estimate

Perform predictor variable selection for Bayesian linear regression models

To estimate the posterior distribution of a standard Bayesian linear regression model, see estimate.

Syntax

PosteriorMdl = estimate(PriorMdl,X,y)
PosteriorMdl = estimate(PriorMdl,X,y,Name,Value)
[PosteriorMdl,Summary] = estimate(___)

Description

example

PosteriorMdl = estimate(PriorMdl,X,y) returns the model that characterizes the joint posterior distributions of β and σ2 of a Bayesian linear regression model. estimate also performs predictor variable selection.

PriorMdl specifies the joint prior distribution of the parameters, the structure of the linear regression model, and the variable selection algorithm. X is the predictor data and y is the response data. PriorMdl and PosteriorMdl are not the same object type.

To produce PosteriorMdl, estimate updates the prior distribution with information about the parameters that it obtains from the data.

NaNs in the data indicate missing values, which estimate removes using list-wise deletion.

example

PosteriorMdl = estimate(PriorMdl,X,y,Name,Value) uses additional options specified by one or more name-value pair arguments. For example, 'Lambda',0.5 specifies that the shrinkage parameter value for Bayesian lasso regression is 0.5 for all coefficients except the intercept.

If you specify Beta or Sigma2, then PosteriorMdl and PriorMdl are equal.

example

[PosteriorMdl,Summary] = estimate(___) uses any of the input argument combinations in the previous syntaxes and also returns a table that includes the following for each parameter: posterior estimates, standard errors, 95% credible intervals, and posterior probability that the parameter is greater than 0.

Examples

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Consider the multiple linear regression model that predicts US real gross national product (GNPR) using a linear combination of industrial production index (IPI), total employment (E), and real wages (WR).

GNPRt=β0+β1IPIt+β2Et+β3WRt+εt.

For all t, εt is a series of independent Gaussian disturbances with a mean of 0 and variance σ2.

Assume the prior distributions are:

  • For k = 0,...,3, βk|σ2 has a Laplace distribution with a mean of 0 and a scale of σ2/λ, where λ is the shrinkage parameter. The coefficients are conditionally independent.

  • σ2IG(A,B). A and B are the shape and scale, respectively, of an inverse gamma distribution.

Create a prior model for Bayesian lasso regression. Specify the number of predictors, the prior model type, and variable names. Specify these shrinkages:

  • 0.01 for the intercept

  • 10 for IPI and WR

  • 1e5 for E because it has a scale that is several orders of magnitude larger than the other variables

The order of the shrinkages follows the order of the specified variable names, but the first element is the shrinkage of the intercept.

p = 3;
PriorMdl = bayeslm(p,'ModelType','lasso','Lambda',[0.01; 10; 1e5; 10],...
    'VarNames',["IPI" "E" "WR"]);

PriorMdl is a lassoblm Bayesian linear regression model object representing the prior distribution of the regression coefficients and disturbance variance.

Load the Nelson-Plosser data set. Create variables for the response and predictor series.

load Data_NelsonPlosser
X = DataTable{:,PriorMdl.VarNames(2:end)};
y = DataTable{:,"GNPR"};

Perform Bayesian lasso regression by passing the prior model and data to estimate, that is, by estimating the posterior distribution of β and σ2. Bayesian lasso regression uses Markov chain Monte Carlo (MCMC) to sample from the posterior. For reproducibility, set a random seed.

rng(1);
PosteriorMdl = estimate(PriorMdl,X,y);
Method: lasso MCMC sampling with 10000 draws
Number of observations: 62
Number of predictors:   4
 
           |   Mean     Std           CI95        Positive  Distribution 
-------------------------------------------------------------------------
 Intercept | -1.3472   6.8160  [-15.169, 11.590]    0.427     Empirical  
 IPI       |  4.4755   0.1646   [ 4.157,  4.799]    1.000     Empirical  
 E         |  0.0001   0.0002   [-0.000,  0.000]    0.796     Empirical  
 WR        |  3.1610   0.3136   [ 2.538,  3.760]    1.000     Empirical  
 Sigma2    | 60.1452  11.1180   [42.319, 85.085]    1.000     Empirical  
 

PosteriorMdl is an empiricalblm model object that stores draws from the posterior distributions of β and σ2 given the data. estimate displays a summary of the marginal posterior distributions in the MATLAB® command line. Rows of the summary correspond to regression coefficients and the disturbance variance, and columns correspond to characteristics of the posterior distribution. The characteristics include:

  • CI95, which contains the 95% Bayesian equitailed credible intervals for the parameters. For example, the posterior probability that the regression coefficient of IPI is in [4.157, 4.799] is 0.95.

  • Positive, which contains the posterior probability that the parameter is greater than 0. For example, the probability that the intercept is greater than 0 is 0.427.

Plot the posterior distributions.

plot(PosteriorMdl)

Given the shrinkages, the distribution of E is fairly dense around 0. Therefore, E might not be an important predictor.

By default, estimate draws and discards a burn-in sample of size 5000. However, a good practice is to inspect a trace plot of the draws for adequate mixing and lack of transience. Plot a trace plot of the draws for each parameter. You can access the draws that compose the distribution (the properties BetaDraws and Sigma2Draws) using dot notation.

figure;
for j = 1:(p + 1)
    subplot(2,2,j);
    plot(PosteriorMdl.BetaDraws(j,:));
    title(sprintf('%s',PosteriorMdl.VarNames{j}));
end

figure;
plot(PosteriorMdl.Sigma2Draws);
title('Sigma2');

The trace plots indicate that the draws seem to mix well. The plots show no detectable transience or serial correlation, and the draws do not jump between states.

Consider the regression model in Select Variables Using Bayesian Lasso Regression.

Create a prior model for performing stochastic search variable selection (SSVS). Assume that β and σ2are dependent (a conjugate mixture model). Specify the number of predictors p and the names of the regression coefficients.

p = 3;
PriorMdl = mixconjugateblm(p,'VarNames',["IPI" "E" "WR"]);

Load the Nelson-Plosser data set. Create variables for the response and predictor series.

load Data_NelsonPlosser
X = DataTable{:,PriorMdl.VarNames(2:end)};
y = DataTable{:,'GNPR'};

Implement SSVS by estimating the marginal posterior distributions of β and σ2. Because SSVS uses Markov chain Monte Carlo for estimation, set a random number seed to reproduce the results.

rng(1);
PosteriorMdl = estimate(PriorMdl,X,y);
Method: MCMC sampling with 10000 draws
Number of observations: 62
Number of predictors:   4
 
           |   Mean      Std           CI95        Positive  Distribution  Regime 
----------------------------------------------------------------------------------
 Intercept | -18.8333  10.1851  [-36.965,  0.716]    0.037     Empirical   0.8806 
 IPI       |   4.4554   0.1543   [ 4.165,  4.764]    1.000     Empirical   0.4545 
 E         |   0.0010   0.0004   [ 0.000,  0.002]    0.997     Empirical   0.0925 
 WR        |   2.4686   0.3615   [ 1.766,  3.197]    1.000     Empirical   0.1734 
 Sigma2    |  47.7557   8.6551   [33.858, 66.875]    1.000     Empirical    NaN   
 

PosteriorMdl is an empiricalblm model object that stores draws from the posterior distributions of β and σ2 given the data. estimate displays a summary of the marginal posterior distributions in the command line. Rows of the summary correspond to regression coefficients and the disturbance variance, and columns correspond to characteristics of the posterior distribution. The characteristics include:

  • CI95, which contains the 95% Bayesian equitailed credible intervals for the parameters. For example, the posterior probability that the regression coefficient of E (standardized) is in [0.000, 0.0.002] is 0.95.

  • Regime, which contains the marginal posterior probability of variable inclusion (γ=1 for a variable). For example, the posterior probability E that should be included in the model is 0.0925.

Assuming that variables with Regime < 0.1 should be removed from the model, the results suggest that you can exclude the unemployment rate from the model.

By default, estimate draws and discards a burn-in sample of size 5000. However, a good practice is to inspect a trace plot of the draws for adequate mixing and lack of transience. Plot a trace plot of the draws for each parameter. You can access the draws that compose the distribution (the properties BetaDraws and Sigma2Draws) using dot notation.

figure;
for j = 1:(p + 1)
    subplot(2,2,j);
    plot(PosteriorMdl.BetaDraws(j,:));
    title(sprintf('%s',PosteriorMdl.VarNames{j}));
end

figure;
plot(PosteriorMdl.Sigma2Draws);
title('Sigma2');

The trace plots indicate that the draws seem to mix well. The plots show no detectable transience or serial correlation, and the draws do not jump between states.

Consider the regression model and prior distribution in Select Variables Using Bayesian Lasso Regression.

Create a Bayesian lasso regression prior model for 3 predictors and specify variable names. Specify the shrinkage values 0.01, 10, 1e5, and 10 for the intercept, and the coefficients of IPI, E, and WR.

p = 3;
PriorMdl = bayeslm(p,'ModelType','lasso','VarNames',["IPI" "E" "WR"],...
    'Lambda',[0.01; 10; 1e5; 10]);

Load the Nelson-Plosser data set. Create variables for the response and predictor series.

load Data_NelsonPlosser
X = DataTable{:,PriorMdl.VarNames(2:end)};
y = DataTable{:,"GNPR"};

Estimate the conditional posterior distributions of β given the data and that σ2=10. Return the estimation summary table.

rng(1); % For reproducibility
[Mdl,SummaryBeta] = estimate(PriorMdl,X,y,'Sigma2',10);
Method: lasso MCMC sampling with 10000 draws
Conditional variable: Sigma2 fixed at  10
Number of observations: 62
Number of predictors:   4
 
           |   Mean     Std          CI95        Positive  Distribution 
------------------------------------------------------------------------
 Intercept | -8.0643  4.1992  [-16.384,  0.018]    0.025     Empirical  
 IPI       |  4.4454  0.0679   [ 4.312,  4.578]    1.000     Empirical  
 E         |  0.0004  0.0002   [ 0.000,  0.001]    0.999     Empirical  
 WR        |  2.9792  0.1672   [ 2.651,  3.305]    1.000     Empirical  
 Sigma2    |   10      0       [10.000, 10.000]    1.000     Empirical  
 

estimate displays a summary of the conditional posterior distribution of β. Because σ2 is fixed during estimation, inferences on it are trivial.

Display Mdl.

Mdl
Mdl = 
  lassoblm with properties:

    NumPredictors: 3
        Intercept: 1
         VarNames: {4x1 cell}
           Lambda: [4x1 double]
                A: 3
                B: 1

 
           |  Mean     Std           CI95         Positive   Distribution  
---------------------------------------------------------------------------
 Intercept |  0       100    [-200.000, 200.000]    0.500   Scale mixture  
 IPI       |  0      0.1000    [-0.200,  0.200]     0.500   Scale mixture  
 E         |  0      0.0000    [-0.000,  0.000]     0.500   Scale mixture  
 WR        |  0      0.1000    [-0.200,  0.200]     0.500   Scale mixture  
 Sigma2    | 0.5000  0.5000    [ 0.138,  1.616]     1.000   IG(3.00,    1) 
 

Because estimate computes the conditional posterior distribution, it returns the model input PriorMdl, not the conditional posterior, in the first position of the output argument list.

Display the estimation summary table.

SummaryBeta
SummaryBeta=5×6 table
                    Mean          Std                  CI95              Positive    Distribution                                  Covariances                              
                 __________    __________    ________________________    ________    ____________    _______________________________________________________________________

    Intercept       -8.0643        4.1992       -16.384       0.01837     0.0254     'Empirical'          17.633        0.17621    -0.00053724        0.11705              0
    IPI              4.4454      0.067949         4.312        4.5783          1     'Empirical'         0.17621      0.0046171    -1.4103e-06     -0.0068855              0
    E            0.00039896    0.00015673    9.4925e-05    0.00070697     0.9987     'Empirical'     -0.00053724    -1.4103e-06     2.4564e-08    -1.8168e-05              0
    WR               2.9792       0.16716        2.6506        3.3046          1     'Empirical'         0.11705     -0.0068855    -1.8168e-05       0.027943              0
    Sigma2               10             0            10            10          1     'Empirical'               0              0              0              0              0

SummaryBeta contains the conditional posterior estimates.

Estimate the conditional posterior distributions of σ2 given that β is the conditional posterior mean of β|σ2,X,y (stored in SummaryBeta.Mean(1:(end – 1))). Return the estimation summary table.

condPostMeanBeta = SummaryBeta.Mean(1:(end - 1));
[~,SummarySigma2] = estimate(PriorMdl,X,y,'Beta',condPostMeanBeta);
Method: lasso MCMC sampling with 10000 draws
Conditional variable: Beta fixed at -8.0643      4.4454  0.00039896      2.9792
Number of observations: 62
Number of predictors:   4
 
           |   Mean     Std          CI95        Positive  Distribution 
------------------------------------------------------------------------
 Intercept | -8.0643   0.0000  [-8.064, -8.064]    0.000     Empirical  
 IPI       |  4.4454   0.0000  [ 4.445,  4.445]    1.000     Empirical  
 E         |  0.0004   0.0000  [ 0.000,  0.000]    1.000     Empirical  
 WR        |  2.9792   0.0000  [ 2.979,  2.979]    1.000     Empirical  
 Sigma2    | 56.8314  10.2921  [39.947, 79.731]    1.000     Empirical  
 

estimate displays an estimation summary of the conditional posterior distribution of σ2 given the data and that β is condPostMeanBeta. In the display, inferences on β are trivial.

Consider the regression model in Select Variables Using Bayesian Lasso Regression.

Create a prior model for performing SSVS. Assume that β and σ2are dependent (a conjugate mixture model). Specify the number of predictors p and the names of the regression coefficients.

p = 3;
PriorMdl = mixconjugateblm(p,'VarNames',["IPI" "E" "WR"]);

Load the Nelson-Plosser data set. Create variables for the response and predictor series.

load Data_NelsonPlosser
X = DataTable{:,PriorMdl.VarNames(2:end)};
y = DataTable{:,'GNPR'};

Implement SSVS by estimating the marginal posterior distributions of β and σ2. Because SSVS uses Markov chain Monte Carlo for estimation, set a random number seed to reproduce the results. Suppress the estimation display, but return the estimation summary table.

rng(1);
[PosteriorMdl,Summary] = estimate(PriorMdl,X,y,'Display',false);

PosteriorMdl is an empiricalblm model object that stores draws from the posterior distributions of β and σ2 given the data. Summary is a table with columns corresponding to posterior characteristics and rows corresponding to the coefficients (PosteriorMdl.VarNames) and disturbance variance (Sigma2).

Display the estimated parameter covariance matrix (Covariances) and proportion of times the algorithm includes each predictor (Regime).

Covariances = Summary(:,"Covariances")
Covariances=5×1 table
                                              Covariances                              
                 ______________________________________________________________________

    Intercept        103.74         1.0486     -0.0031629         0.6791         7.3916
    IPI              1.0486       0.023815    -1.3637e-05      -0.030387        0.06611
    E            -0.0031629    -1.3637e-05     1.3481e-07    -8.8792e-05    -0.00025044
    WR               0.6791      -0.030387    -8.8792e-05        0.13066       0.089039
    Sigma2           7.3916        0.06611    -0.00025044       0.089039         74.911

Regime = Summary(:,"Regime")
Regime=5×1 table
                 Regime
                 ______

    Intercept    0.8806
    IPI          0.4545
    E            0.0925
    WR           0.1734
    Sigma2          NaN

Regime contains the marginal posterior probability of variable inclusion (γ=1 for a variable). For example, the posterior probability that E should be included in the model is 0.0925.

Assuming that variables with Regime < 0.1 should be removed from the model, the results suggest that you can exclude the unemployment rate from the model.

Input Arguments

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Bayesian linear regression model for predictor variable selection, specified as a model object in this table.

Model ObjectDescription
mixconjugateblmDependent, Gaussian-mixture-inverse-gamma conjugate model for SSVS predictor variable selection, returned by bayeslm
mixsemiconjugateblmIndependent, Gaussian-mixture-inverse-gamma semiconjugate model for SSVS predictor variable selection, returned by bayeslm
lassoblmBayesian lasso regression model returned by bayeslm

Predictor data for the multiple linear regression model, specified as a numObservations-by-PriorMdl.NumPredictors numeric matrix. numObservations is the number of observations and must be equal to the length of y.

Data Types: double

Response data for the multiple linear regression model, specified as a numeric vector with numObservations elements.

Data Types: double

Name-Value Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments. Name is the argument name and Value is the corresponding value. Name must appear inside quotes. You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

Example: 'Sigma2',2 specifies estimating the conditional posterior distribution of the regression coefficients given the data and that the specified disturbance variance is 2.

Flag to display Bayesian estimator summary to the command line, specified as the comma-separated pair consisting of 'Display' and a value in this table.

ValueDescription
trueestimate prints estimation information and a table summarizing the Bayesian estimators to the command line.
falseestimate does not print to the command line.

The estimation information includes the estimation method, fixed parameters, the number of observations, and the number of predictors. The summary table contains estimated posterior means, standard deviations (square root of the posterior variance), 95% equitailed credible intervals, the posterior probability that the parameter is greater than 0, and a description of the posterior distribution (if known). For models that perform SSVS, the display table includes a column for variable-inclusion probabilities.

If you specify either Beta or Sigma2, then estimate includes your specification in the display. Corresponding posterior estimates are trivial.

Example: 'Display',false

Data Types: logical

Value of the regression coefficients for conditional posterior distribution estimation of the disturbance variance, specified as the comma-separated pair consisting of 'Beta' and a (PriorMdl.Intercept + PriorMdl.NumPredictors)-by-1 numeric vector. estimate estimates the characteristics of π(σ2|y,X,β = Beta), where y is y, X is X, and Beta is the value of 'Beta'. If PriorMdl.Intercept is true, then Beta(1) corresponds to the model intercept. All other values correspond to the predictor variables that compose the columns of X. Beta cannot contain any NaN values (that is, all coefficients must be known).

You cannot specify Beta and Sigma2 simultaneously.

By default, estimate does not compute characteristics of the conditional posterior of σ2.

Example: 'Beta',1:3

Data Types: double

Value of the disturbance variance for conditional posterior distribution estimation of the regression coefficients, specified as the comma-separated pair consisting of 'Sigma2' and a positive numeric scalar. estimate estimates characteristics of π(β|y,X,Sigma2), where y is y, X is X, and Sigma2 is the value of 'Sigma2'.

You cannot specify Sigma2 and Beta simultaneously.

By default, estimate does not compute characteristics of the conditional posterior of β.

Example: 'Sigma2',1

Data Types: double

Monte Carlo simulation adjusted sample size, specified as the comma-separated pair consisting of 'NumDraws' and a positive integer. estimate actually draws BurnInNumDraws*Thin samples. Therefore, estimate bases the estimates off NumDraws samples. For details on how estimate reduces the full Monte Carlo sample, see Algorithms.

Example: 'NumDraws',1e7

Data Types: double

Number of draws to remove from the beginning of the Monte Carlo sample to reduce transient effects, specified as the comma-separated pair consisting of 'BurnIn' and a nonnegative scalar. For details on how estimate reduces the full Monte Carlo sample, see Algorithms.

Tip

To help you specify the appropriate burn-in period size, determine the extent of the transient behavior in the Monte Carlo sample by specifying 'BurnIn',0, simulating a few thousand observations using simulate, and then plotting the paths.

Example: 'BurnIn',0

Data Types: double

Monte Carlo adjusted sample size multiplier, specified as the comma-separated pair consisting of 'Thin' and a positive integer.

The actual Monte Carlo sample size is BurnIn + NumDraws*Thin. After discarding the burn-in, estimate discards every Thin1 draws, and then retains the next. For details on how estimate reduces the full Monte Carlo sample, see Algorithms.

Tip

To reduce potential large serial correlation in the Monte Carlo sample, or to reduce the memory consumption of the draws stored in PosteriorMdl, specify a large value for Thin.

Example: 'Thin',5

Data Types: double

Starting values of the regression coefficients for the Markov chain Monte Carlo (MCMC) sample, specified as the comma-separated pair consisting of 'BetaStart' and a numeric column vector with (PriorMdl.Intercept + PriorMdl.NumPredictors) elements. By default, BetaStart is the ordinary least-squares (OLS) estimate.

Tip

A good practice is to run estimate multiple times using different parameter starting values. Verify that the solutions from each run converge to similar values.

Example: 'BetaStart',[1; 2; 3]

Data Types: double

Starting values of the disturbance variance for the MCMC sample, specified as the comma-separated pair consisting of 'Sigma2Start' and a positive numeric scalar. By default, Sigma2Start is the OLS residual mean squared error.

Tip

A good practice is to run estimate multiple times using different parameter starting values. Verify that the solutions from each run converge to similar values.

Example: 'Sigma2Start',4

Data Types: double

Output Arguments

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Bayesian linear regression model storing distribution characteristics, returned as a mixconjugateblm, mixsemiconjugateblm, lassoblm, or empiricalblm model object.

  • If you do not specify either Beta or Sigma2 (their values are []), then estimate updates the prior model using the data likelihood to form the posterior distribution. PosteriorMdl characterizes the posterior distribution and is an empiricalblm model object. Information PosteriorMdl stores or displays helps you decide whether predictor variables are important.

  • If you specify either Beta or Sigma2, then PosteriorMdl equals PriorMdl (the two models are the same object storing the same property values). estimate does not update the prior model to form the posterior model. However, Summary stores conditional posterior estimates.

For more details on the display of PosteriorMdl, see Summary.

Summary of Bayesian estimators, returned as a table. Summary contains the same information as the display of the estimation summary (Display). Rows correspond to parameters, and columns correspond to these posterior characteristics:

  • Mean – Posterior mean

  • Std – Posterior standard deviation

  • CI95 – 95% equitailed credible interval

  • Positive – Posterior probability that the parameter is greater than 0

  • Distribution – Description of the marginal or conditional posterior distribution of the parameter, when known

  • Covariances – Estimated covariance matrix of the coefficients and disturbance variance

  • Regime – Variable-inclusion probabilities for models that perform SSVS; low probabilities indicate that the variable should be excluded from the model

Row names are the names in PriorMdl.VarNames. The name of the last row is Sigma2.

Alternatively, pass PosteriorMdl to summarize to obtain a summary of Bayesian estimators.

More About

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Bayesian Linear Regression Model

A Bayesian linear regression model treats the parameters β and σ2 in the multiple linear regression (MLR) model yt = xtβ + εt as random variables.

For times t = 1,...,T:

  • yt is the observed response.

  • xt is a 1-by-(p + 1) row vector of observed values of p predictors. To accommodate a model intercept, x1t = 1 for all t.

  • β is a (p + 1)-by-1 column vector of regression coefficients corresponding to the variables that compose the columns of xt.

  • εt is the random disturbance with a mean of zero and Cov(ε) = σ2IT×T, while ε is a T-by-1 vector containing all disturbances. These assumptions imply that the data likelihood is

    (β,σ2|y,x)=t=1Tϕ(yt;xtβ,σ2).

    ϕ(yt;xtβ,σ2) is the Gaussian probability density with mean xtβ and variance σ2 evaluated at yt;.

Before considering the data, you impose a joint prior distribution assumption on (β,σ2). In a Bayesian analysis, you update the distribution of the parameters by using information about the parameters obtained from the likelihood of the data. The result is the joint posterior distribution of (β,σ2) or the conditional posterior distributions of the parameters.

Tips

  • Monte Carlo simulation is subject to variation. If estimate uses Monte Carlo simulation, then estimates and inferences might vary when you call estimate multiple times under seemingly equivalent conditions. To reproduce estimation results, before calling estimate, set a random number seed by using rng.

Algorithms

This figure shows how estimate reduces the Monte Carlo sample using the values of NumDraws, Thin, and BurnIn.

Rectangles represent successive draws from the distribution. estimate removes the white rectangles from the Monte Carlo sample. The remaining NumDraws black rectangles compose the Monte Carlo sample.

Introduced in R2018b