Example: Bayesian initial condition inversion in an advection-diffusion problem

In this example we tackle the problem of quantifying the uncertainty in the solution of an inverse problem governed by a parabolic PDE via the Bayesian inference framework. The underlying PDE is a time-dependent advection-diffusion equation in which we seek to infer an unknown initial condition from spatio-temporal point measurements.

The Bayesian inverse problem:

Following the Bayesian framework, we utilize a Gaussian prior measure , with where is an elliptic differential operator as described in the PoissonBayesian example, and use an additive Gaussian noise model. Therefore, the solution of the Bayesian inverse problem is the posterior measure, with and .

which can also be interpreted as the regularized functional to be minimized in deterministic inversion. The observation operator extracts the values of the forward solution on a set of locations at times .

The forward problem:

The PDE in the parameter-to-observable map models diffusive transport in a domain ():

Here, is the diffusion coefficient and is the final time. The velocity field is computed by solving the following steady-state Navier-Stokes equation with the side walls driving the flow:

Here, is pressure, is the Reynolds number. The Dirichlet boundary data is given by on the left wall of the domain, on the right wall, and everywhere else.

The adjoint problem:

1. Load modules

from __future__ import absolute_import, division, print_function

import dolfin as dl
import math
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline
import sys
import os
sys.path.append( os.environ.get('HIPPYLIB_BASE_DIR', "../") )
from hippylib import *
sys.path.append( os.environ.get('HIPPYLIB_BASE_DIR', "..") + "/applications/ad_diff/" )
from model_ad_diff import TimeDependentAD

import nb

import logging
logging.getLogger('FFC').setLevel(logging.WARNING)
logging.getLogger('UFL').setLevel(logging.WARNING)
dl.set_log_active(False)

np.random.seed(1)

2. Construct the velocity field

def v_boundary(x,on_boundary):
    return on_boundary

def q_boundary(x,on_boundary):
    return x[0] < dl.DOLFIN_EPS and x[1] < dl.DOLFIN_EPS

def computeVelocityField(mesh):
    Xh = dl.VectorFunctionSpace(mesh,'Lagrange', 2)
    Wh = dl.FunctionSpace(mesh, 'Lagrange', 1)
    if dlversion() <= (1,6,0):
        XW = dl.MixedFunctionSpace([Xh, Wh])
    else:
        mixed_element = dl.MixedElement([Xh.ufl_element(), Wh.ufl_element()])
        XW = dl.FunctionSpace(mesh, mixed_element)

    Re = 1e2

    g = dl.Expression(('0.0','(x[0] < 1e-14) - (x[0] > 1 - 1e-14)'), degree=1)
    bc1 = dl.DirichletBC(XW.sub(0), g, v_boundary)
    bc2 = dl.DirichletBC(XW.sub(1), dl.Constant(0), q_boundary, 'pointwise')
    bcs = [bc1, bc2]

    vq = dl.Function(XW)
    (v,q) = dl.split(vq)
    (v_test, q_test) = dl.TestFunctions (XW)

    def strain(v):
        return dl.sym(dl.nabla_grad(v))

    F = ( (2./Re)*dl.inner(strain(v),strain(v_test))+ dl.inner (dl.nabla_grad(v)*v, v_test)
           - (q * dl.div(v_test)) + ( dl.div(v) * q_test) ) * dl.dx

    dl.solve(F == 0, vq, bcs, solver_parameters={"newton_solver":
                                         {"relative_tolerance":1e-4, "maximum_iterations":100}})

    plt.figure(figsize=(15,5))
    vh = dl.project(v,Xh)
    qh = dl.project(q,Wh)
    nb.plot(nb.coarsen_v(vh), subplot_loc=121,mytitle="Velocity")
    nb.plot(qh, subplot_loc=122,mytitle="Pressure")
    plt.show()

    return v

3. Set up the mesh and finite element spaces

mesh = dl.refine( dl.Mesh("ad_20.xml") )
wind_velocity = computeVelocityField(mesh)
Vh = dl.FunctionSpace(mesh, "Lagrange", 1)
print("Number of dofs: {0}".format( Vh.dim() ) )

png

Number of dofs: 2023

4. Set up model (prior, true/proposed initial condition)

#gamma = 1
#delta = 10
#prior = LaplacianPrior(Vh, gamma, delta)

gamma = 1
delta = 8
prior = BiLaplacianPrior(Vh, gamma, delta)

prior.mean = dl.interpolate(dl.Constant(0.5), Vh).vector()
true_initial_condition = dl.interpolate(dl.Expression('min(0.5,exp(-100*(pow(x[0]-0.35,2) +  pow(x[1]-0.7,2))))', degree=5), Vh).vector()
problem = TimeDependentAD(mesh, [Vh,Vh,Vh], 0., 4., 1., .2, wind_velocity, True, prior)

objs = [dl.Function(Vh,true_initial_condition),
        dl.Function(Vh,prior.mean)]
mytitles = ["True Initial Condition", "Prior mean"]
nb.multi1_plot(objs, mytitles)
plt.show()

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5. Generate the synthetic observations

rel_noise = 0.001
utrue = problem.generate_vector(STATE)
x = [utrue, true_initial_condition, None]
problem.solveFwd(x[STATE], x, 1e-9)
MAX = utrue.norm("linf", "linf")
noise_std_dev = rel_noise * MAX
problem.ud.copy(utrue)
problem.ud.randn_perturb(noise_std_dev)
problem.noise_variance = noise_std_dev*noise_std_dev

nb.show_solution(Vh, true_initial_condition, utrue, "Solution")

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6. Test the gradient and the Hessian of the cost (negative log posterior)

a0 = true_initial_condition.copy()
modelVerify(problem, a0, 1e-12, is_quadratic=True)
(yy, H xx) - (xx, H yy) =  -4.75341826113e-14

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7. Evaluate the gradient

[u,a,p] = problem.generate_vector()
problem.solveFwd(u, [u,a,p], 1e-12)
problem.solveAdj(p, [u,a,p], 1e-12)
mg = problem.generate_vector(PARAMETER)
grad_norm = problem.evalGradientParameter([u,a,p], mg)

print("(g,g) = ", grad_norm)
(g,g) =  1.66716039169e+12

8. The Gaussian approximation of the posterior

H = ReducedHessian(problem, 1e-12, gauss_newton_approx=False, misfit_only=True) 

k = 80
p = 20
print("Single Pass Algorithm. Requested eigenvectors: {0}; Oversampling {1}.".format(k,p))
Omega = np.random.randn(get_local_size(a), k+p)
d, U = singlePassG(H, prior.R, prior.Rsolver, Omega, k)


posterior = GaussianLRPosterior( prior, d, U )

plt.plot(range(0,k), d, 'b*', range(0,k+1), np.ones(k+1), '-r')
plt.yscale('log')
plt.xlabel('number')
plt.ylabel('eigenvalue')

nb.plot_eigenvectors(Vh, U, mytitle="Eigenvector", which=[0,1,2,5,10,20,30,45,60])
Single Pass Algorithm. Requested eigenvectors: 80; Oversampling 20.

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9. Compute the MAP point

H.misfit_only = False

solver = CGSolverSteihaug()
solver.set_operator(H)
solver.set_preconditioner( posterior.Hlr )
solver.parameters["print_level"] = 1
solver.parameters["rel_tolerance"] = 1e-6
solver.solve(a, -mg)
problem.solveFwd(u, [u,a,p], 1e-12)

total_cost, reg_cost, misfit_cost = problem.cost([u,a,p])
print("Total cost {0:5g}; Reg Cost {1:5g}; Misfit {2:5g}".format(total_cost, reg_cost, misfit_cost))

posterior.mean = a

plt.figure(figsize=(7.5,5))
nb.plot(dl.Function(Vh, a), mytitle="Initial Condition")
plt.show()

nb.show_solution(Vh, a, u, "Solution")
 Iterartion :  0  (B r, r) =  30140.7469425
 Iteration :  1  (B r, r) =  0.0653733954192
 Iteration :  2  (B r, r) =  6.28002367536e-06
 Iteration :  3  (B r, r) =  9.57007003125e-10
Relative/Absolute residual less than tol
Converged in  3  iterations with final norm  3.09355297858e-05
Total cost 84.2612; Reg Cost 68.8823; Misfit 15.3789

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10. Prior and posterior pointwise variance fields

compute_trace = True
if compute_trace:
    post_tr, prior_tr, corr_tr = posterior.trace(method="Randomized", r=200)
    print("Posterior trace {0:5g}; Prior trace {1:5g}; Correction trace {2:5g}".format(post_tr, prior_tr, corr_tr))
post_pw_variance, pr_pw_variance, corr_pw_variance = posterior.pointwise_variance(method="Randomized", r=300)

objs = [dl.Function(Vh, pr_pw_variance),
        dl.Function(Vh, post_pw_variance)]
mytitles = ["Prior Variance", "Posterior Variance"]
nb.multi1_plot(objs, mytitles, logscale=True)
plt.show()
Posterior trace 0.000602854; Prior trace 0.0285673; Correction trace 0.0279644

png

11. Draw samples from the prior and posterior distributions

nsamples = 5
noise = dl.Vector()
posterior.init_vector(noise,"noise")
noise_size = get_local_size(noise)
s_prior = dl.Function(Vh, name="sample_prior")
s_post = dl.Function(Vh, name="sample_post")

pr_max =  2.5*math.sqrt( pr_pw_variance.max() ) + prior.mean.max()
pr_min = -2.5*math.sqrt( pr_pw_variance.min() ) + prior.mean.min()
ps_max =  2.5*math.sqrt( post_pw_variance.max() ) + posterior.mean.max()
ps_min = -2.5*math.sqrt( post_pw_variance.max() ) + posterior.mean.min()

for i in range(nsamples):
    noise.set_local( np.random.randn( noise_size ) )
    posterior.sample(noise, s_prior.vector(), s_post.vector())
    plt.figure(figsize=(15,5))
    nb.plot(s_prior, subplot_loc=121,mytitle="Prior sample", vmin=pr_min, vmax=pr_max)
    nb.plot(s_post, subplot_loc=122,mytitle="Posterior sample", vmin=ps_min, vmax=ps_max)
    plt.show()

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