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Bayesian experimental design

From Wikipedia, the free encyclopedia
Experimental design framework
Part of a series on
Bayesian statistics
Posterior =Likelihood ×Prior ÷Evidence
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Bayesian experimental design provides a general probability-theoretical framework from which other theories onexperimental design can be derived. It is based onBayesian inference to interpret the observations/data acquired during the experiment. This allows accounting for both any prior knowledge on the parameters to be determined as well as uncertainties in observations.

The theory of Bayesian experimental design[1] is to a certain extent based on the theory for makingoptimal decisions under uncertainty. The aim when designing an experiment is to maximize the expected utility of the experiment outcome. The utility is most commonly defined in terms of a measure of the accuracy of the information provided by the experiment (e.g., theShannon information or the negative of thevariance) but may also involve factors such as the financial cost of performing the experiment. What will be the optimal experiment design depends on the particular utility criterion chosen.

Relations to more specialized optimal design theory

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Linear theory

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If the model is linear, theprior probability density function (PDF) is homogeneous and observational errors arenormally distributed, the theory simplifies to the classicaloptimal experimental design theory.

Approximate normality

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In numerous publications on Bayesian experimental design, it is (often implicitly) assumed that allposterior probabilities will be approximately normal. This allows for the expected utility to be calculated using linear theory, averaging over the space of model parameters.[2] Caution must however be taken when applying this method, since approximate normality of all possible posteriors is difficult to verify, even in cases of normal observational errors and uniform prior probability.

Posterior distribution

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In many cases, the posterior distribution is not available in closed form and has to be approximated using numerical methods. The most common approach is to useMarkov chain Monte Carlo methods to generate samples from the posterior, which can then be used to approximate the expected utility.

Another approach is to use avariational Bayes approximation of the posterior, which can often be calculated in closed form. This approach has the advantage of being computationally more efficient than Monte Carlo methods, but the disadvantage that the approximation might not be very accurate.

Some authors proposed approaches that use theposterior predictive distribution to assess the effect of new measurements on prediction uncertainty,[3][4] while others suggest maximizing the mutual information between parameters, predictions and potential new experiments.[5]

Mathematical formulation

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Notation
θ{\displaystyle \theta \,}parameters to be determined
y{\displaystyle y\,}observation or data
ξ{\displaystyle \xi \,}design
p(yθ,ξ){\displaystyle p(y\mid \theta ,\xi )\,}PDF for making observationy{\displaystyle y}, given parameter valuesθ{\displaystyle \theta } and designξ{\displaystyle \xi }
p(θ){\displaystyle p(\theta )\,}prior PDF
p(yξ){\displaystyle p(y\mid \xi )\,}marginal PDF in observation space
p(θy,ξ){\displaystyle p(\theta \mid y,\xi )\,}   posterior PDF
U(ξ){\displaystyle U(\xi )\,}   utility of the designξ{\displaystyle \xi }
U(y,ξ){\displaystyle U(y,\xi )\,}   utility of the experiment outcome after observationy{\displaystyle y} with designξ{\displaystyle \xi }

Given a vectorθ{\displaystyle \theta } of parameters to determine, a prior probabilityp(θ){\displaystyle p(\theta )} over those parameters and alikelihoodp(yθ,ξ){\displaystyle p(y\mid \theta ,\xi )} for making observationy{\displaystyle y}, given parameter valuesθ{\displaystyle \theta } and an experiment designξ{\displaystyle \xi }, the posterior probability can be calculated usingBayes' theorem

p(θy,ξ)=p(yθ,ξ)p(θ)p(yξ),{\displaystyle p(\theta \mid y,\xi )={\frac {p(y\mid \theta ,\xi )p(\theta )}{p(y\mid \xi )}}\,,}

wherep(yξ){\displaystyle p(y\mid \xi )} is the marginal probability density in observation space

p(yξ)=p(θ)p(yθ,ξ)dθ.{\displaystyle p(y\mid \xi )=\int p(\theta )p(y\mid \theta ,\xi )\,d\theta \,.}

The expected utility of an experiment with designξ{\displaystyle \xi } can then be defined

U(ξ)=p(yξ)U(y,ξ)dy,{\displaystyle U(\xi )=\int p(y\mid \xi )U(y,\xi )\,dy,}

whereU(y,ξ){\displaystyle U(y,\xi )} is some real-valued functional of the posterior probabilityp(θy,ξ){\displaystyle p(\theta \mid y,\xi )} after making observationy{\displaystyle y} using an experiment designξ{\displaystyle \xi }.

Gain in Shannon information as utility

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Utility may be defined as the prior-posterior gain inShannon information

U(y,ξ)=log(p(θy,ξ))p(θ|y,ξ)dθlog(p(θ))p(θ)dθ.{\displaystyle U(y,\xi )=\int \log(p(\theta \mid y,\xi ))\,p(\theta |y,\xi )\,d\theta -\int \log(p(\theta ))\,p(\theta )\,d\theta \,.}

Another possibility is to define the utility as

U(y,ξ)=DKL(p(θy,ξ)p(θ)),{\displaystyle U(y,\xi )=D_{KL}(p(\theta \mid y,\xi )\|p(\theta ))\,,}

theKullback–Leibler divergence of the prior from the posterior distribution.Lindley (1956) noted that the expected utility will then be coordinate-independent and can be written in two forms

U(ξ)=log(p(θy,ξ))p(θ,yξ)dθdylog(p(θ))p(θ)dθ=log(p(yθ,ξ))p(θ,yξ)dydθlog(p(yξ))p(yξ)dy,{\displaystyle {\begin{alignedat}{2}U(\xi )&=\int \int \log(p(\theta \mid y,\xi ))\,p(\theta ,y\mid \xi )\,d\theta \,dy-\int \log(p(\theta ))\,p(\theta )\,d\theta \\&=\int \int \log(p(y\mid \theta ,\xi ))\,p(\theta ,y\mid \xi )\,dy\,d\theta -\int \log(p(y\mid \xi ))\,p(y\mid \xi )\,dy,\end{alignedat}}\,}

of which the latter can be evaluated without the need for evaluating individual posterior probabilityp(θy,ξ){\displaystyle p(\theta \mid y,\xi )} for all possible observationsy{\displaystyle y}.[6] It is worth noting that the second term on the second equation line will not depend on the designξ{\displaystyle \xi }, as long as the observational uncertainty doesn't. On the other hand, the integral ofp(θ)logp(θ){\displaystyle p(\theta )\log p(\theta )} in the first form is constant for allξ{\displaystyle \xi }, so if the goal is to choose the design with the highest utility, the term need not be computed at all. Several authors have considered numerical techniques for evaluating and optimizing this criterion.[7][8] Note that

U(ξ)=I(θ;y),{\displaystyle U(\xi )=I(\theta ;y)\,,}

the expectedinformation gain being exactly themutual information between the parameterθ and the observationy. An example of Bayesian design for linear dynamical model identification are given in[9][10].

SinceI(θ;y),{\displaystyle I(\theta ;y)\,,} was difficult to calculate, its lower bound has been used as a utility function. The lower bound is then maximized under the signal energy constraint. Proposed Bayesian design has been also compared with classical average D-optimal design. It was shown that the Bayesian design is superior to D-optimal design.

TheKelly criterion also describes such a utility function for a gambler seeking to maximize profit, which is used ingambling and information theory; Kelly's situation is identical to the foregoing, with the side information, or "private wire" taking the place of the experiment.

See also

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References

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  1. ^Lee, Se Yoon (2024)."Using Bayesian statistics in confirmatory clinical trials in the regulatory setting: a tutorial review".BMC Med Res Methodol.24 (1) 110.doi:10.1186/s12874-024-02235-0.PMC 11077897.PMID 38714936.
  2. ^An approach reviewed inChaloner, Kathryn; Verdinelli, Isabella (1995),"Bayesian experimental design: a review"(PDF),Statistical Science,10 (3):273–304,doi:10.1214/ss/1177009939
  3. ^Vanlier; Tiemann; Hilbers; van Riel (2012), "A Bayesian approach to targeted experiment design",Bioinformatics,28 (8):1136–1142,doi:10.1093/bioinformatics/bts092,PMC 3324513,PMID 22368245
  4. ^Thibaut; Laloy; Hermans (2021), "A new framework for experimental design using Bayesian Evidential Learning: The case of wellhead protection area",Journal of Hydrology,603 126903,arXiv:2105.05539,Bibcode:2021JHyd..60326903T,doi:10.1016/j.jhydrol.2021.126903,hdl:1854/LU-8759542,S2CID 234469903
  5. ^Liepe; Filippi; Komorowski; Stumpf (2013), "Maximizing the Information Content of Experiments in Systems Biology",PLOS Computational Biology,9 (1) e1002888,Bibcode:2013PLSCB...9E2888L,doi:10.1371/journal.pcbi.1002888,PMC 3561087,PMID 23382663
  6. ^Lindley, D. V. (1956), "On a measure of information provided by an experiment",Annals of Mathematical Statistics,27 (4):986–1005,doi:10.1214/aoms/1177728069
  7. ^van den Berg; Curtis; Trampert (2003), "Optimal nonlinear Bayesian experimental design: an application to amplitude versus offset experiments",Geophysical Journal International,155 (2):411–421,Bibcode:2003GeoJI.155..411V,doi:10.1046/j.1365-246x.2003.02048.x
  8. ^Ryan, K. J. (2003), "Estimating Expected Information Gains for Experimental Designs With Application to the Random Fatigue-Limit Model",Journal of Computational and Graphical Statistics,12 (3):585–603,doi:10.1198/1061860032012,S2CID 119889630
  9. ^Bania, P. (2019), "Bayesian Input Design for Linear Dynamical Model Discrimination",Entropy,21 (4): 351,Bibcode:2019Entrp..21..351B,doi:10.3390/e21040351,PMC 7514835,PMID 33267065
  10. ^Bania, Piotr; Wojcik, Anna (7 October 2025)."An Approximate Bayesian Approach to Optimal Input Signal Design for System Identification".Entropy.27 (10): 1041.arXiv:2511.04425.Bibcode:2025Entrp..27.1041B.doi:10.3390/e27101041.

Further reading

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