor networks by choosing sensor locations, types, and fidelity in order to improve our ability to identify and locate seismic sources. In this work, we develop the framework necessary to use Bayesian OED to optimize the ability to locate seismic events from arrival time data of detected seismic phases. In order to do utilize Bayesian OED we must develop four elements:1. A likelihood function that describes the uncertainty of detection and travel times; 2. A Bayesian solver that takes a prior and likelihood to identify the posterior; 3. An algorithm to compute EIG; and, 4. An optimizer that finds a sensor network which maximizes EIG. Once we have developed this framework, we can explore many relevant questions to monitoring such as: how and what multiphenomenology data can be used to optimally reduce uncertainty, how to trade off sensor fidelity and earth model uncertainty, and how sensor types, number, and locations influence uncertainty

We consider the problem of A-optimal design of experiment under a Bayesian probabilistic model with both categorical and continuous response variables. The utility function of the local design problem is derived by applying Bayesian experimental design framework. We also develop an efficient optimization algorithm to obtain the local optimal design by combining the particle swarm optimization and the blocked coordinate descent methods. In addition, we discuss two different ways of constructing the global optimal design based on the algorithm for local optimal design. Simulation studies are presented to illustrate the efficiency of our approach.

The concept of design space, as described in the ICH Harmonized Tripartite Guideline Q8 for Pharmaceutical Development (Q8 Pharmaceutical development, ICH harmonized tripartite guidelines, in International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use, 2005), was introduced to justify regulatory flexibility in pharmaceutical manufacturing operations. The basis for this concept is that advanced understanding of variables affecting product quality, obtained either through historical operation or demonstrated through process modeling, justifies replacement of traditional process targets with acceptable operational ranges. Process adjustments that allow operation within the region defined by the design space do not require regulatory oversight. Whereas there are many advantages to having the flexibility to operate within such ranges, the concept is only valid when the design space has been adequately described by appropriate experimentation. Given the complexity of pharmaceutical processes and the number of variables to consider in developing operational ranges, only a well-executed program of experiments, supported by appropriate statistical analyses, could provide the necessary information to truly capture a design space. Thus, the risk of employing a design space is that the model will be applied to a region outside of the approved design space, either through a false statistical inference or by omitting some important factor effects. This article presents a review of the experimental strategies typically employed to develop pharmaceutical processes with special emphasis on the assumptions and limitations of the approaches. An alternative strategy that provides an opportunity to build on previous information efficiently without requiring extraordinary skill in statistics, Bayesian optimal design, is introduced as an alternative to the classical approaches.

Bayesian optimal experimental design (OED) plays an important role in minimizing model uncertainty with limited experimental data in a Bayesian framework. In many applications, rather than minimizing the uncertainty in the inference of model parameters, one seeks to minimize the uncertainty of a model-dependent quantity of interest (QoI). This is known as goal-oriented OED (GOOED). Here, we consider GOOED for linear Bayesian inverse problems governed by large-scale models represented by partial differential equations (PDE) that are computationally expensive to solve. In particular, we consider optimal sensor placement by maximizing an expected information gain (EIG) for the QoI. We develop an efficient method to solve such problems by deriving a new formulation of the goal-oriented EIG. Based on this formulation we propose an offline-online decomposition scheme that achieves significant computational reduction by computing all of the PDE-dependent quantities in an offline stage just once, and optimizing the sensor locations in an online stage without solving any PDEs. Moreover, in the offline stage we need only to compute low-rank approximations of two Hessian-related operators. The computational cost of these low-rank approximations, measured by the number of PDE solves, does not depend on the parameter or data dimensions for a large class of elliptic, parabolic, and sufficiently dissipative hyperbolic inverse problem that exhibit dimension-independent rapid spectra decay. We carry out detailed error analysis for the approximate goal-oriented EIG due to the low-rank approximations of the two operators. Furthermore, in the online stage we extend a swapping greedy method to optimize the sensor locations developed in our recent work that is demonstrated to be more efficient than a standard greedy method. We conduct a numerical experiment for a contaminant transport inverse problem with an infinite-dimensional parameter field to demonstrate the efficiency, accuracy, and both data- and parameter-dimension independence of the proposed algorithm.

We consider the problem of learning structures and parameters of continuous-time Bayesian networks (CTBNs) from time-course data under minimal experimental resources. In practice, the cost of generating experimental data poses a bottleneck, especially in the natural and social sciences. A popular approach to overcome this is Bayesian optimal experimental design (BOED). However, BOED becomes infeasible in high-dimensional settings, as it involves integration over all possible experimental outcomes. We propose a novel criterion for experimental design based on a variational approximation of the expected information gain. We show that for CTBNs, a semi-analytical expression for this criterion can be calculated for structure and parameter learning. By doing so, we can replace sampling over experimental outcomes by solving the CTBNs master-equation, for which scalable approximations exist. This alleviates the computational burden of integrating over possible experimental outcomes in high-dimensions. We employ this framework in order to recommend interventional sequences. In this context, we extend the CTBN model to conditional CTBNs in order to incorporate interventions. We demonstrate the performance of our criterion on synthetic and real-world data.

In high-risk, time-pressure domains, the ability to get only salient information is of paramount importance. Missing or superfluous information in these domains can detract from a decision maker’s ability to make correct judgments. Consequently, decision support systems are being developed to facilitate expert decision-making by modifying the information presented to the operator. In this paper we introduce a method for presenting decision makers with the most environment-relevant information for a given decision task. This study explores a statistical method, Bayesian Optimal Experimental Design (OED), as a means of acquiring and restricting information to improve the probability of selecting the correct decision. We use probability gain theory to acquire the most useful piece of information to present to the decision maker, and we extend this to create a probability loss theory that restricts information that does not aid (probabilistically) or aids the least in the decision-making process.

Derivative-informed projected neural networks for high-dimensional parametric maps governed by PDEs

Optimal Bayesian experimental designs for estimation and prediction in linear models are discussed. The designs are optimal for estimating a linear combination of the regression parameters $\\mathbf{c}^T\\theta$ or prediction at a point where the expected response is $\\mathbf{c}^T\\mathbf{\\theta}$ under squared error loss. A distribution on $\\mathbf{c}$ is introduced to represent the interest in particular linear combinations of the parameters. In the usual notation for linear models minimizing the preposterior expected loss leads to minimizing the quantity $\\mathrm{tr}\\psi(R + XX^T)^{-1}$. The matrix $\\psi$ is defined to be $E(\\mathbf{cc}^T)$ and the matrix $R$ is the prior precision matrix of $\\theta$. A geometric interpretation of the optimal designs is given which leads to a parallel of Elfving's theorem for $\\mathbf{c}$-optimality. A bound is given for the minimum number of points at which it is necessary to take observations. Some examples of optimal Bayesian designs are given and optimal designs for prediction in polynomial regression are derived. The optimality of rounding non-integer designs to integer designs is discussed.