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Sequential design of a (D)GP emulator or a bundle of (D)GP emulators

Source: R/design.R
design.Rd

[Updated]

This function implements sequential design and active learning for a (D)GP emulator or a bundle of (D)GP emulators, supporting an array of popular methods as well as user-specified approaches. It can also be used as a wrapper for Bayesian optimization methods.

Usage

design(
  object,
  N,
  x_cand,
  y_cand,
  n_sample,
  n_cand,
  limits,
  f,
  reps,
  freq,
  x_test,
  y_test,
  reset,
  target,
  method,
  batch_size,
  eval,
  verb,
  autosave,
  new_wave,
  M_val,
  cores,
  ...
)

# S3 method for class 'gp'
design(
  object,
  N,
  x_cand = NULL,
  y_cand = NULL,
  n_sample = 200,
  n_cand = lifecycle::deprecated(),
  limits = NULL,
  f = NULL,
  reps = 1,
  freq = c(1, 1),
  x_test = NULL,
  y_test = NULL,
  reset = FALSE,
  target = NULL,
  method = vigf,
  batch_size = 1,
  eval = NULL,
  verb = TRUE,
  autosave = list(),
  new_wave = TRUE,
  M_val = 50,
  cores = 1,
  ...
)

# S3 method for class 'dgp'
design(
  object,
  N,
  x_cand = NULL,
  y_cand = NULL,
  n_sample = 200,
  n_cand = lifecycle::deprecated(),
  limits = NULL,
  f = NULL,
  reps = 1,
  freq = c(1, 1),
  x_test = NULL,
  y_test = NULL,
  reset = FALSE,
  target = NULL,
  method = vigf,
  batch_size = 1,
  eval = NULL,
  verb = TRUE,
  autosave = list(),
  new_wave = TRUE,
  M_val = 50,
  cores = 1,
  train_N = NULL,
  refit_cores = 1,
  pruning = TRUE,
  control = list(),
  ...
)

# S3 method for class 'bundle'
design(
  object,
  N,
  x_cand = NULL,
  y_cand = NULL,
  n_sample = 200,
  n_cand = lifecycle::deprecated(),
  limits = NULL,
  f = NULL,
  reps = 1,
  freq = c(1, 1),
  x_test = NULL,
  y_test = NULL,
  reset = FALSE,
  target = NULL,
  method = vigf,
  batch_size = 1,
  eval = NULL,
  verb = TRUE,
  autosave = list(),
  new_wave = TRUE,
  M_val = 50,
  cores = 1,
  train_N = NULL,
  refit_cores = 1,
  ...
)

Arguments

object

can be one of the following:

  • the S3 class gp.

  • the S3 class dgp.

  • the S3 class bundle.

N

the number of iterations for the sequential design.

x_cand

a matrix (with each row being a design point and column being an input dimension) that gives a candidate set from which the next design points are determined. Defaults to NULL.

y_cand

a matrix (with each row being a simulator evaluation and column being an output dimension) that gives the realizations from the simulator at input positions in x_cand. Defaults to NULL.

n_sample

[New] an integer that gives the size of a sub-set to be sampled from the candidate set x_cand at each step of the sequential design to determine the next design point, if x_cand is not NULL.

Defaults to 200.

n_cand

[Deprecated] this argument is deprecated. Use n_sample instead.

limits

a two-column matrix that gives the ranges of each input dimension, or a vector of length two if there is only one input dimension. If a vector is provided, it will be converted to a two-column row matrix. The rows of the matrix correspond to input dimensions, and its first and second columns correspond to the minimum and maximum values of the input dimensions. Set limits = NULL if x_cand is supplied. This argument is only used when x_cand is not supplied, i.e., x_cand = NULL. Defaults to NULL. If you provide a custom method function with an argument called limits, the value of limits will be passed to your function.

f

an R function representing the simulator. f must adhere to the following rules:

  • First argument: a matrix where rows correspond to different design points, and columns represent input dimensions.

  • Function output:

    • a matrix where rows correspond to different outputs (matching the input design points) and columns represent output dimensions. If there is only one output dimension, the function should return a matrix with a single column.

    • alternatively, a list where:

      • the first element is the output matrix as described above.

      • additional named elements can optionally update values of arguments with matching names passed via .... This list output is useful if additional arguments to f, method, or eval need to be updated after each sequential design iteration.

See the Note section below for additional details. This argument is required and must be supplied when y_cand = NULL. Defaults to NULL.

reps

an integer that gives the number of repetitions of the located design points to be created and used for evaluations of f. Set the argument to an integer greater than 1 only if f is a stochastic function that can generate different responses given for the same input and the supplied emulator object can deal with stochastic responses, e.g., a (D)GP emulator with nugget_est = TRUE or a DGP emulator with a likelihood layer. The argument is only used when f is supplied. Defaults to 1.

freq

a vector of two integers with the first element indicating the number of iterations taken between re-estimating the emulator hyperparameters, and the second element defining the number of iterations to take between re-calculation of evaluating metrics on the validation set (see x_test below) via the eval function. Defaults to c(1, 1).

x_test

a matrix (with each row being an input testing data point and each column being an input dimension) that gives the testing input data to evaluate the emulator after each freq[2] iterations of the sequential design. Set to NULL for LOO-based emulator validation. Defaults to NULL. This argument is only used if eval = NULL.

y_test

the testing output data corresponding to x_test for emulator validation after each freq[2] iterations of the sequential design:

  • if object is an instance of the gp class, y_test is a matrix with only one column and each row contains a testing output data point from the corresponding row of x_test.

  • if object is an instance of the dgp class, y_test is a matrix with its rows containing testing output data points corresponding to the same rows of x_test and columns representing the output dimensions.

  • if object is an instance of the bundle class, y_test is a matrix with each row representing the outputs for the corresponding row of x_test and each column representing the output of the different emulators in the bundle.

Set to NULL for LOO-based emulator validation. Defaults to NULL. This argument is only used if eval = NULL.

reset

A bool or a vector of bools indicating whether to reset the hyperparameters of the emulator(s) to their initial values (as set during initial construction) before re-fitting. The re-fitting occurs based on the frequency specified by freq[1]. This option is useful when hyperparameters are suspected to have converged to a local optimum affecting validation performance.

  • If a single bool is provided, it applies to every iteration of the sequential design.

  • If a vector is provided, its length must equal N (even if the re-fit frequency specified in freq[1] is not 1) and it will apply to the corresponding iterations of the sequential design.

Defaults to FALSE.

target

a number or vector specifying the target evaluation metric value(s) at which the sequential design should terminate. Defaults to NULL, in which case the sequential design stops after N steps. See the Note section below for further details about target.

method

[Updated] an R function that determines the next design points to be evaluated by f. The function must adhere to the following rules:

  • First argument: an emulator object, which can be one of the following:

    • an instance of the gp class (produced by gp());

    • an instance of the dgp class (produced by dgp());

    • an instance of the bundle class (produced by pack()).

  • Second argument (if x_cand is not NULL): a candidate matrix representing a set of potential design points from which the method function selects the next points.

  • Function output:

    • If x_cand is not NULL:

      • for gp or dgp objects, the output must be a vector of row indices corresponding to the selected design points from the candidate matrix (the second argument).

      • for bundle objects, the output must be a matrix containing the row indices of the selected design points from the candidate matrix. Each column corresponds to the indices for an individual emulator in the bundle.

    • If x_cand is NULL:

      • for gp or dgp objects, the output must be a matrix where each row represents a new design point to be added.

      • for bundle objects, the output must be a list with a length equal to the number of emulators in the bundle. Each element in the list is a matrix where rows represent the new design points for the corresponding emulator.

See alm(), mice(), and vigf() for examples of built-in method functions. Defaults to vigf().

batch_size

[New] an integer specifying the number of design points to select in a single iteration. Defaults to 1. This argument is used by the built-in method functions alm(), mice(), and vigf(). If you provide a custom method function with an argument named batch_size, the value of batch_size will be passed to your function.

eval

an R function that computes a customized metric for evaluating emulator performance. The function must adhere to the following rules:

  • First argument: an emulator object, which can be one of the following:

    • an instance of the gp class (produced by gp());

    • an instance of the dgp class (produced by dgp());

    • an instance of the bundle class (produced by pack()).

  • Function output:

    • for gp objects, the output must be a single metric value.

    • for dgp objects, the output can be a single metric value or a vector of metric values with a length equal to the number of output dimensions.

    • for bundle objects, the output can be a single metric value or a vector of metric values with a length equal to the number of emulators in the bundle.

If no custom function is provided, a built-in evaluation metric (RMSE or log-loss, in the case of DGP emulators with categorical likelihoods) will be used. Defaults to NULL. See the Note section below for additional details.

verb

a bool indicating if trace information will be printed during the sequential design. Defaults to TRUE.

autosave

a list that contains configuration settings for the automatic saving of the emulator:

  • switch: a bool indicating whether to enable automatic saving of the emulator during sequential design. When set to TRUE, the emulator in the final iteration is always saved. Defaults to FALSE.

  • directory: a string specifying the directory path where the emulators will be stored. Emulators will be stored in a sub-directory of directory named 'emulator-id'. Defaults to './check_points'.

  • fname: a string representing the base name for the saved emulator files. Defaults to 'check_point'.

  • save_freq: an integer indicating the frequency of automatic saves, measured in the number of iterations. Defaults to 5.

  • overwrite: a bool value controlling the file saving behavior. When set to TRUE, each new automatic save overwrites the previous one, keeping only the latest version. If FALSE, each automatic save creates a new file, preserving all previous versions. Defaults to FALSE.

new_wave

a bool indicating whether the current call to design() will create a new wave of sequential designs or add the next sequence of designs to the most recent wave. This argument is relevant only if waves already exist in the emulator. Creating new waves can improve the visualization of sequential design performance across different calls to design() via draw(), and allows for specifying a different evaluation frequency in freq. However, disabling this option can help limit the number of waves visualized in draw() to avoid issues such as running out of distinct colors for large numbers of waves. Defaults to TRUE.

M_val

[New] an integer that gives the size of the conditioning set for the Vecchia approximation in emulator validations. This argument is only used if the emulator object was constructed under the Vecchia approximation. Defaults to 50.

cores

an integer that gives the number of processes to be used for emulator validation. If set to NULL, the number of processes is set to max physical cores available %/% 2. Defaults to 1. This argument is only used if eval = NULL.

...

Any arguments with names that differ from those used in design() but are required by f, method, or eval can be passed here. design() will forward relevant arguments to f, method, and eval based on the names of the additional arguments provided.

train_N

the number of training iterations to be used for re-fitting the DGP emulator at each step of the sequential design:

  • If train_N is an integer, the DGP emulator will be re-fitted at each step (based on the re-fit frequency specified in freq[1]) using train_N iterations.

  • If train_N is a vector, its length must be N, even if the re-fit frequency specified in freq[1] is not 1.

  • If train_N is NULL, the DGP emulator will be re-fitted at each step (based on the re-fit frequency specified in freq[1]) using:

    • 100 iterations if the DGP emulator was constructed without the Vecchia approximation, or

    • 50 iterations if the Vecchia approximation was used.

Defaults to NULL.

refit_cores

the number of processes to be used to re-fit GP components (in the same layer of a DGP emulator) at each M-step during the re-fitting. If set to NULL, the number of processes is set to (max physical cores available - 1) if the DGP emulator was constructed without the Vecchia approximation. Otherwise, the number of processes is set to max physical cores available %/% 2. Only use multiple processes when there is a large number of GP components in different layers and optimization of GP components is computationally expensive. Defaults to 1.

pruning

a bool indicating if dynamic pruning of DGP structures will be implemented during the sequential design after the total number of design points exceeds min_size in control. The argument is only applicable to DGP emulators (i.e., object is an instance of dgp class) produced by dgp(). Defaults to TRUE.

control

a list that can supply any of the following components to control the dynamic pruning of the DGP emulator:

  • min_size, the minimum number of design points required to trigger dynamic pruning. Defaults to 10 times the number of input dimensions.

  • threshold, the \(R^2\) value above which a GP node is considered redundant. Defaults to 0.97.

  • nexceed, the minimum number of consecutive iterations that the \(R^2\) value of a GP node must exceed threshold to trigger the removal of that node from the DGP structure. Defaults to 3.

The argument is only used when pruning = TRUE.

Value

An updated object is returned with a slot called design that contains:

  • S slots, named wave1, wave2,..., waveS, that contain information of S waves of sequential design that have been applied to the emulator. Each slot contains the following elements:

    • N, an integer that gives the numbers of iterations implemented in the corresponding wave;

    • rmse, a matrix providing the evaluation metric values for emulators constructed during the corresponding wave, when eval = NULL. Each row of the matrix represents an iteration.

      • for an object of class gp, the matrix contains a single column of RMSE values.

      • for an object of class dgp without a categorical likelihood, each row contains mean/median squared errors corresponding to different output dimensions.

      • for an object of class dgp with a categorical likelihood, the matrix contains a single column of log-loss values.

      • for an object of class bundle, each row contains either mean/median squared errors or log-loss values for the emulators in the bundle.

    • metric: a matrix providing the values of custom evaluation metrics, as computed by the user-supplied eval function, for emulators constructed during the corresponding wave.

    • freq, an integer that gives the frequency that the emulator validations are implemented during the corresponding wave.

    • enrichment, a vector of size N that gives the number of new design points added after each step of the sequential design (if object is an instance of the gp or dgp class), or a matrix that gives the number of new design points added to emulators in a bundle after each step of the sequential design (if object is an instance of the bundle class).

    If target is not NULL, the following additional elements are also included:

    • target: the target evaluating metric computed by the eval or built-in function to stop the sequential design.

    • reached: indicates whether the target was reached at the end of the sequential design:

      • a bool if object is an instance of the gp or dgp class.

      • a vector of bools if object is an instance of the bundle class, with its length determined as follows:

        • equal to the number of emulators in the bundle when eval = NULL.

        • equal to the length of the output from eval when a custom eval function is provided.

  • a slot called type that gives the type of validation:

    • either LOO ('loo') or OOS ('oos') if eval = NULL. See validate() for more information about LOO and OOS.

    • 'customized' if a customized R function is provided to eval.

  • two slots called x_test and y_test that contain the data points for the OOS validation if the type slot is 'oos'.

  • If y_cand = NULL and x_cand is supplied, and there are NAs returned from the supplied f during the sequential design, a slot called exclusion is included that records the located design positions that produced NAs via f. The sequential design will use this information to avoid re-visiting the same locations in later runs of design().

See Note section below for further information.

Details

See further examples and tutorials at https://mingdeyu.github.io/dgpsi-R/.

Note

  • Validation of an emulator is forced after the final step of a sequential design even if N is not a multiple of the second element in freq.

  • Any loo or oos slot that already exists in object will be cleaned, and a new slot called loo or oos will be created in the returned object depending on whether x_test and y_test are provided. The new slot gives the validation information of the emulator constructed in the final step of the sequential design. See validate() for more information about the slots loo and oos.

  • If object has previously been used by design() for sequential design, the information of the current wave of the sequential design will replace those of old waves and be contained in the returned object, unless

    • the validation type (LOO or OOS depending on whether x_test and y_test are supplied or not) of the current wave of the sequential design is the same as the validation types (shown in the type of the design slot of object) in previous waves, and if the validation type is OOS, x_test and y_test in the current wave must also be identical to those in the previous waves;

    • both the current and previous waves of the sequential design supply customized evaluation functions to eval. Users need to ensure the customized evaluation functions are consistent among different waves. Otherwise, the trace plot of RMSEs produced by draw() will show values of different evaluation metrics in different waves.

    For the above two cases, the information of the current wave of the sequential design will be added to the design slot of the returned object under the name waveS.

  • If object is an instance of the gp class and eval = NULL, the matrix in the rmse slot is single-columned. If object is an instance of the dgp or bundle class and eval = NULL, the matrix in the rmse slot can have multiple columns that correspond to different output dimensions or different emulators in the bundle.

  • If object is an instance of the gp class and eval = NULL, target needs to be a single value giving the RMSE threshold. If object is an instance of the dgp or bundle class and eval = NULL, target can be a vector of values that gives the thresholds of evaluating metrics for different output dimensions or different emulators. If a single value is provided, it will be used as the threshold for all output dimensions (if object is an instance of the dgp) or all emulators (if object is an instance of the bundle). If a customized function is supplied to eval and target is given as a vector, the user needs to ensure that the length of target is equal to that of the output from eval.

  • When defining f, it is important to ensure that:

    • the column order of the first argument of f is consistent with the training input used for the emulator;

    • the column order of the output matrix of f is consistent with the order of emulator output dimensions (if object is an instance of the dgp class), or the order of emulators placed in object (if object is an instance of the bundle class).

  • The output matrix produced by f may include NAs. This is especially beneficial as it allows the sequential design process to continue without interruption, even if errors or NA outputs are encountered from f at certain input locations identified by the sequential design. Users should ensure that any errors within f are handled by appropriately returning NAs.

  • When defining eval, the output metric needs to be positive if draw() is used with log = T. And one needs to ensure that a lower metric value indicates a better emulation performance if target is set.

Examples

if (FALSE) { # \dontrun{

# load packages and the Python env
library(lhs)
library(dgpsi)

# construct a 2D non-stationary function that takes a matrix as the input
f <- function(x) {
  sin(1/((0.7*x[,1,drop=F]+0.3)*(0.7*x[,2,drop=F]+0.3)))
}

# generate the initial design
X <- maximinLHS(5,2)
Y <- f(X)

# generate the validation data
validate_x <- maximinLHS(30,2)
validate_y <- f(validate_x)

# training a 2-layered DGP emulator with the initial design
m <- dgp(X, Y)

# specify the ranges of the input dimensions
lim_1 <- c(0, 1)
lim_2 <- c(0, 1)
lim <- rbind(lim_1, lim_2)

# 1st wave of the sequential design with 10 steps
m <- design(m, N=10, limits = lim, f = f, x_test = validate_x, y_test = validate_y)

# 2nd wave of the sequential design with 10 steps
m <- design(m, N=10, limits = lim, f = f, x_test = validate_x, y_test = validate_y)

# 3rd wave of the sequential design with 10 steps
m <- design(m, N=10, limits = lim, f = f, x_test = validate_x, y_test = validate_y)

# draw the design created by the sequential design
draw(m,'design')

# inspect the trace of RMSEs during the sequential design
draw(m,'rmse')

# reduce the number of imputations for faster OOS
m_faster <- set_imp(m, 5)

# plot the OOS validation with the faster DGP emulator
plot(m_faster, x_test = validate_x, y_test = validate_y)
} # }