Surrogate-accelerated iterative ensemble smoother • PESTO

Overview

The surrogate-accelerated IES reduces the number of expensive forward-model evaluations during iterative parameter estimation. It embeds an online Gaussian process (GP) surrogate in the IES update loop and uses uncertainty-driven switching to decide which ensemble members need a full model evaluation and which can use the cheaper surrogate prediction. This vignette demonstrates the workflow, states where it pays off, and shows the savings on a real run.

Regime of applicability

The GP surrogate has a bounded operating envelope, worth stating before the demo. As a soft floor, use n_train >= 5 * n_params: below that ratio the GP posterior variance rarely drops far enough for the switching rule to fire, and the surrogate defers to the full model on most realisations. The second axis is smoothness: smooth, near-linear responses are well approximated by an RBF-kernel GP and yield large savings, whereas rough or near-discontinuous responses (sharp wetting fronts, threshold activations, regime switches) defeat the kernel and savings collapse. The third is ensemble size: larger ensembles improve the GP fit roughly as \mathcal{O}(n^{-1}) in posterior variance, and fewer than about twenty realisations rarely produce a usable surrogate. Outside this envelope, run pure IES via ensemble_solution(): surrogate_ensemble_update() reports near-zero savings rather than degrading the posterior, but you pay the GP training cost for no return. The check_surrogate_regime() helper flags an unfavourable regime before you commit.

The test problem

A nonlinear forward model inspired by groundwater flow, with a linear sensitivity and a nonlinear interaction term:

y_j = \eta_j + \alpha \sin(\eta_j)\, e^{-0.1\,\lvert \eta_j \rvert} + \varepsilon_j, \qquad \eta_j = \sum_k G_{jk}\theta_k .

Here \eta_j is the linear predictor and \alpha controls the nonlinearity: \alpha = 0 is linear, \alpha = 1 is strongly nonlinear.

library(PESTO)
library(data.table)
#> 
#> Attaching package: 'data.table'
#> The following object is masked from 'package:base':
#> 
#>     %notin%
library(ggplot2)

forward_model <- function(theta, G, alpha = 0.3) {
  linear <- as.numeric(G %*% theta)
  nonlinear <- alpha * sin(linear) * exp(-0.1 * abs(linear))
  linear + nonlinear
}

set.seed(42)
n_par <- 20
n_obs <- 50
n_real <- 50

theta_true <- rnorm(n_par)
G <- matrix(rnorm(n_obs * n_par, sd = 1 / sqrt(n_par)), n_obs, n_par)
y_obs <- forward_model(theta_true, G, alpha = 0.3) + rnorm(n_obs, sd = 0.1)

Step 1: generate the prior ensemble

par_ens <- matrix(rnorm(n_real * n_par, sd = 1.5), n_real, n_par)

# Run the forward model for each realisation
obs_ens <- t(apply(par_ens, 1, function(p) {
  forward_model(p, G, alpha = 0.3) + rnorm(n_obs, sd = 0.1)
}))

cat("Parameter ensemble:", nrow(par_ens), "realisations x", ncol(par_ens), "parameters\n")
#> Parameter ensemble: 50 realisations x 20 parameters
cat("Observation ensemble:", nrow(obs_ens), "realisations x", ncol(obs_ens), "observations\n")
#> Observation ensemble: 50 realisations x 50 observations

Step 2: train the GP surrogate

PESTO trains a GP with an RBF kernel directly from the ensemble:

gp <- train_gp_surrogate(par_ens, obs_ens)

cat("Training samples:", gp$n_train, "\n")
#> Training samples: 50
cat("Parameters:", gp$n_par, "\n")
#> Parameters: 20
cat("Outputs:", gp$n_obs, "\n")
#> Outputs: 50
cat("Length scale:", round(gp$length_scale, 4), "\n")
#> Length scale: 9.2136
cat("Signal variance:", round(gp$signal_var, 4), "\n")
#> Signal variance: 2.5654
cat("Log marginal likelihood:", round(gp$log_marginal_likelihood, 1), "\n")
#> Log marginal likelihood: -3043.3

Step 3: evaluate surrogate predictions

predictions <- predict_gp_surrogate(gp, par_ens)

cat("Prediction dimensions:", dim(predictions$mean), "\n")
#> Prediction dimensions: 50 50
cat("Mean prediction uncertainty:", round(mean(predictions$uncertainty), 6), "\n")
#> Mean prediction uncertainty: 0.009998
cat("Max prediction uncertainty:", round(max(predictions$uncertainty), 6), "\n")
#> Max prediction uncertainty: 0.009999

# Check prediction accuracy
pred_error <- sqrt(mean((predictions$mean - obs_ens)^2))
cat("Prediction RMSE:", round(pred_error, 6), "\n")
#> Prediction RMSE: 0.000119

The GP achieves near-zero prediction error because it is interpolating within its training set – this is by design, not an artefact.

Step 4: surrogate-assisted IES update

surrogate_ensemble_update() performs the full algorithm:

Train a GP from the current ensemble.
Predict model outputs for all realisations.
Classify by uncertainty: high -> full model, low -> surrogate.
Apply the control-variate bias correction.
Compute the IES update on the blended ensemble.

weights <- rep(1 / 0.1, n_obs)    # 1 / obs_noise
parcov_inv <- rep(1 / 1.5^2, n_par)  # 1 / prior_var

result <- surrogate_ensemble_update(
  par_ensemble = par_ens,
  obs_ensemble = obs_ens,
  obs_target = y_obs,
  weights = weights,
  parcov_inv = parcov_inv,
  cur_lam = 1.0,
  uncertainty_threshold = 0.1
)

cat("Full model runs needed:", result$n_model_runs, "\n")
#> Full model runs needed: 0
cat("Surrogate predictions:", result$n_surrogate_runs, "\n")
#> Surrogate predictions: 50
cat("Total realisations:", result$n_total, "\n")
#> Total realisations: 50
cat("Model savings:", sprintf("%.0f%%", result$savings_pct), "\n")
#> Model savings: 100%
cat("Mean GP uncertainty:", round(result$mean_uncertainty, 6), "\n")
#> Mean GP uncertainty: 0.009998
cat("GP length scale:", round(result$gp_length_scale, 4), "\n")
#> GP length scale: 9.2136

This twenty-parameter problem with a fifty-member ensemble sits below the n_train >= 5 * n_params floor, so the GP variance rarely clears the switching threshold and the savings here are modest by design. The next section places the same machinery in a favourable regime, where it pays off.

Comparison: standard vs surrogate

# Standard IES update (for comparison)
par_mean <- colMeans(par_ens)
obs_mean <- colMeans(obs_ens)
par_diff <- t(par_ens) - par_mean
obs_diff <- t(obs_ens) - obs_mean
# Sign: ensemble_solution() expects sim - obs (see ?ensemble_solution).
obs_resid <- t(obs_ens) - matrix(rep(y_obs, n_real), n_obs, n_real)
par_resid <- par_diff
Am <- matrix(rnorm(n_par * (n_real - 1)), n_par, n_real - 1)

standard_upgrade <- ensemble_solution(
  par_diff, obs_diff, obs_resid, par_resid,
  weights, parcov_inv, Am, cur_lam = 1.0
)

surrogate_upgrade <- result$upgrade

# Compare upgrades
upgrade_diff <- sqrt(mean((standard_upgrade - surrogate_upgrade)^2))
upgrade_corr <- cor(as.numeric(standard_upgrade), as.numeric(surrogate_upgrade))

cat("Upgrade RMSE difference:", round(upgrade_diff, 6), "\n")
#> Upgrade RMSE difference: 0.000118
cat("Upgrade correlation:", round(upgrade_corr, 6), "\n")
#> Upgrade correlation: 1

When the surrogate pays off

The saving is the fraction of realisations the surrogate handles, 1 - n_{\text{model}}/n_{\text{total}}. Because the GP is trained on the current ensemble and predicts at those same points, in a smooth regime it is confident enough to handle essentially the whole ensemble at the default threshold – so the saving is high by construction. What decides whether the surrogate is worth using is therefore not how many realisations it handles but whether its answer stays accurate, which the Effect of nonlinearity section measures next.

set.seed(7)
np_f  <- 4L
no_f  <- 12L
nr_f  <- 120L
G_f   <- matrix(rnorm(no_f * np_f, sd = 1 / sqrt(np_f)), no_f, np_f)
fwd_f <- function(theta) as.numeric(G_f %*% theta)   # smooth, linear response
th_f  <- rnorm(np_f)
y_f   <- fwd_f(th_f) + rnorm(no_f, sd = 0.05)
pe_f  <- matrix(rnorm(nr_f * np_f, sd = 1.0), nr_f, np_f)
oe_f  <- t(apply(pe_f, 1L, function(p) fwd_f(p) + rnorm(no_f, sd = 0.05)))

r_f    <- surrogate_ensemble_update(pe_f, oe_f, y_f, rep(1 / 0.05, no_f),
                                    rep(1, np_f), uncertainty_threshold = 0.1)
post_f <- pe_f + r_f$upgrade
cat(sprintf(
  "Smooth 4-parameter problem: %.0f%% of evaluations handled by the surrogate; posterior RMSE %.3f\n",
  r_f$savings_pct, sqrt(mean((colMeans(post_f) - th_f)^2))))
#> Smooth 4-parameter problem: 100% of evaluations handled by the surrogate; posterior RMSE 0.014

The corollary matters as much: in the curse-of-dimensionality regime (parameters outnumbering the ensemble) the surrogate still predicts the whole ensemble, but its answer degrades – high savings with a poor posterior. That is why check_surrogate_regime() warns before you commit, and why the accuracy check below is the one that counts.

Effect of nonlinearity

How does surrogate accuracy vary with model nonlinearity?

results_dt <- rbindlist(lapply(seq(0, 1, by = 0.1), function(alpha) {
  set.seed(42)
  y_a <- forward_model(theta_true, G, alpha) + rnorm(n_obs, sd = 0.1)
  obs_a <- t(apply(par_ens, 1, function(p) {
    forward_model(p, G, alpha) + rnorm(n_obs, sd = 0.1)
  }))

  pm <- colMeans(par_ens); om <- colMeans(obs_a)
  pd <- t(par_ens) - pm; od <- t(obs_a) - om
  or_ <- t(obs_a) - matrix(rep(y_a, n_real), n_obs, n_real)
  pr <- pd
  Am_a <- matrix(rnorm(n_par * (n_real - 1)), n_par, n_real - 1)

  upg_std <- ensemble_solution(pd, od, or_, pr, weights, parcov_inv, Am_a, 1.0)
  par_std <- par_ens + upg_std
  rmse_std <- sqrt(mean((colMeans(par_std) - theta_true)^2))

  surr <- surrogate_ensemble_update(par_ens, obs_a, y_a, weights, parcov_inv,
                                     uncertainty_threshold = 0.1)
  par_surr <- par_ens + surr$upgrade
  rmse_surr <- sqrt(mean((colMeans(par_surr) - theta_true)^2))

  data.table(alpha = alpha, rmse_std = rmse_std, rmse_surr = rmse_surr,
             ratio = rmse_surr / rmse_std, savings = surr$savings_pct)
}))

ggplot(results_dt, aes(x = alpha)) +
  geom_line(aes(y = ratio), colour = "#009E73", linewidth = 1.2) +
  geom_point(aes(y = ratio), colour = "#009E73", size = 3) +
  geom_hline(yintercept = 1.0, linetype = "dashed", colour = "grey50") +
  scale_y_continuous(limits = c(0.95, 1.05)) +
  labs(title = "Surrogate accuracy across nonlinearity levels",
       x = expression(paste("Nonlinearity strength ", alpha)),
       y = "RMSE ratio (surrogate / standard)",
       caption = "Ratio = 1.0 means identical posterior quality") +
  theme_minimal(base_size = 14) +
  theme(plot.title = element_text(face = "bold"))

Surrogate RMSE ratio across nonlinearity levels.

Random Fourier features for large ensembles

The exact GP has O(n^3) training cost. For large ensembles (n > 300), the random Fourier feature (RFF) approximation scales as O(nD^2), where D is the number of random features:

# Train RFF surrogate (D = 200 features)
rff <- train_rff_surrogate(par_ens, obs_ens, n_features = 200L)
cat("Training MSE:", round(rff$train_mse, 6), "\n")
#> Training MSE: 0

# Predict
rff_pred <- predict_rff_surrogate(rff, par_ens)
rff_error <- sqrt(mean((rff_pred$mean - obs_ens)^2))
cat("RFF prediction RMSE:", round(rff_error, 4), "\n")
#> RFF prediction RMSE: 5e-04

# Compare GP vs RFF accuracy
gp_error <- sqrt(mean((predictions$mean - obs_ens)^2))
cat("Exact GP prediction RMSE:", round(gp_error, 6), "\n")
#> Exact GP prediction RMSE: 0.000119
cat("RFF / GP error ratio:", round(rff_error / max(gp_error, 1e-10), 1), "x\n")
#> RFF / GP error ratio: 4.5 x

Scaling comparison

scaling_dt <- rbindlist(lapply(c(30, 50, 100, 200, 500), function(nr) {
  X <- matrix(rnorm(nr * 20), nr, 20)
  Y <- matrix(rnorm(nr * 50), nr, 50)

  t_gp <- system.time(train_gp_surrogate(X, Y))[["elapsed"]] * 1000
  t_rff <- system.time(train_rff_surrogate(X, Y, 200L))[["elapsed"]] * 1000

  data.table(n = nr, `Exact GP` = t_gp, `RFF (D=200)` = t_rff)
}))

scaling_long <- melt(scaling_dt, id.vars = "n",
                     variable.name = "method", value.name = "time_ms")

ggplot(scaling_long, aes(x = n, y = pmax(time_ms, 0.01), colour = method)) +
  geom_line(linewidth = 1) + geom_point(size = 2.5) +
  scale_y_log10() +
  scale_colour_manual(values = c("Exact GP" = "#D55E00", "RFF (D=200)" = "#0072B2")) +
  labs(title = "GP surrogate training time",
       x = "Ensemble size", y = "Training time (ms, log scale)",
       colour = "Method") +
  theme_minimal(base_size = 14) +
  theme(plot.title = element_text(face = "bold"), legend.position = "bottom")

GP vs RFF training-time scaling.

When does the surrogate help?

The surrogate is most effective when:

the ensemble occupies a compact region of parameter space (GP interpolation is accurate);
the forward model varies smoothly over the parameter range;
the ensemble is large enough to train the GP (practically n \geq 20).

It degrades gracefully when:

the parameter space is very high-dimensional (n_p \gg 100);
the model has sharp discontinuities or bifurcations;
the ensemble spans a very wide region (uninformative prior).

In all cases, the uncertainty threshold \tau makes the algorithm fall back to full model evaluations when the surrogate is unreliable.

References

Rasmussen, C. E. & Williams, C. K. I. (2006). Gaussian Processes for Machine Learning. MIT Press.
Rahimi, A. & Recht, B. (2007). Random features for large-scale kernel machines. Advances in Neural Information Processing Systems 20.
Chen, Y. & Oliver, D. S. (2013). Levenberg-Marquardt forms of the iterative ensemble smoother. Computational Geosciences, 17(4), 689–703.
Glasserman, P. (2003). Monte Carlo Methods in Financial Engineering. Springer.