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templateGP

Gaussian process template

Since R2023b

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Syntax

t = templateGP
t = templateGP(Name=Value)

Description

t = templateGP returns a Gaussian process (GP) template suitable for training regression models. After you create the template t, you can specify it as a learner during training.

example

t = templateGP(Name=Value) specifies additional options using one or more name-value arguments. For example, you can specify the basis function and method for estimating the parameters of the Gaussian process regression (GPR) model.

If you display t in the Command Window, then all options appear empty ([]), except those that you specify using name-value arguments. During training, the training function uses default values for empty options.

example

Examples

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Open Live Script

Create a default Gaussian process template using the templateGP function.

t = templateGP
t = 
Fit template for regression GP.

                     KernelFunction: []
                   KernelParameters: []
                      BasisFunction: []
                               Beta: []
                              Sigma: []
                          FitMethod: []
                      PredictMethod: []
                          ActiveSet: []
                      ActiveSetSize: []
                    ActiveSetMethod: []
                        Standardize: []
                            Verbose: []
                          CacheSize: []
                            Options: [1x1 struct]
                          Optimizer: []
                   OptimizerOptions: []
           ConstantKernelParameters: []
                      ConstantSigma: []
                    InitialStepSize: []
    InitialSigmaLowerBoundTolerance: []
                            Version: 1
                             Method: 'GP'
                               Type: 'regression'

t is a template object for a Gaussian process learner. All properties of the template object are empty except Version, Method, and Type. When you pass t to the training function, the function fills in the empty properties with their respective default values. For example, the directforecaster function sets the ConstantSigma property to false when you specify t as a learner. For details on other default values, see Name-Value Arguments.

Open Live Script

Create a Gaussian process template that specifies a linear basis for the GPR model, and exact methods for fitting and prediction.

t = templateGP(BasisFunction="linear",FitMethod="exact",PredictMethod="exact")
t = 
Fit template for regression GP.

                     KernelFunction: []
                   KernelParameters: []
                      BasisFunction: 'Linear'
                               Beta: []
                              Sigma: []
                          FitMethod: 'Exact'
                      PredictMethod: 'Exact'
                          ActiveSet: []
                      ActiveSetSize: []
                    ActiveSetMethod: []
                        Standardize: []
                            Verbose: []
                          CacheSize: []
                            Options: [1x1 struct]
                          Optimizer: []
                   OptimizerOptions: []
           ConstantKernelParameters: []
                      ConstantSigma: []
                    InitialStepSize: []
    InitialSigmaLowerBoundTolerance: []
                            Version: 1
                             Method: 'GP'
                               Type: 'regression'

t is a template object for a Gaussian process learner. The object display shows the specified properties of the template object. By default, Method and Type are specified as GP and regression, respectively. When you pass t to a training function, the software sets the empty properties to their respective default values.

Input Arguments

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Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: templateGP(BasisFunction="linear",Standardize=true) specifies a linear basis function and to standardize the predictors.

Fitting

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Method to estimate the parameters of the GPR model, specified as one of the following.

Fit MethodDescription
"none"No estimation. Use the initial parameter values as the known parameter values.
"exact"Exact Gaussian process regression. This value is the default if n ≤ 2000, where n is the number of observations.
"sd"Subset of data points approximation. This value is the default if n > 2000, where n is the number of observations. "sd" is a sparse method.
"sr"Subset of regressors approximation. "sr" is a sparse method.
"fic"Fully independent conditional approximation. "fic" is a sparse method.

Example: FitMethod="fic"

Explicit basis in the GPR model, specified as "constant", "none", "linear", "pureQuadratic", or a function handle. If n is the number of observations, the basis function adds the term H*β to the model, where H is the basis matrix and β is a p-by-1 vector of basis coefficients.

Explicit BasisBasis Matrix
"none"Empty matrix
"constant"

H=1

H is an n-by-1 vector of 1s, where n is the number of observations.

"linear"

H=[1,X]

X is the expanded predictor data after the software creates dummy variables for the categorical variables. For details about creating dummy variables, see CategoricalPredictors.

"pureQuadratic"

H=[1,X,X2],

where

X2=[x112x122⋯x1d2x212x222⋯x2d2⋮⋮⋮⋮xn12xn22⋯xnd2].

For this basis option, the software does not support X with categorical predictors.

Function handle

Function handle hfcn, which fitrgp calls as

H=hfcn(X),

where X is an n-by-d matrix of predictors, d is the number of predictors after the software creates dummy variables for the categorical variables, and H is an n-by-p matrix of basis functions.

Example: BasisFunction="pureQuadratic"

Data Types: char | string | function_handle

Initial value of the coefficients for the explicit basis, specified as a p-by-1 vector, where p is the number of columns in the basis matrix H.

The basis matrix depends on the specified basis function. For more information, see BasisFunction.

The training function uses the coefficient initial values as the known coefficient values only when FitMethod is "none".

Data Types: double

Initial value for the noise standard deviation of the Gaussian process model, specified as a positive scalar value.

The training function parameterizes the noise standard deviation as the sum of SigmaLowerBound and exp(η), where η is an unconstrained value. Therefore, Sigma must be larger than SigmaLowerBound by a small tolerance so that the function can initialize η to a finite value. Otherwise, the function resets Sigma to a compatible value.

The tolerance is 1e-3 when ConstantSigma is false (default) and 1e-6 otherwise. If the tolerance is not small enough relative to the scale of the response variable, you can scale up the response variable so that the tolerance value can be considered small for the response variable.

Example: Sigma=2

Data Types: double

Constant value of Sigma for the noise standard deviation of the Gaussian process model, specified as a numeric or logical 0 (false) or 1 (true). When ConstantSigma is true, the training function does not optimize the value of Sigma, but instead uses the initial value throughout its computations.

Example: ConstantSigma=true

Data Types: logical

Lower bound on the noise standard deviation (Sigma), specified as a positive scalar value.

Sigma must be larger than SigmaLowerBound by a small tolerance.

Example: SigmaLowerBound=0.02

Data Types: double

Indicator to standardize data, specified as a numeric or logical 0 (false) or 1 (true).

If you set Standardize=1, then the software centers and scales each column of the predictor data by the column mean and standard deviation. The software does not standardize the data contained in the dummy variable columns generated for categorical predictors.

Example: Standardize=1

Example: Standardize=true

Data Types: logical

Regularization standard deviation for the subset of regressors ("sr") and fully independent conditional ("fic") approximation methods, specified as a positive scalar value. For more information, see FitMethod.

Example: Regularization=0.2

Data Types: double

Method for computing the loglikelihood and gradient for parameter estimation, specified as "qr" or "v". This argument is valid when FitMethod is "sr" or "fic".

  • "qr" — Use the QR-factorization-based approach, which provides better accuracy.

  • "v" — Use the V-method-based approach, which provides faster computation.

For more information about these approaches, see Foster, et. al. [7].

Example: ComputationMethod="v"

Kernel (Covariance) Function

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Form of the covariance function, specified as one of the following.

ValueDescription
"exponential"Exponential kernel
"squaredexponential"Squared exponential kernel
"matern32"Matern kernel with parameter 3/2
"matern52"Matern kernel with parameter 5/2
"rationalquadratic"Rational quadratic kernel
"ardexponential"Exponential kernel with a separate length scale per predictor
"ardsquaredexponential"Squared exponential kernel with a separate length scale per predictor
"ardmatern32"Matern kernel with parameter 3/2 and a separate length scale per predictor
"ardmatern52"Matern kernel with parameter 5/2 and a separate length scale per predictor
"ardrationalquadratic"Rational quadratic kernel with a separate length scale per predictor
Function handleFunction handle in the form:
Kmn = kfcn(Xm,Xn,theta),
where Xm is an m-by-d matrix, Xn is an n-by-d matrix, and Kmn is an m-by-n matrix of kernel products such that Kmn(i,j) is the kernel product between Xm(i,:) and Xn(j,:). d is the number of predictor variables after the software creates dummy variables for the categorical variables. For details about creating dummy variables, see CategoricalPredictors.
theta is the r-by-1 unconstrained parameter vector for kfcn.

For more information on the kernel functions, see Kernel (Covariance) Function Options.

Example: KernelFunction="matern32"

Data Types: char | string | function_handle

Initial values for the kernel parameters, specified as a numeric vector. The size of the vector and the values depend on the form of the covariance function, specified by the KernelFunction name-value argument.

KernelFunction ValueKernelParameters Value
"exponential", "squaredexponential", "matern32", or "matern52"2-by-1 vector phi, where phi(1) contains the length scale and phi(2) contains the signal standard deviation.
The default initial value of the length scale parameter is the mean of the standard deviations of the predictors. The signal standard deviation is the standard deviation of the responses divided by the square root of 2. That is,
phi = [mean(std(X));std(y)/sqrt(2)].
"rationalquadratic"3-by-1 vector phi, where phi(1) contains the length scale, phi(2) contains the scale-mixture parameter, and phi(3) contains the signal standard deviation.
The default initial value of the length scale parameter is the mean of the standard deviations of the predictors. The signal standard deviation is the standard deviation of the responses divided by the square root of 2. The default initial value for the scale-mixture parameter is 1. That is,
phi = [mean(std(X));1;std(y)/sqrt(2)].
"ardexponential", "ardsquaredexponential", "ardmatern32", or "ardmatern52"(d+1)-by-1 vector phi, where phi(i) contains the length scale for predictor i, and phi(d+1) contains the signal standard deviation. d is the number of predictor variables after the software creates dummy variables for the categorical variables. For details about creating dummy variables, see CategoricalPredictors.
The default initial values of the length scale parameters are the standard deviations of the predictors. The signal standard deviation is the standard deviation of the responses divided by the square root of 2. That is,
phi = [std(X)';std(y)/sqrt(2)].
"ardrationalquadratic"(d+2)-by-1 vector phi, where phi(i) contains the length scale for predictor i, phi(d+1) contains the scale-mixture parameter, and phi(d+2) contains the signal standard deviation. d is the number of predictor variables after the software creates dummy variables for the categorical variables. For details about creating dummy variables, see CategoricalPredictors.
The default initial values of the length scale parameters are the standard deviations of the predictors. The signal standard deviation is the standard deviation of the responses divided by the square root of 2. The default initial value of the scale-mixture parameter is 1. That is,
phi = [std(X)';1;std(y)/sqrt(2)].
Function handler-by-1 vector for the initial value of the unconstrained parameter vector phi for the custom kernel function kfcn.
When KernelFunction is a function handle, you must supply initial values for the kernel parameters.

For more information on the kernel functions, see Kernel (Covariance) Function Options.

Example: KernelParameters=phi

Data Types: double | single

Method for computing inter-point distances to evaluate built-in kernel functions, specified as "fast" or "accurate". When you specify "fast", the training function computes (x−y)2 as x2+y2−2*x*y. When you specify "accurate", the training function computes (x−y)2.

Example: DistanceMethod="accurate"

Active Set Selection

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Size of the active set, specified as an integer m, 1 ≤ m ≤ n, where n is the number of observations. This argument is valid when FitMethod is "sd", "sr", or "fic".

The default value is min(1000,n) when FitMethod is "sr" or "fic", and min(2000,n) otherwise.

Example: ActiveSetSize=100

Data Types: double

Active set selection method, specified as one of the following values.

ValueDescription
"random"Random selection
"sgma"Sparse greedy matrix approximation
"entropy"Differential entropy-based selection
"likelihood"Subset of regressors loglikelihood-based selection

All active set selection methods (except "random") require the storage of an n-by-m matrix, where m is the size of the active set and n is the number of observations.

Example: ActiveSetMethod="entropy"

Random search set size per greedy inclusion for active set selection, specified as an integer value.

Example: RandomSearchSetSize=30

Data Types: double

Relative tolerance for terminating active set selection, specified as a positive scalar.

Example: ToleranceActiveset=0.0002

Data Types: double

Number of repetitions for interleaved active set selection and parameter estimation when ActiveSetMethod is not "random", specified as an integer value.

Example: NumActiveSetRepeats=5

Data Types: double

Prediction

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Method used to make predictions from a Gaussian process model given the parameters, specified as one of the following values.

ValueDescription
"exact"Exact Gaussian process regression method. This value is the default if n ≤ 10,000.
"bcd"Block coordinate descent (BCD). This value is the default if n > 10,000.
"sd"Subset of data points approximation
"sr"Subset of regressors approximation
"fic"Fully independent conditional approximation

Example: PredictMethod="bcd"

Block size for the block coordinate descent method ("bcd"), specified as an integer in the range 1 to n, where n is the number of observations.

Example: BlockSizeBCD=1500

Data Types: double

Number of greedy selections for the block coordinate descent method ("bcd"), specified as an integer in the range 1 to BlockSizeBCD.

Example: NumGreedyBCD=150

Data Types: double

Relative tolerance on the gradient norm for terminating the block coordinate descent method ("bcd") iterations, specified as a positive scalar.

Example: ToleranceBCD=0.002

Data Types: double

Absolute tolerance on the step size for terminating the block coordinate descent method ("bcd") iterations, specified as a positive scalar.

Example: StepToleranceBCD=0.002

Data Types: double

Maximum number of block coordinate descent method ("bcd") iterations, specified as a positive integer.

Example: IterationLimitBCD=10000

Data Types: double

Optimization

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Optimizer to use for parameter estimation, specified as one of the values in this table.

ValueDescription
"quasinewton"Dense, symmetric rank-1-based, quasi-Newton approximation to the Hessian
"lbfgs"LBFGS-based quasi-Newton approximation to the Hessian
"fminsearch"Unconstrained nonlinear optimization using the simplex search method of Lagarias et al. [5]
"fminunc"Unconstrained nonlinear optimization (requires an Optimization Toolbox™ license)
"fmincon"Constrained nonlinear optimization (requires an Optimization Toolbox license)

For more information on the optimizers, see Algorithms.

Example: Optimizer="fmincon"

Options for the optimizer set by the Optimizer name-value argument, specified as a structure or object created by optimset, statset("fitrgp"), or optimoptions.

OptimizerFunction for Creating Optimizer Options
"fminsearch"optimset (structure)
"quasinewton" or "lbfgs"statset("fitrgp") (structure)
"fminunc" or "fmincon"optimoptions (object)

The default options depend on the specified optimizer.

Example: OptimizerOptions=opt

Initial step size, specified as a real positive scalar or "auto".

InitialStepSize is the approximate maximum absolute value of the first optimization step when the optimizer is "quasinewton" or "lbfgs". The initial step size can determine the initial Hessian approximation during optimization.

By default, the training function does not use the initial step size to determine the initial Hessian approximation. To use the initial step size, set a value for the InitialStepSize name-value argument, or specify InitialStepSize="auto" to have the software determine a value automatically. For more information on "auto", see Algorithms.

Example: InitialStepSize="auto"

Other

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Verbosity level, specified as 0 or 1.

  • 0 — The training function suppresses diagnostic messages related to active set selection and block coordinate descent, but displays the messages related to parameter estimation, depending on the value of Display in OptimizerOptions.

  • 1 — The training function displays the iterative diagnostic messages related to parameter estimation, active set selection, and block coordinate descent.

Example: Verbose=1

Cache size in megabytes (MB), specified as a positive scalar. Cache size is the extra memory available in addition to the memory required for fitting and active set selection. The training function uses CacheSize to:

  • Decide whether inter-point distances are cached when estimating parameters.

  • Decide how matrix vector products are computed for the block coordinate descent method and for making predictions.

Example: CacheSize=2000

Data Types: double

Output Arguments

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Gaussian process learner template suitable for training regression models, returned as a template object. During training, the training function (such as directforecaster) uses default values for empty options.

More About

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Active Set Selection and Parameter Estimation

For subset of data, subset of regressors, or fully independent conditional approximation fitting methods (FitMethod equal to "sd", "sr", or "fic"), the software selects the active set and computes the parameter estimates in a series of iterations.

In the first iteration, the software uses the initial parameter values in vector η0 = [β0,σ0,θ0] to select an active set A1. The software maximizes the GPR marginal loglikelihood or its approximation using η0 as the initial values and A1 to compute the new parameter estimates η1. Next, the software computes the new loglikelihood L1 using η1 and A1.

In the second iteration, the software selects the active set A2 using the parameter values in η1. Then, using η1 as the initial values and A2, the software maximizes the GPR marginal loglikelihood or its approximation and estimates the new parameter values η2. Then, using η2 and A2, the software computes the new loglikelihood value L2.

The following table summarizes the iterations and the computations at each iteration.

Iteration NumberActive SetParameter VectorLoglikelihood
1A1η1L1
2A2η2L2
3A3η3L3
…………

The software iterates similarly for a specified number of repetitions. You can specify the number of replications for active set selection using the NumActiveSetRepeats name-value argument.

Algorithms

  • Fitting a GPR model involves estimating the following model parameters from the data:

    • Covariance function k(xi,xj|θ) parameterized in terms of kernel parameters in vector θ (see Kernel (Covariance) Function Options)

    • Noise variance σ2

    • Coefficient vector of fixed-basis functions β

    The value of the KernelParameters name-value argument is a vector that consists of initial values for the signal standard deviation σf and the characteristic length scales σl. The software uses these values to determine the kernel parameters. Similarly, the Sigma name-value argument contains the initial value for the noise standard deviation σ.

  • During optimization, the software creates a vector of unconstrained initial parameter values η0 by using the initial values for the noise standard deviation and the kernel parameters.

  • The software analytically determines the explicit basis coefficients β, specified by the Beta name-value argument, from estimated values of θ and σ2. Therefore, β does not appear in the η0 vector when the software initializes numerical optimization.

    Note

    If you do not specify the estimation of parameters for the GPR model, the software uses the value of the Beta name-value argument and other initial parameter values as the known GPR parameter values (see Beta). In all other cases, the value of Beta is optimized analytically from the objective function.

  • The quasi-Newton optimizer uses a trust-region method with a dense, symmetric rank-1-based (SR1), quasi-Newton approximation to the Hessian. The LBFGS optimizer uses a standard line-search method with a limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) quasi-Newton approximation to the Hessian. See Nocedal and Wright [6].

  • If you set the InitialStepSize name-value argument to "auto" the software determines the initial step size ‖s0‖∞ by using ‖s0‖∞=0.5‖η0‖∞+0.1.

    s0 is the initial step vector, and η0 is the vector of unconstrained initial parameter values.

  • During optimization, the software uses the initial step size ‖s0‖∞ as follows:

    If you specify Optimizer="quasinewton" with the initial step size, then the initial Hessian approximation is ‖g0‖∞‖s0‖∞I.

    If you specify Optimizer="lbfgs" with the initial step size, then the initial inverse-Hessian approximation is ‖s0‖∞‖g0‖∞I.

    g0 is the initial gradient vector, and I is the identity matrix.

References

[1] Nash, W.J., T. L. Sellers, S. R. Talbot, A. J. Cawthorn, and W. B. Ford. "The Population Biology of Abalone (Haliotis species) in Tasmania. I. Blacklip Abalone (H. rubra) from the North Coast and Islands of Bass Strait." Sea Fisheries Division, Technical Report No. 48, 1994.

[2] Waugh, S. "Extending and Benchmarking Cascade-Correlation: Extensions to the Cascade-Correlation Architecture and Benchmarking of Feed-forward Supervised Artificial Neural Networks." University of Tasmania Department of Computer Science thesis, 1995.

[3] Lichman, M. UCI Machine Learning Repository, Irvine, CA: University of California, School of Information and Computer Science, 2013. http://archive.ics.uci.edu/ml.

[4] Rasmussen, C. E. and C. K. I. Williams. "Gaussian Processes for Machine Learning". MIT Press. Cambridge, Massachusetts, 2006.

[5] Lagarias, J. C., J. A. Reeds, M. H. Wright, and P. E. Wright. "Convergence Properties of the Nelder-Mead Simplex Method in Low Dimensions." SIAM Journal of Optimization. vol. 9, no. 1, January 1998, pp. 112–147.

[6] Nocedal, J. and S. J. Wright. Numerical Optimization, Second Edition. Springer Series in Operations Research, Springer Verlag, 2006.

[7] Foster, L., et. al. "Stable and Efficient Gaussian Process Calculations", Journal of Machine Learning Research. vol. 10, no. 31, April 2009, pp. 857–882.

Version History

Introduced in R2023b

See Also

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