Bayesian calibration of a computer code

In this example we compute the parameters of a computer model thanks to Bayesian estimation. We use the RandomWalkMetropolisHastings and Gibbs classes and simulate a sample of the posterior distribution using The Metropolis-Hastings Algorithm.

Let us denote (y_1, \dots, y_n) the observation sample, (\vect z_1, \ldots, \vect z_n) = (f(x_1|\vect\theta), \ldots, f(x_n|\vect\theta)) the model prediction, p(y |\vect z) the density function of observation y conditional on model prediction \vect z, and \vect\theta \in \mathbb{R}^p the calibration parameters we wish to estimate.

The posterior distribution is given by Bayes theorem:

\pi(\vect\theta | \vect y) \quad \propto \quad L\left(\vect y | \vect\theta\right) \times \pi(\vect\theta)

where \propto means “proportional to”, regarded as a function of \vect\theta.

The posterior distribution is approximated here by the empirical distribution of the sample \vect\theta^1, \ldots, \vect\theta^N generated by the Metropolis-Hastings algorithm. This means that any quantity characteristic of the posterior distribution (mean, variance, quantile, …) is approximated by its empirical counterpart.

Our model (i.e. the compute code to calibrate) is a standard normal linear regression, where

y_i = \theta_1 + x_i \theta_2 + x_i^2 \theta_3 + \varepsilon_i

where \varepsilon_i \stackrel{i.i.d.}{\sim} \mathcal N(0, 1).

The “true” value of \theta is:

\vect \theta_{true} = (-4.5,4.8,2.2)^T.

We use a normal prior on \vect\theta:

\pi(\vect\theta) = \mathcal N(\vect{\mu}_\vect{\theta}, \mat{\Sigma}_\vect{\theta})


\vect{\mu}_\vect{\theta} =
 -3 \\
  4 \\

is the mean of the prior and

\mat{\Sigma}_\vect{\theta} =
  \sigma_{\theta_1}^2 & 0 & 0 \\
  0 & \sigma_{\theta_2}^2 & 0 \\
  0 & 0 & \sigma_{\theta_3}^2

is the prior covariance matrix with

\sigma_{\theta_1} = 2, \qquad \sigma_{\theta_2} = 1, \qquad \sigma_{\theta_3} = 1.5.

The following objects need to be defined in order to perform Bayesian calibration:

  • The conditional density p(y|\vect z) must be defined as a probability distribution.

  • The computer model must be implemented thanks to the ParametricFunction class. This takes a value of \vect\theta as input, and outputs the vector of model predictions \vect z, as defined above (the vector of covariates \vect x = (x_1, \ldots, x_n) is treated as a known constant). When doing that, we have to keep in mind that \vect z will be used as the vector of parameters corresponding to the distribution specified for p(y |\vect z). For instance, if p(y|\vect z) is normal, this means that \vect z must be a vector containing the mean and standard deviation of y.

  • The prior density \pi(\vect\theta) encoding the set of possible values for the calibration parameters, each value being weighted by its a priori probability, reflecting the beliefs about the possible values of \vect\theta before consideration of the experimental data. Again, this is implemented as a probability distribution.

  • Metropolis-Hastings algorithm(s), possibly used in tandem with a Gibbs algorithm in order to sample from the posterior distribution of the calibration parameters.

This example uses the ParametricFunction class. Please read its documentation and Create a parametric function for a detailed example.

import openturns as ot
import openturns.viewer as viewer
from matplotlib import pylab as plt


Dimension of the vector of parameters to calibrate

paramDim = 3
# The number of obesrvations
obsSize = 10

Define the observed inputs x_i.

xmin = -2.0
xmax = 3.0
step = (xmax - xmin) / (obsSize - 1)
rg = ot.RegularGrid(xmin, step, obsSize)
x_obs = rg.getVertices()

Define the parametric model \vect z = f(x,\vect\theta) that associates each observation x and value of \vect \theta to the parameters of the distribution of the corresponding observation y: here \vect z=(\mu, \sigma) where \mu, the first output of the model, is the mean and \sigma, the second output of the model, is the standard deviation.

fullModel = ot.SymbolicFunction(
    ["x", "theta1", "theta2", "theta3"], ["theta1+theta2*x+theta3*x^2", "1.0"]

To differentiate between the two classes of inputs (x and \vect\theta), we define a ParametricFunction from fullModel and make the first input (the observations x) its parameter: f_x(\vect \theta) := f(x, \vect \theta). We set x = 1 as a placeholder, but x will actually take the values x_i of the observations when we sample \vect\theta.

linkFunction = ot.ParametricFunction(fullModel, [0], [1.0])
ParametricEvaluation([x,theta1,theta2,theta3]->[theta1+theta2*x+theta3*x^2,1.0], parameters positions=[0], parameters=[x : 1], input positions=[1,2,3])

Define the observation noise \varepsilon {\sim} \mathcal N(0, 1) and create a sample from it.

noiseStandardDeviation = 1.0
noise = ot.Normal(0, noiseStandardDeviation)
noiseSample = noise.getSample(obsSize)

Define the vector of observations y_i, here sampled using the “true” value of \vect \theta: \vect \theta_{true}.

thetaTrue = [-4.5, 4.8, 2.2]
y_obs = ot.Sample(obsSize, 1)
for i in range(obsSize):
    y_obs[i, 0] = linkFunction(thetaTrue)[0] + noiseSample[i, 0]

Draw the model predictions vs the observations.

functionnalModel = ot.ParametricFunction(fullModel, [1, 2, 3], thetaTrue)
graphModel = functionnalModel.getMarginal(0).draw(xmin, xmax)
observations = ot.Cloud(x_obs, y_obs)
graphModel.setLegends(["Model", "Observations"])
graphModel.setLegendPosition("upper left")
view = viewer.View(graphModel)
y0 as a function of x

Define the distribution of observations y | \vect{z} conditional on model predictions.

Note that its parameter dimension is the one of \vect{z}, so the model must be adjusted accordingly.

conditional = ot.Normal()

Define the mean \mu_\theta, the covariance matrix \Sigma_\theta, then the prior distribution \pi(\vect\theta) of the parameter \vect\theta.

thetaPriorMean = [-3.0, 4.0, 1.0]
sigma0 = [2.0, 1.0, 1.5]  # standard deviations
thetaPriorCovarianceMatrix = ot.CovarianceMatrix(paramDim)
for i in range(paramDim):
    thetaPriorCovarianceMatrix[i, i] = sigma0[i] ** 2

prior = ot.Normal(thetaPriorMean, thetaPriorCovarianceMatrix)
prior.setDescription(["theta1", "theta2", "theta3"])

The proposed steps for \theta_1, \theta_2 and \theta_3 will all follow a uniform distribution.

proposal = ot.Uniform(-1.0, 1.0)

Test the Metropolis-Hastings sampler

Creation of a single component random walk Metropolis-Hastings (RWMH) sampler. This involves a combination of the RWMH and the Gibbs algorithms.

initialState = thetaPriorMean

We create a RandomWalkMetropolisHastings sampler for each component. Each sampler must be aware of the joint prior distribution. We also use the same proposal distribution, but this is not mandatory.

mh_coll = [
    ot.RandomWalkMetropolisHastings(prior, initialState, proposal, [i])
    for i in range(paramDim)

Each sampler must be made aware of the likelihood. Otherwise we would sample from the prior!

for mh in mh_coll:
    mh.setLikelihood(conditional, y_obs, linkFunction, x_obs)

Finally, the Gibbs algorithm is constructed from all Metropolis-Hastings samplers.

sampler = ot.Gibbs(mh_coll)

Generate a sample from the posterior distribution of the parameters \vect \theta.

sampleSize = 10000
sample = sampler.getSample(sampleSize)

Look at the acceptance rate (basic check of the sampling efficiency: values close to 0.2 are usually recommended for Normal posterior distributions).

[mh.getAcceptanceRate() for mh in sampler.getMetropolisHastingsCollection()]
[0.282, 0.2944, 0.3035]

Build the distribution of the posterior by kernel smoothing.

kernel = ot.KernelSmoothing()
posterior =

Display prior vs posterior for each parameter.

def plot_bayesian_prior_vs_posterior_pdf(prior, posterior):
    Plot the prior and posterior distribution of a Bayesian calibration

    prior : ot.Distribution(dimension)
        The prior.
    posterior : ot.Distribution(dimension)
        The posterior.

    grid : ot.GridLayout(1, dimension)
        The prior and posterior PDF for each marginal.
    palette = ot.Drawable.BuildDefaultPalette(2)
    paramDim = prior.getDimension()
    grid = ot.GridLayout(1, paramDim)
    parameterNames = prior.getDescription()
    for parameter_index in range(paramDim):
        graph = ot.Graph("", parameterNames[parameter_index], "PDF", True)
        # Prior
        curve = prior.getMarginal(parameter_index).drawPDF().getDrawable(0)
        # Posterior
        curve = posterior.getMarginal(parameter_index).drawPDF().getDrawable(0)
        if parameter_index < paramDim - 1:
        if parameter_index > 0:
        graph.setLegendPosition("upper right")
        grid.setGraph(0, parameter_index, graph)
    grid.setTitle("Bayesian calibration")
    return grid

sphinx_gallery_thumbnail_number = 2

grid = plot_bayesian_prior_vs_posterior_pdf(prior, posterior)
    figure_kw={"figsize": (8.0, 3.0)},
    legend_kw={"bbox_to_anchor": (1.0, 1.0), "loc": "upper left"},
plt.subplots_adjust(right=0.8, bottom=0.2, wspace=0.3)
Bayesian calibration