fitcgam
Syntax
Description
returns a generalized additive model
Mdl
= fitcgam(Tbl
,ResponseVarName
)Mdl
trained using the sample data contained in the table
Tbl
. The input argument ResponseVarName
is the
name of the variable in Tbl
that contains the class labels for binary
classification.
specifies options using one or more name-value arguments in addition to any of the input
argument combinations in the previous syntaxes. For example,
Mdl
= fitcgam(___,Name,Value
)'Interactions',5
specifies to include five interaction terms in the
model. You can also specify a list of interaction terms using the
Interactions
name-value argument.
[
also returns Mdl
,AggregateOptimizationResults
] = fitcgam(___)AggregateOptimizationResults
, which contains
hyperparameter optimization results when you specify the
OptimizeHyperparameters
and
HyperparameterOptimizationOptions
name-value arguments. You must
also specify the ConstraintType
and
ConstraintBounds
options of
HyperparameterOptimizationOptions
. You can use this syntax to
optimize on compact model size instead of cross-validation loss, and to perform a set of
multiple optimization problems that have the same options but different constraint
bounds.
Examples
Train Generalized Additive Model
Train a univariate generalized additive model, which contains linear terms for predictors. Then, interpret the prediction for a specified data instance by using the plotLocalEffects
function.
Load the ionosphere
data set. This data set has 34 predictors and 351 binary responses for radar returns, either bad ('b'
) or good ('g'
).
load ionosphere
Train a univariate GAM that identifies whether the radar return is bad ('b'
) or good ('g'
).
Mdl = fitcgam(X,Y)
Mdl = ClassificationGAM ResponseName: 'Y' CategoricalPredictors: [] ClassNames: {'b' 'g'} ScoreTransform: 'logit' Intercept: 2.2715 NumObservations: 351
Mdl
is a ClassificationGAM
model object. The model display shows a partial list of the model properties. To view the full list of properties, double-click the variable name Mdl
in the Workspace. The Variables editor opens for Mdl
. Alternatively, you can display the properties in the Command Window by using dot notation. For example, display the class order of Mdl
.
classOrder = Mdl.ClassNames
classOrder = 2x1 cell
{'b'}
{'g'}
Classify the first observation of the training data, and plot the local effects of the terms in Mdl
on the prediction.
label = predict(Mdl,X(1,:))
label = 1x1 cell array
{'g'}
plotLocalEffects(Mdl,X(1,:))
The predict
function classifies the first observation X(1,:)
as 'g'
. The plotLocalEffects
function creates a horizontal bar graph that shows the local effects of the 10 most important terms on the prediction. Each local effect value shows the contribution of each term to the classification score for 'g'
, which is the logit of the posterior probability that the classification is 'g'
for the observation.
Train GAM with Interaction Terms
Train a generalized additive model that contains linear and interaction terms for predictors in three different ways:
Specify the interaction terms using the
formula
input argument.Specify the
'Interactions'
name-value argument.Build a model with linear terms first and add interaction terms to the model by using the
addInteractions
function.
Load Fisher's iris data set. Create a table that contains observations for versicolor and virginica.
load fisheriris inds = strcmp(species,'versicolor') | strcmp(species,'virginica'); tbl = array2table(meas(inds,:),'VariableNames',["x1","x2","x3","x4"]); tbl.Y = species(inds,:);
Specify formula
Train a GAM that contains the four linear terms (x1
, x2
, x3
, and x4
) and two interaction terms (x1*x2
and x2*x3
). Specify the terms using a formula in the form 'Y ~ terms'
.
Mdl1 = fitcgam(tbl,'Y ~ x1 + x2 + x3 + x4 + x1:x2 + x2:x3');
The function adds interaction terms to the model in the order of importance. You can use the Interactions
property to check the interaction terms in the model and the order in which fitcgam
adds them to the model. Display the Interactions
property.
Mdl1.Interactions
ans = 2×2
2 3
1 2
Each row of Interactions
represents one interaction term and contains the column indexes of the predictor variables for the interaction term.
Specify 'Interactions'
Pass the training data (tbl
) and the name of the response variable in tbl
to fitcgam
, so that the function includes the linear terms for all the other variables as predictors. Specify the 'Interactions'
name-value argument using a logical matrix to include the two interaction terms, x1*x2
and x2*x3
.
Mdl2 = fitcgam(tbl,'Y','Interactions',logical([1 1 0 0; 0 1 1 0])); Mdl2.Interactions
ans = 2×2
2 3
1 2
You can also specify 'Interactions'
as the number of interaction terms or as 'all'
to include all available interaction terms. Among the specified interaction terms, fitcgam
identifies those whose p-values are not greater than the 'MaxPValue'
value and adds them to the model. The default 'MaxPValue'
is 1 so that the function adds all specified interaction terms to the model.
Specify 'Interactions','all'
and set the 'MaxPValue'
name-value argument to 0.01.
Mdl3 = fitcgam(tbl,'Y','Interactions','all','MaxPValue',0.01); Mdl3.Interactions
ans = 5×2
3 4
2 4
1 4
2 3
1 3
Mdl3
includes five of the six available pairs of interaction terms.
Use addInteractions
Function
Train a univariate GAM that contains linear terms for predictors, and then add interaction terms to the trained model by using the addInteractions
function. Specify the second input argument of addInteractions
in the same way you specify the 'Interactions'
name-value argument of fitcgam
. You can specify the list of interaction terms using a logical matrix, the number of interaction terms, or 'all'
.
Specify the number of interaction terms as 5 to add the five most important interaction terms to the trained model.
Mdl4 = fitcgam(tbl,'Y');
UpdatedMdl4 = addInteractions(Mdl4,5);
UpdatedMdl4.Interactions
ans = 5×2
3 4
2 4
1 4
2 3
1 3
Mdl4
is a univariate GAM, and UpdatedMdl4
is an updated GAM that contains all the terms in Mdl4
and five additional interaction terms.
Create Cross-Validated GAM Using fitcgam
Train a cross-validated GAM with 10 folds, which is the default cross-validation option, by using fitcgam
. Then, use kfoldPredict
to predict class labels for validation-fold observations using a model trained on training-fold observations.
Load the ionosphere
data set. This data set has 34 predictors and 351 binary responses for radar returns, either bad ('b'
) or good ('g'
).
load ionosphere
Create a cross-validated GAM by using the default cross-validation option. Specify the 'CrossVal'
name-value argument as 'on'
.
rng('default') % For reproducibility CVMdl = fitcgam(X,Y,'CrossVal','on')
CVMdl = ClassificationPartitionedGAM CrossValidatedModel: 'GAM' PredictorNames: {'x1' 'x2' 'x3' 'x4' 'x5' 'x6' 'x7' 'x8' 'x9' 'x10' 'x11' 'x12' 'x13' 'x14' 'x15' 'x16' 'x17' 'x18' 'x19' 'x20' 'x21' 'x22' 'x23' 'x24' 'x25' 'x26' 'x27' 'x28' 'x29' 'x30' 'x31' 'x32' 'x33' 'x34'} ResponseName: 'Y' NumObservations: 351 KFold: 10 Partition: [1x1 cvpartition] NumTrainedPerFold: [1x1 struct] ClassNames: {'b' 'g'} ScoreTransform: 'logit'
The fitcgam
function creates a ClassificationPartitionedGAM
model object CVMdl
with 10 folds. During cross-validation, the software completes these steps:
Randomly partition the data into 10 sets.
For each set, reserve the set as validation data, and train the model using the other 9 sets.
Store the 10 compact, trained models in a 10-by-1 cell vector in the
Trained
property of the cross-validated model objectClassificationPartitionedGAM
.
You can override the default cross-validation setting by using the 'CVPartition'
, 'Holdout'
, 'KFold'
, or 'Leaveout'
name-value argument.
Classify the observations in X
by using kfoldPredict
. The function predicts class labels for every observation using the model trained without that observation.
label = kfoldPredict(CVMdl);
Create a confusion matrix to compare the true classes of the observations to their predicted labels.
C = confusionchart(Y,label);
Compute the classification error.
L = kfoldLoss(CVMdl)
L = 0.0712
The average misclassification rate over 10 folds is about 7%.
Optimize GAM Using OptimizeHyperparameters
Optimize the hyperparameters of a GAM with respect to cross-validation loss by using the OptimizeHyperparameters name-value argument.
Load the 1994 census data stored in census1994.mat
. The data set consists of demographic data from the US Census Bureau to predict whether an individual makes over $50,000 per year. The classification task is to fit a model that predicts the salary category of people given their age, working class, education level, marital status, race, and so on.
load census1994
census1994
contains the training data set adultdata
and the test data set adulttest
. To reduce the running time for this example, subsample 500 training observations and 500 test observations by using the datasample
function.
rng('default') NumSamples = 5e2; adultdata = datasample(adultdata,NumSamples,'Replace',false); adulttest = datasample(adulttest,NumSamples,'Replace',false);
Train a GAM classifier by passing the training data adultdata
to the fitcgam
function, and include the OptimizeHyperparameters
argument. Specify OptimizeHyperparameters
as 'auto'
so that fitcgam
finds optimal values of InitialLearnRateForPredictors
, NumTreesPerPredictor
, Interactions
, InitialLearnRateForInteractions
, and NumTreesPerInteraction
. For reproducibility, choose the 'expected-improvement-plus'
acquisition function. The default acquisition function depends on run time and, therefore, can give varying results.
Mdl = fitcgam(adultdata,'salary','OptimizeHyperparameters','auto', ... 'HyperparameterOptimizationOptions', ... struct('AcquisitionFunctionName','expected-improvement-plus'))
|==========================================================================================================================================================| | Iter | Eval | Objective | Objective | BestSoFar | BestSoFar | InitialLearnRate-| NumTreesPerP-| Interactions | InitialLearnRate-| NumTreesPerI-| | | result | | runtime | (observed) | (estim.) | ForPredictors | redictor | | ForInteractions | nteraction | |==========================================================================================================================================================| | 1 | Best | 0.148 | 11.721 | 0.148 | 0.148 | 0.001555 | 356 | 5 | 0.068117 | 16 | | 2 | Accept | 0.182 | 0.88258 | 0.148 | 0.14977 | 0.94993 | 25 | 0 | - | - | | 3 | Accept | 0.174 | 0.5938 | 0.148 | 0.148 | 0.016784 | 11 | 3 | 0.12025 | 12 | | 4 | Accept | 0.176 | 10.466 | 0.148 | 0.148 | 0.14207 | 179 | 71 | 0.0020629 | 22 | | 5 | Accept | 0.176 | 9.6859 | 0.148 | 0.1502 | 0.0010025 | 104 | 12 | 0.0052651 | 178 | | 6 | Accept | 0.152 | 9.212 | 0.148 | 0.15035 | 0.0017566 | 323 | 4 | 0.079281 | 16 | | 7 | Accept | 0.166 | 16.319 | 0.148 | 0.14801 | 0.0011656 | 497 | 10 | 0.17479 | 92 | | 8 | Accept | 0.172 | 10.99 | 0.148 | 0.14914 | 0.0014435 | 397 | 0 | - | - | | 9 | Accept | 0.16 | 11.9 | 0.148 | 0.14801 | 0.0016398 | 432 | 2 | 0.045129 | 11 | | 10 | Accept | 0.172 | 4.414 | 0.148 | 0.14855 | 0.0013589 | 146 | 9 | 0.065204 | 12 | | 11 | Accept | 0.156 | 10.724 | 0.148 | 0.14911 | 0.002082 | 368 | 7 | 0.0011513 | 12 | | 12 | Accept | 0.178 | 11.031 | 0.148 | 0.14801 | 0.13309 | 360 | 6 | 0.67104 | 13 | | 13 | Accept | 0.154 | 11.475 | 0.148 | 0.15192 | 0.0014287 | 380 | 5 | 0.027919 | 18 | | 14 | Accept | 0.164 | 10.497 | 0.148 | 0.15151 | 0.0015368 | 318 | 5 | 0.022401 | 93 | | 15 | Best | 0.144 | 9.6966 | 0.144 | 0.14515 | 0.0020403 | 331 | 8 | 0.12167 | 11 | | 16 | Accept | 0.168 | 9.6039 | 0.144 | 0.14401 | 0.0016201 | 329 | 10 | 0.74319 | 12 | | 17 | Accept | 0.16 | 9.0822 | 0.144 | 0.1526 | 0.002317 | 313 | 9 | 0.093554 | 18 | | 18 | Accept | 0.158 | 9.8266 | 0.144 | 0.15425 | 0.0016865 | 331 | 5 | 0.023535 | 11 | | 19 | Accept | 0.146 | 11.464 | 0.144 | 0.15096 | 0.0019238 | 386 | 6 | 0.043578 | 14 | | 20 | Accept | 0.156 | 11.165 | 0.144 | 0.15234 | 0.0023502 | 385 | 6 | 0.063029 | 11 | |==========================================================================================================================================================| | Iter | Eval | Objective | Objective | BestSoFar | BestSoFar | InitialLearnRate-| NumTreesPerP-| Interactions | InitialLearnRate-| NumTreesPerI-| | | result | | runtime | (observed) | (estim.) | ForPredictors | redictor | | ForInteractions | nteraction | |==========================================================================================================================================================| | 21 | Accept | 0.146 | 11.203 | 0.144 | 0.15105 | 0.0023381 | 383 | 6 | 0.042149 | 21 | | 22 | Best | 0.142 | 11.922 | 0.142 | 0.14959 | 0.0024173 | 400 | 7 | 0.022884 | 18 | | 23 | Accept | 0.152 | 13.325 | 0.142 | 0.14972 | 0.0017718 | 443 | 8 | 0.022974 | 18 | | 24 | Best | 0.14 | 12.785 | 0.14 | 0.14681 | 0.0032302 | 417 | 7 | 0.01295 | 23 | | 25 | Accept | 0.148 | 11.121 | 0.14 | 0.14672 | 0.0043102 | 371 | 6 | 0.016624 | 27 | | 26 | Accept | 0.14 | 11.871 | 0.14 | 0.14433 | 0.0029528 | 410 | 6 | 0.011766 | 25 | | 27 | Accept | 0.15 | 13.058 | 0.14 | 0.14441 | 0.0038288 | 455 | 6 | 0.038686 | 14 | | 28 | Accept | 0.144 | 13.992 | 0.14 | 0.14374 | 0.0030969 | 471 | 7 | 0.0093565 | 39 | | 29 | Accept | 0.144 | 14.149 | 0.14 | 0.14331 | 0.0033063 | 487 | 5 | 0.0033831 | 26 | | 30 | Best | 0.138 | 12.442 | 0.138 | 0.14213 | 0.0031221 | 420 | 5 | 0.0035267 | 26 |
__________________________________________________________ Optimization completed. MaxObjectiveEvaluations of 30 reached. Total function evaluations: 30 Total elapsed time: 326.2596 seconds Total objective function evaluation time: 316.6185 Best observed feasible point: InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction _____________________________ ____________________ ____________ _______________________________ ______________________ 0.0031221 420 5 0.0035267 26 Observed objective function value = 0.138 Estimated objective function value = 0.14267 Function evaluation time = 12.4417 Best estimated feasible point (according to models): InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction _____________________________ ____________________ ____________ _______________________________ ______________________ 0.0029528 410 6 0.011766 25 Estimated objective function value = 0.14213 Estimated function evaluation time = 12.2594
Mdl = ClassificationGAM PredictorNames: {'age' 'workClass' 'fnlwgt' 'education' 'education_num' 'marital_status' 'occupation' 'relationship' 'race' 'sex' 'capital_gain' 'capital_loss' 'hours_per_week' 'native_country'} ResponseName: 'salary' CategoricalPredictors: [2 4 6 7 8 9 10 14] ClassNames: [<=50K >50K] ScoreTransform: 'logit' Intercept: -1.3924 Interactions: [6×2 double] NumObservations: 500 HyperparameterOptimizationResults: [1×1 BayesianOptimization] Properties, Methods
fitcgam
returns a ClassificationGAM
model object that uses the best estimated feasible point. The best estimated feasible point is the set of hyperparameters that minimizes the upper confidence bound of the cross-validation loss based on the underlying Gaussian process model of the Bayesian optimization process.
The Bayesian optimization process internally maintains a Gaussian process model of the objective function. The objective function is the cross-validated misclassification rate for classification. For each iteration, the optimization process updates the Gaussian process model and uses the model to find a new set of hyperparameters. Each line of the iterative display shows the new set of hyperparameters and these column values:
Objective
— Objective function value computed at the new set of hyperparameters.Objective runtime
— Objective function evaluation time.Eval result
— Result report, specified asAccept
,Best
, orError
.Accept
indicates that the objective function returns a finite value, andError
indicates that the objective function returns a value that is not a finite real scalar.Best
indicates that the objective function returns a finite value that is lower than previously computed objective function values.BestSoFar(observed)
— The minimum objective function value computed so far. This value is either the objective function value of the current iteration (if theEval result
value for the current iteration isBest
) or the value of the previousBest
iteration.BestSoFar(estim.)
— At each iteration, the software estimates the upper confidence bounds of the objective function values, using the updated Gaussian process model, at all the sets of hyperparameters tried so far. Then the software chooses the point with the minimum upper confidence bound. TheBestSoFar(estim.)
value is the objective function value returned by thepredictObjective
function at the minimum point.
The plot below the iterative display shows the BestSoFar(observed)
and BestSoFar(estim.)
values in blue and green, respectively.
The returned object Mdl
uses the best estimated feasible point, that is, the set of hyperparameters that produces the BestSoFar(estim.)
value in the final iteration based on the final Gaussian process model.
Obtain the best estimated feasible point from Mdl
in the HyperparameterOptimizationResults
property.
Mdl.HyperparameterOptimizationResults.XAtMinEstimatedObjective
ans=1×5 table
InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction
_____________________________ ____________________ ____________ _______________________________ ______________________
0.0029528 410 6 0.011766 25
Alternatively, you can use the bestPoint
function. By default, the bestPoint
function uses the 'min-visited-upper-confidence-interval'
criterion.
[x,CriterionValue,iteration] = bestPoint(Mdl.HyperparameterOptimizationResults)
x=1×5 table
InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction
_____________________________ ____________________ ____________ _______________________________ ______________________
0.0029528 410 6 0.011766 25
CriterionValue = 0.1464
iteration = 26
The 'min-visited-upper-confidence-interval'
criterion chooses the hyperparameters obtained from the 26th iteration as the best point. CriterionValue
is the upper bound of the cross-validated loss computed by the final Gaussian process model.
You can also extract the best observed feasible point (that is, the last Best
point in the iterative display) from the HyperparameterOptimizationResults
property or by specifying Criterion
as 'min-observed'
.
Mdl.HyperparameterOptimizationResults.XAtMinObjective
ans=1×5 table
InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction
_____________________________ ____________________ ____________ _______________________________ ______________________
0.0031221 420 5 0.0035267 26
[x_observed,CriterionValue_observed,iteration_observed] = bestPoint(Mdl.HyperparameterOptimizationResults,'Criterion','min-observed')
x_observed=1×5 table
InitialLearnRateForPredictors NumTreesPerPredictor Interactions InitialLearnRateForInteractions NumTreesPerInteraction
_____________________________ ____________________ ____________ _______________________________ ______________________
0.0031221 420 5 0.0035267 26
CriterionValue_observed = 0.1380
iteration_observed = 30
The 'min-observed'
criterion chooses the hyperparameters obtained from the 30th iteration as the best point. CriterionValue_observed
is the actual cross-validated loss computed using the selected hyperparameters. For more information, see the Criterion name-value argument of bestPoint
.
Evaluate the performance of the classifier on the test set by computing the test set classification error.
L = loss(Mdl,adulttest,'salary')
L = 0.1564
Optimize Cross-Validated GAM Using bayesopt
Optimize the parameters of a GAM with respect to cross-validation by using the bayesopt
function.
Alternatively, you can find optimal values of fitcgam
name-value arguments by using the OptimizeHyperparameters name-value argument. For an example, see Optimize GAM Using OptimizeHyperparameters.
Load the 1994 census data stored in census1994.mat
. The data set consists of demographic data from the US Census Bureau to predict whether an individual makes over $50,000 per year. The classification task is to fit a model that predicts the salary category of people given their age, working class, education level, marital status, race, and so on.
load census1994
census1994
contains the training data set adultdata
and the test data set adulttest
. To reduce the running time for this example, subsample 500 training observations from adultdata
by using the datasample
function.
rng('default') NumSamples = 5e2; adultdata = datasample(adultdata,NumSamples,'Replace',false);
Set up a partition for cross-validation. This step fixes the cross-validation sets that the optimization uses at each step.
c = cvpartition(adultdata.salary,'KFold',5);
Prepare optimizableVariable
objects for the name-value arguments that you want to optimize using Bayesian optimization. This example finds optimal values for the MaxNumSplitsPerPredictor
and NumTreesPerPredictor
arguments of fitcgam
.
maxNumSplits = optimizableVariable('maxNumSplits',[1,10],'Type','integer'); numTrees = optimizableVariable('numTrees',[1,500],'Type','integer');
Create an objective function that takes an input z = [maxNumSplits,numTrees]
and returns the cross-validated loss value of z
.
minfun = @(z)kfoldLoss(fitcgam(adultdata,'salary','CVPartition',c, ... 'MaxNumSplitsPerPredictor',z.maxNumSplits, ... 'NumTreesPerPredictor',z.numTrees));
If you specify a cross-validation option, then the fitcgam
function returns a cross-validated model object ClassificationPartitionedGAM
. The kfoldLoss
function returns the classification loss obtained by the cross-validated model. Therefore, the function handle minfun
computes the cross-validation loss at the parameters in z
.
Search for the best parameters [maxNumSplits,numTrees]
using bayesopt
. For reproducibility, choose the 'expected-improvement-plus'
acquisition function. The default acquisition function depends on run time and, therefore, can give varying results.
results = bayesopt(minfun,[maxNumSplits,numTrees],'Verbose',0, ... 'IsObjectiveDeterministic',true, ... 'AcquisitionFunctionName','expected-improvement-plus');
Obtain the best point from results
.
zbest = bestPoint(results)
zbest=1×2 table
maxNumSplits numTrees
____________ ________
1 5
Train an optimized GAM using the zbest
values.
Mdl = fitcgam(adultdata,'salary', ... 'MaxNumSplitsPerPredictor',zbest.maxNumSplits, ... 'NumTreesPerPredictor',zbest.numTrees);
Input Arguments
Tbl
— Sample data
table
Sample data used to train the model, specified as a table. Each row of
Tbl
corresponds to one observation, and each column corresponds
to one predictor variable. Multicolumn variables and cell arrays other than cell arrays
of character vectors are not allowed.
Optionally, Tbl
can contain a column for the response variable
and a column for the observation weights.
The response variable must be a categorical, character, or string array, a logical or numeric vector, or a cell array of character vectors.
fitcgam
supports only binary classification. Either the response variable must contain exactly two distinct classes, or you must specify two classes for training by using theClassNames
name-value argument.A good practice is to specify the order of the classes in the response variable by using the
ClassNames
name-value argument.
The column for the weights must be a numeric vector.
You must specify the response variable in
Tbl
by usingResponseVarName
orformula
and specify the observation weights inTbl
by usingWeights
.Specify the response variable by using
ResponseVarName
—fitcgam
uses the remaining variables as predictors. To use a subset of the remaining variables inTbl
as predictors, specify predictor variables by usingPredictorNames
.Define a model specification by using
formula
—fitcgam
uses a subset of the variables inTbl
as predictor variables and the response variable, as specified informula
.
If Tbl
does not contain the response variable, then specify a
response variable by using Y
. The length of the response variable
Y
and the number of rows in Tbl
must be
equal. To use a subset of the variables in Tbl
as predictors,
specify predictor variables by using PredictorNames
.
fitcgam
considers NaN
,
''
(empty character vector), ""
(empty string),
<missing>
, and <undefined>
values in
Tbl
to be missing values.
fitcgam
does not use observations with all missing values in the fit.fitcgam
does not use observations with missing response values in the fit.fitcgam
uses observations with some missing values for predictors to find splits on variables for which these observations have valid values.
Data Types: table
ResponseVarName
— Response variable name
name of variable in Tbl
Response variable name, specified as a character vector or string scalar containing the name
of the response variable in Tbl
. For example, if the response
variable Y
is stored in Tbl.Y
, then specify it as
'Y'
.
Data Types: char
| string
formula
— Model specification
character vector | string scalar
Model specification, specified as a character vector or string scalar in the form
'Y ~ terms'
. The formula
argument specifies
a response variable and linear and interaction terms for predictor variables. Use
formula
to specify a subset of variables in
Tbl
as predictors for training the model. If you specify a
formula, then the software does not use any variables in Tbl
that
do not appear in formula
.
For example, specify 'Y~x1+x2+x3+x1:x2'
. In this form,
Y
represents the response variable, and x1
,
x2
, and x3
represent the linear terms for the
predictor variables. x1:x2
represents the interaction term for
x1
and x2
.
The variable names in the formula must be both variable names in Tbl
(Tbl.Properties.VariableNames
) and valid MATLAB® identifiers. You can verify the variable names in Tbl
by
using the isvarname
function. If the variable names
are not valid, then you can convert them by using the matlab.lang.makeValidName
function.
Alternatively, you can specify a response variable and linear terms for predictors
using formula
, and specify interaction terms for predictors using
'Interactions'
.
fitcgam
builds a set of interaction trees using only the
terms whose p-values are not greater than the
'MaxPValue'
value.
Example: 'Y~x1+x2+x3+x1:x2'
Data Types: char
| string
Y
— Class labels
categorical array | character array | string array | logical vector | numeric vector | cell array of character vectors
Class labels, specified as a categorical, character, or string array, a logical or numeric vector, or a cell array of character vectors.
fitcgam
supports only binary classification. EitherY
must contain exactly two distinct classes, or you must specify two classes for training by using theClassNames
name-value argument.The length of
Y
must be equal to the number of observations inX
orTbl
.If
Y
is a character array, then each label must correspond to one row of the array.A good practice is to specify the class order using the
ClassNames
name-value pair argument.fitcgam
considersNaN
,''
(empty character vector),""
(empty string),<missing>
, and<undefined>
values inY
to be missing values.fitcgam
does not use observations with missing response values in the fit.
Data Types: single
| double
| categorical
| logical
| char
| string
| cell
X
— Predictor data
numeric matrix
Predictor data, specified as a numeric matrix. Each row of X
corresponds to one observation, and each column corresponds to one predictor variable.
fitcgam
considers NaN
values in
X
as missing values. The function does not use observations
with all missing values in the fit. fitcgam
uses observations
with some missing values for X
to find splits on variables for
which these observations have valid values.
Data Types: single
| double
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.
Before R2021a, use commas to separate each name and value, and enclose
Name
in quotes.
Example: 'Interactions','all','MaxPValue',0.05
specifies to include
all available interaction terms whose p-values are not greater than
0.05.
InitialLearnRateForInteractions
— Initial learning rate of gradient boosting for interaction terms
1
(default) | numeric scalar in (0,1]
Initial learning rate of gradient boosting for interaction terms, specified as a numeric scalar in the interval (0,1].
For each boosting iteration for interaction trees,
fitcgam
starts fitting with the initial learning rate. The
function halves the learning rate until it finds a rate that improves the model
fit.
Training a model using a small learning rate requires more learning iterations, but often achieves better accuracy.
For more details about gradient boosting, see Gradient Boosting Algorithm.
Example: 'InitialLearnRateForInteractions',0.1
Data Types: single
| double
InitialLearnRateForPredictors
— Initial learning rate of gradient boosting for linear terms
1
(default) | numeric scalar in (0,1]
Initial learning rate of gradient boosting for linear terms, specified as a numeric scalar in the interval (0,1].
For each boosting iteration for predictor trees, fitcgam
starts fitting with the initial learning rate. The function halves the learning rate
until it finds a rate that improves the model fit.
Training a model using a small learning rate requires more learning iterations, but often achieves better accuracy.
For more details about gradient boosting, see Gradient Boosting Algorithm.
Example: 'InitialLearnRateForPredictors',0.1
Data Types: single
| double
Interactions
— Number or list of interaction terms
0
(default) | nonnegative integer scalar | logical matrix | 'all'
Number or list of interaction terms to include in the candidate set S,
specified as a nonnegative integer scalar, a logical matrix, or
'all'
.
Number of interaction terms, specified as a nonnegative integer — S includes the specified number of important interaction terms, selected based on the p-values of the terms.
List of interaction terms, specified as a logical matrix — S includes the terms specified by a
t
-by-p
logical matrix, wheret
is the number of interaction terms, andp
is the number of predictors used to train the model. For example,logical([1 1 0; 0 1 1])
represents two pairs of interaction terms: a pair of the first and second predictors, and a pair of the second and third predictors.If
fitcgam
uses a subset of input variables as predictors, then the function indexes the predictors using only the subset. That is, the column indexes of the logical matrix do not count the response and observation weight variables. The indexes also do not count any variables not used by the function.'all'
— S includes all possible pairs of interaction terms, which isp*(p – 1)/2
number of terms in total.
Among the interaction terms in S, the fitcgam
function identifies those whose p-values are not greater than the
'MaxPValue'
value and uses them to build a set of
interaction trees. Use the default value ('MaxPValue'
,1) to
build interaction trees using all terms in S.
Example: 'Interactions','all'
Data Types: single
| double
| logical
| char
| string
MaxNumSplitsPerInteraction
— Maximum number of decision splits per interaction tree
4 (default) | positive integer scalar
Maximum number of decision splits (or branch nodes) for each interaction tree (boosted tree for an interaction term), specified as a positive integer scalar.
Example: 'MaxNumSplitsPerInteraction',5
Data Types: single
| double
MaxNumSplitsPerPredictor
— Maximum number of decision splits per predictor tree
1 (default) | positive integer scalar
Maximum number of decision splits (or branch nodes) for each predictor tree (boosted tree for
a linear term), specified as a positive integer
scalar. By default,
fitcgam
uses a tree stump
for a predictor tree.
Example: 'MaxNumSplitsPerPredictor',5
Data Types: single
| double
MaxPValue
— Maximum p-value for detecting interaction terms
1 (default) | numeric scalar in [0,1]
Maximum p-value for detecting interaction terms, specified as a numeric scalar in the interval [0,1].
fitcgam
first finds the candidate set S of
interaction terms from formula
or
'Interactions'
. Then the function identifies the interaction
terms whose p-values are not greater than the
'MaxPValue'
value and uses them to build a set of interaction
trees.
The default value ('MaxPValue',1
) builds interaction trees for all
interaction terms in the candidate set S.
For more details about detecting interaction terms, see Interaction Term Detection.
Example: 'MaxPValue',0.05
Data Types: single
| double
NumBins
— Number of bins for numeric predictors
256
(default) | positive integer scalar | []
(empty)
Number of bins for numeric predictors, specified as a positive integer scalar or
[]
(empty).
If you specify the
'NumBins'
value as a positive integer scalar (numBins
), thenfitcgam
bins every numeric predictor into at mostnumBins
equiprobable bins, and then grows trees on the bin indices instead of the original data.The number of bins can be less than
numBins
if a predictor has fewer thannumBins
unique values.fitcgam
does not bin categorical predictors.
If the
'NumBins'
value is empty ([]
), thenfitcgam
does not bin any predictors.
When you use a large training data set, this binning option speeds up training but might cause
a decrease in accuracy. You can first use the default value of
'NumBins'
, and then change the value depending on the accuracy
and training speed.
The trained model Mdl
stores the bin edges in the
BinEdges
property.
Example: 'NumBins',50
Data Types: single
| double
NumTreesPerInteraction
— Number of trees per interaction term
100 (default) | positive integer scalar
Number of trees per interaction term, specified as a positive integer scalar.
The 'NumTreesPerInteraction'
value is equivalent to the number of
gradient boosting iterations for the interaction terms for predictors. For each
iteration, fitcgam
adds a set of interaction trees to the
model, one tree for each interaction term. To learn about the gradient boosting
algorithm, see Gradient Boosting Algorithm.
You can determine whether the fitted model has the specified number of trees by
viewing the diagnostic message displayed when 'Verbose'
is 1 or 2,
or by checking the ReasonForTermination
property value of the model
Mdl
.
Example: 'NumTreesPerInteraction',500
Data Types: single
| double
NumTreesPerPredictor
— Number of trees per linear term
300 (default) | positive integer scalar
Number of trees per linear term, specified as a positive integer scalar.
The 'NumTreesPerPredictor'
value is equivalent to the number of
gradient boosting iterations for the linear terms for predictors. For each iteration,
fitcgam
adds a set of predictor trees to the model, one
tree for each predictor. To learn about the gradient boosting algorithm, see Gradient Boosting Algorithm.
You can determine whether the fitted model has the specified number of trees by
viewing the diagnostic message displayed when 'Verbose'
is 1 or 2,
or by checking the ReasonForTermination
property value of the model
Mdl
.
Example: 'NumTreesPerPredictor',500
Data Types: single
| double
CategoricalPredictors
— Categorical predictors list
vector of positive integers | logical vector | character matrix | string array | cell array of character vectors | 'all'
Categorical predictors list, specified as one of the values in this table.
Value | Description |
---|---|
Vector of positive integers |
Each entry in the vector is an index value indicating that the corresponding predictor is
categorical. The index values are between 1 and If |
Logical vector |
A |
Character matrix | Each row of the matrix is the name of a predictor variable. The names must match the entries in PredictorNames . Pad the names with extra blanks so each row of the character matrix has the same length. |
String array or cell array of character vectors | Each element in the array is the name of a predictor variable. The names must match the entries in PredictorNames . |
"all" | All predictors are categorical. |
By default, if the predictor data is a table
(Tbl
), fitcgam
assumes that a variable is
categorical if it is a logical vector, unordered categorical vector, character array, string
array, or cell array of character vectors. If the predictor data is a matrix
(X
), fitcgam
assumes that all predictors are
continuous. To identify any other predictors as categorical predictors, specify them by using
the CategoricalPredictors
name-value argument.
Example: 'CategoricalPredictors','all'
Data Types: single
| double
| logical
| char
| string
| cell
ClassNames
— Names of classes to use for training
categorical array | character array | string array | logical vector | numeric vector | cell array of character vectors
Names of classes to use for training, specified as a categorical, character, or string
array; a logical or numeric vector; or a cell array of character vectors.
ClassNames
must have the same data type as the response variable
in Tbl
or Y
.
If ClassNames
is a character array, then each element must correspond to one row of the array.
Use ClassNames
to:
Specify the order of the classes during training.
Specify the order of any input or output argument dimension that corresponds to the class order. For example, use
ClassNames
to specify the order of the dimensions ofCost
or the column order of classification scores returned bypredict
.Select a subset of classes for training. For example, suppose that the set of all distinct class names in
Y
is["a","b","c"]
. To train the model using observations from classes"a"
and"c"
only, specify"ClassNames",["a","c"]
.
The default value for ClassNames
is the set of all distinct class names in the response variable in Tbl
or Y
.
Example: "ClassNames",["b","g"]
Data Types: categorical
| char
| string
| logical
| single
| double
| cell
Cost
— Misclassification cost
[0 1; 1 0]
(default) | 2-by-2 numeric matrix | structure
Misclassification cost of a point, specified as one of the following:
2-by-2 numeric matrix, where
Cost(i,j)
is the cost of classifying a point into classj
if its true class isi
(that is, the rows correspond to the true class and the columns correspond to the predicted class). To specify the class order for the corresponding rows and columns ofCost
, set the'ClassNames'
name-value argument.Structure
S
with two fields:S.ClassNames
, which contains the group names as a variable of the same data type as the response variable inTbl
orY
; andS.ClassificationCosts
, which contains the cost matrix.
Example: 'Cost',[0 2; 1 0]
Data Types: single
| double
| struct
NumPrint
— Number of iterations between diagnostic message printouts
10
(default) | nonnegative integer scalar
Number of iterations between diagnostic message printouts, specified as a nonnegative integer
scalar. This argument is valid only when you specify 'Verbose'
as 1.
If you specify 'Verbose',1
and 'NumPrint',numPrint
, then
the software displays diagnostic messages every numPrint
iterations in the Command Window.
Example: 'NumPrint',500
Data Types: single
| double
PredictorNames
— Predictor variable names
string array of unique names | cell array of unique character vectors
Predictor variable names, specified as a string array of unique names or cell array of unique
character vectors. The functionality of PredictorNames
depends on the
way you supply the training data.
If you supply
X
andY
, then you can usePredictorNames
to assign names to the predictor variables inX
.The order of the names in
PredictorNames
must correspond to the column order ofX
. That is,PredictorNames{1}
is the name ofX(:,1)
,PredictorNames{2}
is the name ofX(:,2)
, and so on. Also,size(X,2)
andnumel(PredictorNames)
must be equal.By default,
PredictorNames
is{'x1','x2',...}
.
If you supply
Tbl
, then you can usePredictorNames
to choose which predictor variables to use in training. That is,fitcgam
uses only the predictor variables inPredictorNames
and the response variable during training.PredictorNames
must be a subset ofTbl.Properties.VariableNames
and cannot include the name of the response variable.By default,
PredictorNames
contains the names of all predictor variables.A good practice is to specify the predictors for training using either
PredictorNames
orformula
, but not both.
Example: "PredictorNames",["SepalLength","SepalWidth","PetalLength","PetalWidth"]
Data Types: string
| cell
Prior
— Prior probabilities
'empirical'
(default) | 'uniform'
| vector of scalar values | structure
Prior probabilities for each class, specified as one of the following:
Character vector or string scalar.
Vector (one scalar value for each class). To specify the class order for the corresponding elements of
'Prior'
, set the'ClassNames'
name-value argument.Structure
S
with two fields.S.ClassNames
contains the class names as a variable of the same type as the response variable inY
orTbl
.S.ClassProbs
contains a vector of corresponding probabilities.
fitcgam
normalizes the weights in each class
('Weights'
) to add up to the value of the prior probability of
the respective class.
Example: 'Prior','uniform'
Data Types: char
| string
| single
| double
| struct
ResponseName
— Response variable name
"Y"
(default) | character vector | string scalar
Response variable name, specified as a character vector or string scalar.
If you supply
Y
, then you can useResponseName
to specify a name for the response variable.If you supply
ResponseVarName
orformula
, then you cannot useResponseName
.
Example: ResponseName="response"
Data Types: char
| string
ScoreTransform
— Score transformation
'logit'
(default) | 'none'
| function handle | ...
Score transformation, specified as a built-in transformation function name or function handle.
This table summarizes the available score transformations. Specify one using its corresponding character vector or string scalar.
Value | Description |
---|---|
"doublelogit" | 1/(1 + e–2x) |
"invlogit" | log(x / (1 – x)) |
"ismax" | Sets the score for the class with the largest score to 1, and sets the scores for all other classes to 0 |
"logit" | 1/(1 + e–x) |
"none" or "identity" | x (no transformation) |
"sign" | –1 for x < 0 0 for x = 0 1 for x > 0 |
"symmetric" | 2x – 1 |
"symmetricismax" | Sets the score for the class with the largest score to 1, and sets the scores for all other classes to –1 |
"symmetriclogit" | 2/(1 + e–x) – 1 |
For a MATLAB function or a function you define, use its function handle for the score transform. The function handle must accept a matrix (the original scores) and return a matrix of the same size (the transformed scores).
This argument determines the output score computation for object functions such as
predict
,
margin
, and
edge
. Use
'logit'
(default) to compute posterior probabilities, and use
'none'
to compute the logit of posterior probabilities.
Example: 'ScoreTransform','none'
Data Types: char
| string
| function_handle
Verbose
— Verbosity level
0
(default) | 1
| 2
Verbosity level, specified as 0
, 1
, or
2
. The Verbose
value controls the amount of
information that the software displays in the Command Window.
This table summarizes the available verbosity level options.
Value | Description |
---|---|
0 | The software displays no information. |
1 | The software displays diagnostic messages every numPrint iterations, where
numPrint is the 'NumPrint'
value. |
2 | The software displays diagnostic messages at every iteration. |
Each line of the diagnostic messages shows the information about each boosting iteration and includes the following columns:
Type
— Type of trained trees,1D
(predictor trees, or boosted trees for linear terms for predictors) or2D
(interaction trees, or boosted trees for interaction terms for predictors)NumTrees
— Number of trees per linear term or interaction term thatfitcgam
added to the model so farDeviance
— Deviance of the modelRelTol
— Relative change of model predictions: , where is a column vector of model predictions at iteration kLearnRate
— Learning rate used for the current iteration
Example: 'Verbose',1
Data Types: single
| double
Weights
— Observation weights
ones(size(X,1),1)
(default) | vector of scalar values | name of variable in Tbl
Observation weights, specified as a vector of scalar values or the name of a variable in Tbl
. The software weights the observations in each row of X
or Tbl
with the corresponding value in Weights
. The size of Weights
must equal the number of rows in X
or Tbl
.
If you specify the input data as a table Tbl
, then
Weights
can be the name of a variable in Tbl
that contains a numeric vector. In this case, you must specify
Weights
as a character vector or string scalar. For example, if
the weights vector W
is stored in Tbl.W
, then
specify it as 'W'
.
fitcgam
normalizes the weights in each class to add up to the value of the prior probability of the respective class.
Data Types: single
| double
| char
| string
Note
You cannot use any cross-validation name-value argument together with the
OptimizeHyperparameters
name-value argument. You can modify the
cross-validation for OptimizeHyperparameters
only by using the
HyperparameterOptimizationOptions
name-value argument.
CrossVal
— Flag to train cross-validated model
'off'
(default) | 'on'
Flag to train a cross-validated model, specified as 'on'
or 'off'
.
If you specify 'on'
, then the software trains a
cross-validated model with 10 folds.
You can override this cross-validation setting using the
'CVPartition'
, 'Holdout'
,
'KFold'
, or 'Leaveout'
name-value argument. You can use only one cross-validation name-value
argument at a time to create a cross-validated model.
Alternatively, cross-validate after creating a model by passing
Mdl
to crossval
.
Example: 'Crossval','on'
CVPartition
— Cross-validation partition
[]
(default) | cvpartition
object
Cross-validation partition, specified as a cvpartition
object that specifies the type of cross-validation and the
indexing for the training and validation sets.
To create a cross-validated model, you can specify only one of these four name-value
arguments: CVPartition
, Holdout
,
KFold
, or Leaveout
.
Example: Suppose you create a random partition for 5-fold cross-validation on 500
observations by using cvp = cvpartition(500,KFold=5)
. Then, you can
specify the cross-validation partition by setting
CVPartition=cvp
.
Holdout
— Fraction of data for holdout validation
scalar value in the range (0,1)
Fraction of the data used for holdout validation, specified as a scalar value in the range
(0,1). If you specify Holdout=p
, then the software completes these
steps:
Randomly select and reserve
p*100
% of the data as validation data, and train the model using the rest of the data.Store the compact trained model in the
Trained
property of the cross-validated model.
To create a cross-validated model, you can specify only one of these four name-value
arguments: CVPartition
, Holdout
,
KFold
, or Leaveout
.
Example: Holdout=0.1
Data Types: double
| single
KFold
— Number of folds
10
(default) | positive integer value greater than 1
Number of folds to use in the cross-validated model, specified as a positive integer value
greater than 1. If you specify KFold=k
, then the software completes
these steps:
Randomly partition the data into
k
sets.For each set, reserve the set as validation data, and train the model using the other
k
– 1 sets.Store the
k
compact trained models in ak
-by-1 cell vector in theTrained
property of the cross-validated model.
To create a cross-validated model, you can specify only one of these four name-value
arguments: CVPartition
, Holdout
,
KFold
, or Leaveout
.
Example: KFold=5
Data Types: single
| double
Leaveout
— Leave-one-out cross-validation flag
"off"
(default) | "on"
Leave-one-out cross-validation flag, specified as "on"
or
"off"
. If you specify Leaveout="on"
, then for
each of the n observations (where n is the number
of observations, excluding missing observations, specified in the
NumObservations
property of the model), the software completes
these steps:
Reserve the one observation as validation data, and train the model using the other n – 1 observations.
Store the n compact trained models in an n-by-1 cell vector in the
Trained
property of the cross-validated model.
To create a cross-validated model, you can specify only one of these four name-value
arguments: CVPartition
, Holdout
,
KFold
, or Leaveout
.
Example: Leaveout="on"
Data Types: char
| string
OptimizeHyperparameters
— Parameters to optimize
'none'
(default) | 'auto'
| 'auto-univariate'
| 'auto-bivariate'
| 'all'
| 'all-univariate'
| 'all-bivariate'
| string array or cell array of eligible parameter names | vector of optimizableVariable
objects
Parameters to optimize, specified as one of these values:
'none'
— Do not optimize.'auto'
— OptimizeInitialLearnRateForPredictors
,NumTreesPerPredictor
,Interactions
,InitialLearnRateForInteractions
, andNumTreesPerInteraction
.'auto-univariate'
— OptimizeInitialLearnRateForPredictors
andNumTreesPerPredictor
.'auto-bivariate'
— OptimizeInteractions
,InitialLearnRateForInteractions
, andNumTreesPerInteraction
.'all'
— Optimize all eligible parameters.'all-univariate'
— Optimize all eligible univariate parameters.'all-bivariate'
— Optimize all eligible bivariate parameters.String array or cell array of eligible parameter names.
Vector of
optimizableVariable
objects, typically the output ofhyperparameters
.
The eligible parameters for fitcgam
are:
Univariate hyperparameters
InitialLearnRateForPredictors
—fitcgam
searches among real values, log-scaled in the range[1e-3,1]
.MaxNumSplitsPerPredictor
—fitcgam
searches among integers in the range[1,maxNumSplits]
, wheremaxNumSplits
ismin(30,max(2,NumObservations–1))
.NumObservations
is the number of observations, excluding missing observations, stored in theNumObservations
property of the returned modelMdl
.NumTreesPerPredictor
—fitcgam
searches among integers, log-scaled in the range[10,500]
.
Bivariate hyperparameters
Interactions
—fitcgam
searches among integers, log-scaled in the range[0,MaxNumInteractions]
t, whereMaxNumInteractions
isNumPredictors*(NumPredictors – 1)/2
, andNumPredictors
is the number of predictors used to train the model.InitialLearnRateForInteractions
—fitcgam
searches among real values, log-scaled in the range[1e-3,1]
.MaxNumSplitsPerInteraction
—fitcgam
searches among integers in the range[1,maxNumSplits]
.NumTreesPerInteraction
—fitcgam
searches among integers, log-scaled in the range[10,500]
.
Use 'auto'
or 'all'
to find optimal
hyperparameter values for both univariate and bivariate parameters. Alternatively, you
can find optimal values for univariate parameters using
'auto-univariate'
or 'all-univariate'
and then
find optimal values for bivariate parameters using 'auto-bivariate'
or 'all-bivariate'
. For examples, see Optimize GAM Using OptimizeHyperparameters and Train Generalized Additive Model for Binary Classification.
The optimization attempts to minimize the cross-validation loss
(error) for fitcgam
by varying the parameters. To control the
cross-validation type and other aspects of the optimization, use the
HyperparameterOptimizationOptions
name-value argument. When you use
HyperparameterOptimizationOptions
, you can use the (compact) model size
instead of the cross-validation loss as the optimization objective by setting the
ConstraintType
and ConstraintBounds
options.
Note
The values of OptimizeHyperparameters
override any values you
specify using other name-value arguments. For example, setting
OptimizeHyperparameters
to "auto"
causes
fitcgam
to optimize hyperparameters corresponding to the
"auto"
option and to ignore any specified values for the
hyperparameters.
Set nondefault parameters by passing a vector of
optimizableVariable
objects that have nondefault values. For
example:
load fisheriris params = hyperparameters('fitcgam',meas,species); params(1).Range = [1e-4,1e6];
Pass params
as the value of
OptimizeHyperparameters
.
By default, the iterative display appears at the command line,
and plots appear according to the number of hyperparameters in the optimization. For the
optimization and plots, the objective function is the misclassification rate. To control the
iterative display, set the Verbose
option of the
HyperparameterOptimizationOptions
name-value argument. To control the
plots, set the ShowPlots
field of the
HyperparameterOptimizationOptions
name-value argument.
Example: 'OptimizeHyperparameters','auto'
HyperparameterOptimizationOptions
— Options for optimization
HyperparameterOptimizationOptions
object | structure
Options for optimization, specified as a HyperparameterOptimizationOptions
object or a structure. This argument
modifies the effect of the OptimizeHyperparameters
name-value
argument. If you specify HyperparameterOptimizationOptions
, you must
also specify OptimizeHyperparameters
. All the options are optional.
However, you must set ConstraintBounds
and
ConstraintType
to return
AggregateOptimizationResults
. The options that you can set in a
structure are the same as those in the
HyperparameterOptimizationOptions
object.
Option | Values | Default |
---|---|---|
Optimizer |
| "bayesopt" |
ConstraintBounds | Constraint bounds for N optimization problems,
specified as an N-by-2 numeric matrix or
| [] |
ConstraintTarget | Constraint target for the optimization problems, specified as
| If you specify ConstraintBounds and
ConstraintType , then the default value is
"matlab" . Otherwise, the default value is
[] . |
ConstraintType | Constraint type for the optimization problems, specified as
| [] |
AcquisitionFunctionName | Type of acquisition function:
Acquisition functions whose names include
| "expected-improvement-per-second-plus" |
MaxObjectiveEvaluations | Maximum number of objective function evaluations. If you specify multiple
optimization problems using ConstraintBounds , the value of
MaxObjectiveEvaluations applies to each optimization
problem individually. | 30 for "bayesopt" and
"randomsearch" , and the entire grid for
"gridsearch" |
MaxTime | Time limit for the optimization, specified as a nonnegative real
scalar. The time limit is in seconds, as measured by | Inf |
NumGridDivisions | For Optimizer="gridsearch" , the number of values in each
dimension. The value can be a vector of positive integers giving the number of
values for each dimension, or a scalar that applies to all dimensions. This
option is ignored for categorical variables. | 10 |
ShowPlots | Logical value indicating whether to show plots of the optimization progress.
If this option is true , the software plots the best observed
objective function value against the iteration number. If you use Bayesian
optimization (Optimizer ="bayesopt" ), then
the software also plots the best estimated objective function value. The best
observed objective function values and best estimated objective function values
correspond to the values in the BestSoFar (observed) and
BestSoFar (estim.) columns of the iterative display,
respectively. You can find these values in the properties ObjectiveMinimumTrace and EstimatedObjectiveMinimumTrace of
Mdl.HyperparameterOptimizationResults . If the problem
includes one or two optimization parameters for Bayesian optimization, then
ShowPlots also plots a model of the objective function
against the parameters. | true |
SaveIntermediateResults | Logical value indicating whether to save the optimization results. If this
option is true , the software overwrites a workspace variable
named "BayesoptResults" at each iteration. The variable is a
BayesianOptimization object. If you
specify multiple optimization problems using
ConstraintBounds , the workspace variable is an AggregateBayesianOptimization object named
"AggregateBayesoptResults" . | false |
Verbose | Display level at the command line:
For details, see the | 1 |
UseParallel | Logical value indicating whether to run the Bayesian optimization in parallel, which requires Parallel Computing Toolbox™. Due to the nonreproducibility of parallel timing, parallel Bayesian optimization does not necessarily yield reproducible results. For details, see Parallel Bayesian Optimization. | false |
Repartition | Logical value indicating whether to repartition the cross-validation at
every iteration. If this option is A value of
| false |
Specify only one of the following three options. | ||
CVPartition | cvpartition object created by cvpartition | Kfold=5 if you do not specify a
cross-validation option |
Holdout | Scalar in the range (0,1) representing the holdout
fraction | |
Kfold | Integer greater than 1 |
Example: HyperparameterOptimizationOptions=struct(UseParallel=true)
Output Arguments
Mdl
— Trained generalized additive model
ClassificationGAM
model object | ClassificationPartitionedGAM
cross-validated model object
Trained generalized additive model, returned as one of the model objects in this table.
Model Object | Cross-Validation Options to Train Model Object | Ways to Classify Observations Using Model Object |
---|---|---|
ClassificationGAM | None | Use predict to classify new observations, and use resubPredict to classify training observations. |
ClassificationPartitionedGAM | Specify KFold , Holdout ,
Leaveout , CrossVal , or
CVPartition | Use kfoldPredict to classify
observations that fitcgam holds out during training.
kfoldPredict predicts a class label for every
observation by using the model trained without that observation. |
To reference properties of Mdl
, use dot notation. For example,
enter Mdl.Interactions
in the Command Window to display the
interaction terms in Mdl
.
If you specify OptimizeHyperparameters
and
set the ConstraintType
and ConstraintBounds
options of
HyperparameterOptimizationOptions
, then Mdl
is an
N-by-1 cell array of model objects, where N is equal
to the number of rows in ConstraintBounds
. If none of the optimization
problems yields a feasible model, then each cell array value is []
.
AggregateOptimizationResults
— Aggregate optimization results
AggregateBayesianOptimization
object
Aggregate optimization results for multiple optimization problems, returned as an AggregateBayesianOptimization
object. To return
AggregateOptimizationResults
, you must specify
OptimizeHyperparameters
and
HyperparameterOptimizationOptions
. You must also specify the
ConstraintType
and ConstraintBounds
options of HyperparameterOptimizationOptions
. For an example that
shows how to produce this output, see Hyperparameter Optimization with Multiple Constraint Bounds.
More About
Generalized Additive Model (GAM) for Binary Classification
A generalized additive model (GAM) is an interpretable model that explains class scores (the logit of class probabilities) using a sum of univariate and bivariate shape functions of predictors.
fitcgam
uses a boosted tree as a shape function for each predictor
and, optionally, each pair of predictors; therefore, the function can capture a nonlinear
relation between a predictor and the response variable. Because contributions of individual
shape functions to the prediction (classification score) are well separated, the model is
easy to interpret.
The standard GAM uses a univariate shape function for each predictor.
where y is a response variable that follows the binomial distribution with the probability of success (probability of positive class) μ in n observations. g(μ) is a logit link function, and c is an intercept (constant) term. fi(xi) is a univariate shape function for the ith predictor, which is a boosted tree for a linear term for the predictor (predictor tree).
You can include interactions between predictors in a model by adding bivariate shape functions of important interaction terms to the model.
where fij(xixj) is a bivariate shape function for the ith and jth predictors, which is a boosted tree for an interaction term for the predictors (interaction tree).
fitcgam
finds important interaction terms based on the
p-values of F-tests. For details, see Interaction Term Detection.
Deviance
Deviance is a generalization of the residual sum of squares. It measures the goodness of fit compared to the saturated model.
The deviance of a fitted model is twice the difference between the loglikelihoods of the model and the saturated model:
-2(logL - logLs),
where L and Ls are the likelihoods of the fitted model and the saturated model, respectively. The saturated model is the model with the maximum number of parameters that you can estimate.
fitcgam
uses the deviance to measure the goodness of model fit
and finds a learning rate that reduces the deviance at each iteration. Specify
'Verbose'
as 1 or 2 to display the deviance and learning rate in
the Command Window.
Algorithms
Gradient Boosting Algorithm
fitcgam
fits a generalized additive model using a gradient
boosting algorithm (Adaptive Logistic Regression).
fitcgam
first builds sets of predictor trees (boosted trees for
linear terms for predictors) and then builds sets of interaction trees (boosted trees for
interaction terms for predictors). The boosting algorithm iterates for at most
'NumTreesPerPredictor'
times for predictor trees, and then iterates
for at most 'NumTreesPerInteraction'
times for interaction
trees.
For each boosting iteration, fitcgam
builds a set of predictor
trees with the initial learning rate 'InitialLearnRateForPredictors'
,
or builds a set of interaction trees with the initial learning rate
'InitialLearnRateForInteractions'
.
When building a set of trees, the function trains one tree at a time. It fits a tree to the residual that is the difference between the response and the aggregated prediction from all trees grown previously. To control the boosting learning speed, the function shrinks the tree by the learning rate and then adds the tree to the model and updates the residual.
Updated model = current model + (learning rate)·(new tree)
Updated residual = current residual – (learning rate)·(response explained by new tree)
If adding the set of trees improves the model fit (that is, reduces the deviance of the fit by a value larger than a tolerance), then
fitcgam
moves to the next iteration.Otherwise,
fitcgam
halves the learning rate and uses it to update the model and residual. The function continues to halve the learning rate until it finds a rate that improves the model fit.If the function cannot find such a learning rate when training predictor trees, then it stops boosting iterations for linear terms and starts boosting iterations for interaction terms.
If the function cannot find such a learning rate when training interaction trees, then it terminates the model fitting.
You can determine why training stopped by checking the
ReasonForTermination
property of the trained model.
Interaction Term Detection
For each pairwise interaction term
xixj
(specified by formula
or 'Interactions'
), the
software performs an F-test to examine whether the term is statistically
significant.
To speed up the process, fitcgam
bins numeric predictors into at
most 8 equiprobable bins. The number of bins can be less than 8 if a predictor has fewer
than 8 unique values. The F-test examines the null hypothesis that the
bins created by xi and
xj have equal responses versus the
alternative that at least one bin has a different response value from the others. A small
p-value indicates that differences are significant, which implies
that the corresponding interaction term is significant and, therefore, including the term
can improve the model fit.
fitcgam
builds a set of interaction trees using the terms whose
p-values are not greater than the 'MaxPValue'
value. You can use the default 'MaxPValue'
value 1
to build interaction trees using all terms specified by formula
or
'Interactions'
.
fitcgam
adds interaction terms to the model in the order of
importance based on the p-values. Use the
Interactions
property of the returned model to check the order of
the interaction terms added to the model.
Cost
, Prior
, and Weights
If you specify the
Cost
,Prior
, andWeights
name-value arguments, the output model object stores the specified values in theCost
,Prior
, andW
properties, respectively. TheCost
property stores the user-specified cost matrix as is. ThePrior
andW
properties store the prior probabilities and observation weights, respectively, after normalization. For details, see Misclassification Cost Matrix, Prior Probabilities, and Observation Weights.The software uses the
Cost
property for prediction, but not training. Therefore,Cost
is not read-only; you can change the property value by using dot notation after creating the trained model.
References
[1] Lou, Yin, Rich Caruana, and Johannes Gehrke. "Intelligible Models for Classification and Regression." Proceedings of the 18th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD ’12). Beijing, China: ACM Press, 2012, pp. 150–158.
[2] Lou, Yin, Rich Caruana, Johannes Gehrke, and Giles Hooker. "Accurate Intelligible Models with Pairwise Interactions." Proceedings of the 19th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD ’13) Chicago, Illinois, USA: ACM Press, 2013, pp. 623–631.
Extended Capabilities
Automatic Parallel Support
Accelerate code by automatically running computation in parallel using Parallel Computing Toolbox™.
To perform parallel hyperparameter optimization, use the UseParallel=true
option in the HyperparameterOptimizationOptions
name-value argument in
the call to the fitcgam
function.
For more information on parallel hyperparameter optimization, see Parallel Bayesian Optimization.
For general information about parallel computing, see Run MATLAB Functions with Automatic Parallel Support (Parallel Computing Toolbox).
Version History
Introduced in R2021a
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