partialDependence
Syntax
Description
computes the partial dependence pd
= partialDependence(RegressionMdl
,Vars
)pd
between the predictor variables
listed in Vars
and the responses predicted by using the regression
model RegressionMdl
, which contains predictor data.
computes the partial dependence pd
= partialDependence(ClassificationMdl
,Vars
,Labels
)pd
between the predictor variables
listed in Vars
and the scores for the classes specified in
Labels
by using the classification model
ClassificationMdl
, which contains predictor data.
uses additional options specified by one or more namevalue arguments. For example, if you
specify pd
= partialDependence(___,Name,Value
)"UseParallel","true"
, the
partialDependence
function uses parallel computing to perform the
partial dependence calculations.
Examples
Compute and Plot Partial Dependence on One Variable
Train a naive Bayes classification model with the fisheriris
data set, and compute partial dependence values that show the relationship between the predictor variable and the predicted scores (posterior probabilities) for multiple classes.
Load the fisheriris
data set, which contains species (species
) and measurements (meas
) on sepal length, sepal width, petal length, and petal width for 150 iris specimens. The data set contains 50 specimens from each of three species: setosa, versicolor, and virginica.
load fisheriris
Train a naive Bayes classification model with species
as the response and meas
as predictors.
Mdl = fitcnb(meas,species,"PredictorNames",["Sepal Length","Sepal Width","Petal Length","Petal Width"]);
Compute partial dependence values on the third predictor variable (petal length) of the scores predicted by Mdl
for all three classes of species
. Specify the class labels by using the ClassNames
property of Mdl
.
[pd,x] = partialDependence(Mdl,3,Mdl.ClassNames);
pd contains the partial dependence values for the query points x. You can plot the computed partial dependence values by using plotting functions such as plot
and bar
. Plot pd
against x
by using the bar
function.
bar(x,pd) legend(Mdl.ClassNames) xlabel("Petal Length") ylabel("Scores") title("Partial Dependence Plot")
According to this model, the probability of virginica
increases with petal length. The probability of setosa
is about 0.33, from where petal length is 0 to around 2.5, and then the probability drops to almost 0.
Alternatively, you can use the plotPartialDependence
function to compute and plot partial dependence values.
plotPartialDependence(Mdl,3,Mdl.ClassNames)
Compute and Plot Partial Dependence on Two Variables for Multiple Classes
Train an ensemble of classification models and compute partial dependence values on two variables for multiple classes. Then plot the partial dependence values for each class.
Load the census1994
data set, which contains US yearly salary data, categorized as <=50K
or >50K
, and several demographic variables.
load census1994
Extract a subset of variables to analyze from the table adultdata
.
X = adultdata(1:500,["age","workClass","education_num","marital_status","race", ... "sex","capital_gain","capital_loss","hours_per_week","salary"]);
Train a random forest of classification trees by using fitcensemble
and specifying Method
as "Bag"
. For reproducibility, use a template of trees created by using templateTree
with the Reproducible
option.
rng("default") t = templateTree("Reproducible",true); Mdl = fitcensemble(X,"salary","Method","Bag","Learners",t);
Inspect the class names in Mdl
.
Mdl.ClassNames
ans = 2x1 categorical
<=50K
>50K
Compute partial dependence values of the scores on the predictors age
and education_num
for both classes (<=50K
and >50K
). Specify the number of observations to sample as 100.
[pd,x,y] = partialDependence(Mdl,["age","education_num"],Mdl.ClassNames,"NumObservationsToSample",100);
Create a surface plot of the partial dependence values for the first class (<=50K
) by using the surf
function.
figure surf(x,y,squeeze(pd(1,:,:))) xlabel("age") ylabel("education\_num") zlabel("Score of class <=50K") title("Partial Dependence Plot") view([130 30]) % Modify the viewing angle
Create a surface plot of the partial dependence values for the second class (>50K
).
figure surf(x,y,squeeze(pd(2,:,:))) xlabel("age") ylabel("education\_num") zlabel("Score of class >50K") title("Partial Dependence Plot") view([130 30]) % Modify the viewing angle
The two plots show different partial dependence patterns depending on the class.
Compute Partial Dependence for Noisy Data
Load the carbig
sample data set.
load carbig
The vectors Displacement
, Cylinders
, and Model_Year
contain data for car engine displacement, number of engine cylinders, and year the car was manufactured, respectively.
Fit a multinomial regression model using Displacement
and Cylinders
as predictor variables and Model_Year
as the response.
predvars = [Displacement,Cylinders]; Mdl = fitmnr(predvars,Model_Year,PredictorNames=["Displacement","Cylinders"]);
Create a vector of noisy predictor data from the predictor variables by using the rand
function.
Data = predvars(1:10:end,:);
rng("default")
rows = length(Data);
Data = Data + 10*rand([rows,2]);
Calculate the partial dependence of the response category probability corresponding to cars manufactured in 1980 on Displacement
. Use the noisy predictor data to calculate the partial dependence.
[pd,x,~] = partialDependence(Mdl,"Displacement",80,Data)
pd = 1×100
0.0030 0.0031 0.0031 0.0032 0.0032 0.0033 0.0033 0.0033 0.0034 0.0034 0.0035 0.0035 0.0036 0.0036 0.0036 0.0037 0.0037 0.0037 0.0038 0.0038 0.0038 0.0039 0.0039 0.0039 0.0039 0.0039 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0040 0.0039 0.0039 0.0039 0.0039 0.0038 0.0038 0.0038 0.0037 0.0037 0.0036
x = 100×1
73.7850
77.1781
80.5713
83.9644
87.3575
90.7507
94.1438
97.5370
100.9301
104.3232
⋮
The output shows the calculated values for the partial dependence of the category probability on Displacement
. Because Displacement
is a continuous variable, the partialDependence
function calculates the partial dependence at 100 equally spaced query points x
.
Plot the partial dependence using plotPartialDependence
.
plotPartialDependence(Mdl,"Displacement",80,Data)
The plot shows that when Displacement
increases from approximately 70 to approximately 180, the probability of a car being manufactured in 1980 increases. As Displacement
continues to increase, the probability of a car being manufactured in 1980 decreases.
Compute and Plot Partial Dependence on Multiple Variables for Regression
Train a support vector machine (SVM) regression model using the carsmall
data set, and compute the partial dependence on two predictor variables. Then, create a figure that shows the partial dependence on the two variables along with the histogram on each variable.
Load the carsmall
data set.
load carsmall
Create a table that contains Weight
, Cylinders
, Displacement
, and Horsepower
.
Tbl = table(Weight,Cylinders,Displacement,Horsepower);
Train an SVM regression model using the predictor variables in Tbl
and the response variable MPG
. Use a Gaussian kernel function with an automatic kernel scale.
Mdl = fitrsvm(Tbl,MPG,"ResponseName","MPG", ... "CategoricalPredictors","Cylinders","Standardize",true, ... "KernelFunction","gaussian","KernelScale","auto");
Compute the partial dependence of the predicted response (MPG
) on the predictor variables Weight
and Horsepower
. Specify query points to compute the partial dependence by using the QueryPoints
namevalue argument.
numPoints = 10; ptX = linspace(min(Weight),max(Weight),numPoints)'; ptY = linspace(min(Horsepower),max(Horsepower),numPoints)'; [pd,x,y] = partialDependence(Mdl,["Weight","Horsepower"],"QueryPoints",[ptX ptY]);
Create a figure that contains a 5by5 tiled chart layout. Plot the partial dependence on the two variables by using the imagesc
function. Then draw the histogram for each variable by using the histogram
function. Specify the edges of the histograms so that the centers of the histogram bars align with the query points. Change the axes properties to align the axes of the plots.
t = tiledlayout(5,5,"TileSpacing","compact"); ax1 = nexttile(2,[4,4]); imagesc(x,y,pd) title("Partial Dependence Plot") colorbar("eastoutside") ax1.YDir = "normal"; ax2 = nexttile(22,[1,4]); dX = diff(ptX(1:2)); edgeX = [ptXdX/2;ptX(end)+dX]; histogram(Weight,edgeX); xlabel("Weight") xlim(ax1.XLim); ax3 = nexttile(1,[4,1]); dY = diff(ptY(1:2)); edgeY = [ptYdY/2;ptY(end)+dY]; histogram(Horsepower,edgeY) xlabel("Horsepower") xlim(ax1.YLim); ax3.XDir = "reverse"; camroll(90)
Each element of pd
specifies the color for one pixel of the image plot. The histograms aligned with the axes of the image show the distribution of the predictors.
Specify Model Using Function Handle
Compute the partial dependence of label scores on predictor variables for a SemiSupervisedSelfTrainingModel
object. You cannot pass a SemiSupervisedSelfTrainingModel
object directly to the partialDependence
function. Instead, define a custom function that returns label scores for the object, and then pass the function to partialDependence
.
Randomly generate 15 observations of labeled data, with five observations in each of three classes.
rng("default") % For reproducibility labeledX = [randn(5,2)*0.25 + ones(5,2); randn(5,2)*0.25  ones(5,2); randn(5,2)*0.5]; Y = [ones(5,1); ones(5,1)*2; ones(5,1)*3];
Randomly generate 300 additional observations of unlabeled data, with 100 observations per class.
unlabeledX = [randn(100,2)*0.25 + ones(100,2); randn(100,2)*0.25  ones(100,2); randn(100,2)*0.5];
Fit labels to the unlabeled data by using a semisupervised selftraining method. The function fitsemiself
returns a SemiSupervisedSelfTrainingModel
object.
Mdl = fitsemiself(labeledX,Y,unlabeledX);
Define the custom function myLabelScores
, which returns label scores computed by the predict
function of SemiSupervisedSelfTrainingModel
; the custom function definition appears at the end of this example.
Compute the partial dependence of the scores for unlabeledX
on each variable for all classes. partialDependence
accepts a custom model in the form of a function handle. The function represented by the function handle must accept predictor data and return a column vector or matrix with one row for each observation. Specify the custom model as @(X)myLabelScores(Mdl,X)
so that the custom function uses the trained model Mdl
and accepts predictor data.
[pd1,x1] = partialDependence(@(X)myLabelScores(Mdl,X),1,unlabeledX); [pd2,x2] = partialDependence(@(X)myLabelScores(Mdl,X),2,unlabeledX);
You can plot the computed partial dependence values by using plotting functions such as plot
and bar
. Alternatively, you can use the plotPartialDependence
function to compute and plot partial dependence values.
Create partial dependence plots for the first variable and all classes.
plotPartialDependence(@(X)myLabelScores(Mdl,X),1,unlabeledX) xlabel("1st Variable of unlabeledX") ylabel("Scores") legend("Class 1","Class 2","Class 3")
Custom Function myLabelScores
function scores = myLabelScores(Mdl,X) [~,scores] = predict(Mdl,X); end
Input Arguments
RegressionMdl
— Regression model
regression model object
Regression model, specified as a full or compact regression model object, as given in the following tables of supported models.
Model  Full or Compact Model Object 

Generalized linear model  GeneralizedLinearModel , CompactGeneralizedLinearModel 
Generalized linear mixedeffect model  GeneralizedLinearMixedModel 
Linear regression  LinearModel , CompactLinearModel 
Linear mixedeffect model  LinearMixedModel 
Nonlinear regression  NonLinearModel 
Ensemble of regression models  RegressionEnsemble , RegressionBaggedEnsemble ,
CompactRegressionEnsemble 
Generalized additive model (GAM)  RegressionGAM , CompactRegressionGAM 
Gaussian process regression  RegressionGP , CompactRegressionGP 
Gaussian kernel regression model using random feature expansion  RegressionKernel 
Linear regression for highdimensional data  RegressionLinear 
Neural network regression model  RegressionNeuralNetwork , CompactRegressionNeuralNetwork 
Support vector machine (SVM) regression  RegressionSVM , CompactRegressionSVM 
Regression tree  RegressionTree , CompactRegressionTree 
Bootstrap aggregation for ensemble of decision trees  TreeBagger , CompactTreeBagger 
If RegressionMdl
is a model object that does not contain
predictor data (for example, a compact model), you must provide the input argument
Data
.
partialDependence
does not support a model object trained with a sparse
matrix. When you train a model, use a full numeric matrix or table for predictor data
where rows correspond to individual observations.
ClassificationMdl
— Classification model
classification model object
Classification model, specified as a full or compact classification model object, as given in the following table of supported models.
Model  Full or Compact Model Object 

Discriminant analysis classifier  ClassificationDiscriminant , CompactClassificationDiscriminant 
Multiclass model for support vector machines or other classifiers  ClassificationECOC , CompactClassificationECOC 
Ensemble of learners for classification  ClassificationEnsemble , CompactClassificationEnsemble , ClassificationBaggedEnsemble 
Generalized additive model (GAM)  ClassificationGAM , CompactClassificationGAM 
Gaussian kernel classification model using random feature expansion  ClassificationKernel 
knearest neighbor classifier  ClassificationKNN 
Linear classification model  ClassificationLinear 
Multiclass naive Bayes model  ClassificationNaiveBayes , CompactClassificationNaiveBayes 
Neural network classifier  ClassificationNeuralNetwork , CompactClassificationNeuralNetwork 
Support vector machine (SVM) classifier for oneclass and binary classification  ClassificationSVM , CompactClassificationSVM 
Binary decision tree for multiclass classification  ClassificationTree , CompactClassificationTree 
Bagged ensemble of decision trees  TreeBagger , CompactTreeBagger 
Multinomial regression model  MultinomialRegression 
If ClassificationMdl
is a model object that does not contain predictor
data (for example, a compact model), you must provide the input argument
Data
.
partialDependence
does not support a model object trained with a sparse matrix. When you train a model, use a full numeric matrix or table for predictor data where rows correspond to individual observations.
fun
— Custom model
function handle
Custom model, specified as a function handle. The function handle fun
must represent a function that accepts the predictor data Data
and
returns an output in the form of a column vector or matrix. Each row of the output must
correspond to each observation (row) in the predictor data.
By default, partialDependence
uses all output columns of
fun
for the partial dependence computation. You can specify
which output columns to use by setting the OutputColumns
namevalue
argument.
If the predictor data (Data
) is in a table,
partialDependence
assumes that a variable is categorical if it is a
logical vector, categorical vector, character array, string array, or cell array of
character vectors. If the predictor data is a matrix, partialDependence
assumes that all predictors are continuous. To identify any other predictors as
categorical predictors, specify them by using the
CategoricalPredictors
namevalue argument.
Data Types: function_handle
Vars
— Predictor variables
vector of positive integers  character vector  string scalar  string array  cell array of character vectors
Predictor variables, specified as a vector of positive integers, character vector, string scalar, string array, or cell array of character vectors. You can specify one or two predictor variables, as shown in the following tables.
One Predictor Variable
Value  Description 

positive integer  Index value corresponding to the column of the predictor data. 
character vector or string scalar  Name of the predictor variable. The name must match the entry in the

Two Predictor Variables
Value  Description 

vector of two positive integers  Index values corresponding to the columns of the predictor data. 
string array or cell array of character vectors  Names of the predictor variables. Each element in the array is the name of a predictor
variable. The names must match the entries in the

Example: ["x1","x3"]
Data Types: single
 double
 char
 string
 cell
Labels
— Class labels
categorical array  character array  logical vector  numeric vector  cell array of character vectors
Class labels, specified as a categorical or character array, logical or numeric
vector, or cell array of character vectors. The values and data types in
Labels
must match those of the class names in the
ClassNames
property of ClassificationMdl
(ClassificationMdl.ClassNames
).
You can specify one or multiple class labels.
This argument is valid only when you specify a classification model object
ClassificationMdl
.
Example: ["red","blue"]
Example: ClassificationMdl.ClassNames([1 3])
specifies
Labels
as the first and third classes in
ClassificationMdl
.
Data Types: single
 double
 logical
 char
 cell
 categorical
Data
— Predictor data
numeric matrix  table
Predictor data, specified as a numeric matrix or table. Each row of
Data
corresponds to one observation, and each column
corresponds to one variable.
For both a regression model (RegressionMdl
) and a classification
model (ClassificationMdl
), Data
must be
consistent with the predictor data that trained the model, stored in either the
X
or Variables
property.
If you trained the model using a numeric matrix, then
Data
must be a numeric matrix. The variables that make up the columns ofData
must have the same number and order as the predictor variables that trained the model.If you trained the model using a table (for example,
Tbl
), thenData
must be a table. All predictor variables inData
must have the same variable names and data types as the names and types inTbl
. However, the column order ofData
does not need to correspond to the column order ofTbl
.Data
must not be sparse.
If you specify a regression or classification model that does not contain predictor
data, you must provide Data
. If the model is a full model object
that contains predictor data and you specify the Data
argument,
then partialDependence
ignores the predictor data in the model and uses
Data
only.
If you specify a custom model fun
, you must provide
Data
.
Data Types: single
 double
 table
NameValue Arguments
Specify optional pairs of arguments as
Name1=Value1,...,NameN=ValueN
, where Name
is
the argument name and Value
is the corresponding value.
Namevalue 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: partialDependence(Mdl,Vars,Data,"NumObservationsToSample",100,"UseParallel",true)
computes the partial dependence values by using 100 sampled observations in
and executing Data
for
loop
iterations in parallel.
IncludeInteractions
— Flag to include interaction terms
true
 false
Flag to include interaction terms of the generalized additive model (GAM) in the partial
dependence computation, specified as true
or
false
. This argument is valid only for a GAM. That is, you can
specify this argument only when RegressionMdl
is RegressionGAM
or CompactRegressionGAM
, or ClassificationMdl
is ClassificationGAM
or CompactClassificationGAM
.
The default IncludeInteractions
value is true
if the
model contains interaction terms. The value must be false
if the
model does not contain interaction terms.
Example: "IncludeInteractions",false
Data Types: logical
IncludeIntercept
— Flag to include intercept term
true
(default)  false
Flag to include an intercept term of the generalized additive model (GAM) in the partial
dependence computation, specified as true
or
false
. This argument is valid only for a GAM. That is, you can
specify this argument only when RegressionMdl
is RegressionGAM
or CompactRegressionGAM
, or ClassificationMdl
is ClassificationGAM
or CompactClassificationGAM
.
Example: "IncludeIntercept",false
Data Types: logical
NumObservationsToSample
— Number of observations to sample
number of total observations (default)  positive integer
Number of observations to sample, specified as a positive integer. The default value is the
number of total observations in Data
or the model
(RegressionMdl
or ClassificationMdl
). If you
specify a value larger than the number of total observations, then
partialDependence
uses all observations.
partialDependence
samples observations without replacement by using the
datasample
function and uses the sampled observations to compute partial
dependence.
Example: "NumObservationsToSample",100
Data Types: single
 double
QueryPoints
— Points to compute partial dependence
numeric column vector  numeric twocolumn matrix  cell array of two numeric column vectors
Points to compute partial dependence for numeric predictors, specified as a numeric column vector, a numeric twocolumn matrix, or a cell array of two numeric column vectors.
If you select one predictor variable in
Vars
, use a numeric column vector.If you select two predictor variables in
Vars
:Use a numeric twocolumn matrix to specify the same number of points for each predictor variable.
Use a cell array of two numeric column vectors to specify a different number of points for each predictor variable.
The default value is a numeric column vector or a numeric twocolumn matrix, depending on the number of selected predictor variables. Each column contains 100 evenly spaced points between the minimum and maximum values of the sampled observations for the corresponding predictor variable.
You cannot modify QueryPoints
for a categorical variable. The
partialDependence
function uses all categorical values in the
selected variable.
If you select one numeric variable and one categorical variable, you can specify
QueryPoints
for a numeric variable by using a cell array
consisting of a numeric column vector and an empty array.
Example: "QueryPoints",{pt,[]}
Data Types: single
 double
 cell
UseParallel
— Flag to run in parallel
false
(default)  true
Flag to run in parallel, specified as true
or
false
. If you specify "UseParallel",true
, the
partialDependence
function executes for
loop
iterations by using parfor
when predicting responses or
scores for each observation and averaging them. The loop runs in parallel when you have
Parallel Computing Toolbox™.
Example: "UseParallel",true
Data Types: logical
CategoricalPredictors
— Categorical predictors list for custom model
vector of positive integers  logical vector  character matrix  string array  cell array of character vectors  "all"
Categorical predictors list for the custom model fun
, 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 
Logical vector  A 
Character matrix  Each row of the matrix is the name of a predictor variable. The names must match the variable names of the predictor data Data in a table. 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 variable names of the predictor data Data in a table. 
"all"  All predictors are categorical. 
By default, if the predictor data Data
is in a table, partialDependence
assumes that a variable is categorical if it is a logical vector, categorical vector, character array, string array, or cell array of character vectors. If the predictor data is a matrix, partialDependence
assumes that all predictors are continuous. To identify any other predictors as categorical predictors, specify them by using the CategoricalPredictors
namevalue argument.
This argument is valid only when you specify a custom model by using fun
.
Example: "CategoricalPredictors","all"
Data Types: single
 double
 logical
 char
 string
 cell
OutputColumns
— Output columns of custom model
"all"
(default)  vector of positive integers  logical vector
Output columns of the custom model fun
to use for the partial dependence computation, 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 
Logical vector  A 
"all"  partialDependence uses all output columns for the partial dependence computation. 
This argument is valid only when you specify a custom model by using
fun
.
Example: "OutputColumns",[1 2]
Data Types: single
 double
 logical
 char
 string
PredictionForMissingValue
— Predicted response value to use for observations with missing predictor values
"median"
(default)  "mean"
 numeric scalar
Since R2024a
Predicted response value to use for observations with missing predictor values,
specified as "median"
, "mean"
, or a numeric
scalar.
Value  Description 

"median"  partialDependence uses the median of the observed response
values in the training data as the predicted response value for observations
with missing predictor values. 
"mean"  partialDependence uses the mean of the observed response
values in the training data as the predicted response value for observations
with missing predictor values. 
Numeric scalar 
If you specify 
If an observation has a missing value in a Vars
predictor
variable, then partialDependence
does not use the observation in
partial dependence computations.
Note
This namevalue argument is valid only for these types of regression models:
Gaussian process regression, kernel, linear, neural network, and support vector
machine. That is, you can specify this argument only when
RegressionMdl
is a RegressionGP
,
CompactRegressionGP
, RegressionKernel
,
RegressionLinear
, RegressionNeuralNetwork
,
CompactRegressionNeuralNetwork
, RegressionSVM
,
or CompactRegressionSVM
object.
Example: "PredictionForMissingValue","mean"
Example: "PredictionForMissingValue",NaN
Data Types: single
 double
 char
 string
Output Arguments
pd
— Partial dependence values
numeric array
Partial dependence values, returned as a numeric array.
The dimension of pd
depends on the type of model (regression,
classification or custom), number of variables specified in Vars
,
number of classes specified in Labels
(classification model only),
and number of columns specified in OutputColumns
(custom model
only).
For a regression model (RegressionMdl
), the following
conditions apply:
If you specify two variables in
Vars
,pd
is anumY
bynumX
matrix, wherenumY
andnumX
are the number of query points of the second and first variables inVars
, respectively. The value inpd(i,j)
is the partial dependence value of the query point corresponding to
andy
(i)
.x
(j)
is they
(i)i
th query point of the second predictor variable, and
is thex
(j)j
th query point of the first predictor variable.If you specify one variable in
Vars
,pd
is a1
bynumX
vector.
For a classification model (ClassificationMdl
), the following
conditions apply:
If you specify two variables in
Vars
,pd
is anum
bynumY
bynumX
array, wherenum
is the number of class labels inLabels
. The value inpd(i,j,k)
is the partial dependence value of the query point
andy
(j)
for thex
(k)i
th class label inLabels
.If you specify one variable in
Vars
,pd
is anum
bynumX
matrix.If you specify one class in
Labels
,pd
is anumY
bynumX
matrix.If you specify one variable and one class,
pd
is a1
bynumX
vector.
For a custom model (fun
), the following conditions apply:
If you specify two variables in
Vars
,pd
is anum
bynumY
bynumX
array, wherenum
is the number of output columns inOutputColumns
. The value inpd(i,j,k)
is the partial dependence value of the query point
andy
(j)
for thex
(k)i
th column inOutputColumns
.If you specify one variable in
Vars
,pd
is anum
bynumX
matrix.If you specify one column in
OutputColumns
,pd
is anumY
bynumX
matrix.If you specify one variable and one column,
pd
is a1
bynumX
vector.
x
— Query points of first predictor variable
numeric column vector  categorical column vector
Query points of the first predictor variable in Vars
, returned
as a numeric or categorical column vector.
If the predictor variable is numeric, then you can specify the query points by using
the QueryPoints
namevalue argument.
Data Types: single
 double
 categorical
y
— Query points of second predictor variable
numeric column vector  categorical column vector  []
Query points of the second predictor variable in Vars
, returned
as a numeric or categorical column vector. This output argument is empty
([]
) if you specify only one variable in
Vars
.
If the predictor variable is numeric, then you can specify the query points by using
the QueryPoints
namevalue argument.
Data Types: single
 double
 categorical
More About
Partial Dependence for Regression Models
Partial dependence[1] represents the relationships between
predictor variables and predicted responses in a trained regression model.
partialDependence
computes the partial dependence of predicted responses
on a subset of predictor variables by marginalizing over the other variables.
Consider partial dependence on a subset X^{S} of the whole predictor variable set X = {x_{1}, x_{2}, …, x_{m}}. A subset X^{S} includes either one variable or two variables: X^{S} = {x_{S1}} or X^{S} = {x_{S1}, x_{S2}}. Let X^{C} be the complementary set of X^{S} in X. A predicted response f(X) depends on all variables in X:
f(X) = f(X^{S}, X^{C}).
The partial dependence of predicted responses on X^{S} is defined by the expectation of predicted responses with respect to X^{C}:
$${f}^{S}\left({X}^{S}\right)={E}_{C}\left[f\left({X}^{S},{X}^{C}\right)\right]={\displaystyle \int f\left({X}^{S},{X}^{C}\right)}{p}_{C}\left({X}^{C}\right)d{X}^{C},$$
where
p_{C}(X^{C})
is the marginal probability of X^{C}, that is, $${p}_{C}\left({X}^{C}\right)\approx {\displaystyle \int p}\left({X}^{S},{X}^{C}\right)d{X}^{S}$$. Assuming that each observation is equally likely, and the dependence
between X^{S} and
X^{C} and the interactions of
X^{S} and
X^{C} in responses is not strong,
partialDependence
estimates the partial dependence by using observed
predictor data as follows:
$${f}^{S}\left({X}^{S}\right)\approx \frac{1}{N}{\displaystyle \sum _{i=1}^{N}f\left({X}^{S},{X}_{i}{}^{C}\right)},$$  (1) 
where N is the number of observations and X_{i} = (X_{i}^{S}, X_{i}^{C}) is the ith observation.
When you call the partialDependence
function, you can specify a trained
model (f(·)) and select variables
(X^{S}) by using the input arguments
RegressionMdl
and Vars
, respectively.
partialDependence
computes the partial dependence at 100 evenly spaced
points of X^{S} or the points that you specify by
using the QueryPoints
namevalue argument. You can specify the number
(N) of observations to sample from given predictor data by using the
NumObservationsToSample
namevalue argument.
Partial Dependence Classification Models
In the case of classification models,
partialDependence
computes the partial dependence in the same way as
for regression models, with one exception: instead of using the predicted responses from the
model, the function uses the predicted scores for the classes specified in
Labels
.
Weighted Traversal Algorithm
The weighted traversal algorithm[1] is a method to estimate partial dependence for a treebased model. The estimated partial dependence is the weighted average of response or score values corresponding to the leaf nodes visited during the tree traversal.
Let X^{S} be a subset of the whole variable set X and X^{C} be the complementary set of X^{S} in X. For each X^{S} value to compute partial dependence, the algorithm traverses a tree from the root (beginning) node down to leaf (terminal) nodes and finds the weights of leaf nodes. The traversal starts by assigning a weight value of one at the root node. If a node splits by X^{S}, the algorithm traverses to the appropriate child node depending on the X^{S} value. The weight of the child node becomes the same value as its parent node. If a node splits by X^{C}, the algorithm traverses to both child nodes. The weight of each child node becomes a value of its parent node multiplied by the fraction of observations corresponding to each child node. After completing the tree traversal, the algorithm computes the weighted average by using the assigned weights.
For an ensemble of bagged trees, the estimated partial dependence is an average of the weighted averages over the individual trees.
Algorithms
For both a regression model (RegressionMdl
) and a classification
model (ClassificationMdl
), partialDependence
uses a
predict
function to predict responses or scores.
partialDependence
chooses the proper predict
function according to the model and runs predict
with its default settings.
For details about each predict
function, see the predict
functions in the following two tables. If the specified model is a treebased model (not
including a boosted ensemble of trees), then partialDependence
uses the
weighted traversal algorithm instead of the predict
function. For details,
see Weighted Traversal Algorithm.
Regression Model Object
Model Type  Full or Compact Regression Model Object  Function to Predict Responses 

Bootstrap aggregation for ensemble of decision trees  CompactTreeBagger  predict 
Bootstrap aggregation for ensemble of decision trees  TreeBagger  predict 
Ensemble of regression models  RegressionEnsemble , RegressionBaggedEnsemble , CompactRegressionEnsemble  predict 
Gaussian kernel regression model using random feature expansion  RegressionKernel  predict 
Gaussian process regression  RegressionGP , CompactRegressionGP  predict 
Generalized additive model  RegressionGAM , CompactRegressionGAM  predict 
Generalized linear mixedeffect model  GeneralizedLinearMixedModel  predict 
Generalized linear model  GeneralizedLinearModel , CompactGeneralizedLinearModel  predict 
Linear mixedeffect model  LinearMixedModel  predict 
Linear regression  LinearModel , CompactLinearModel  predict 
Linear regression for highdimensional data  RegressionLinear  predict 
Neural network regression model  RegressionNeuralNetwork , CompactRegressionNeuralNetwork  predict 
Nonlinear regression  NonLinearModel  predict 
Regression tree  RegressionTree , CompactRegressionTree  predict 
Support vector machine  RegressionSVM , CompactRegressionSVM  predict 
Classification Model Object
Alternative Functionality
plotPartialDependence
computes and plots partial dependence values. The function can also create individual conditional expectation (ICE) plots.
References
[1] Friedman, Jerome. H. “Greedy Function Approximation: A Gradient Boosting Machine.” The Annals of Statistics 29, no. 5 (2001): 11891232.
[2] Hastie, Trevor, Robert Tibshirani, and Jerome Friedman. The Elements of Statistical Learning. New York, NY: Springer New York, 2009.
Extended Capabilities
Automatic Parallel Support
Accelerate code by automatically running computation in parallel using Parallel Computing Toolbox™.
To run in parallel, set the UseParallel
namevalue argument to
true
in the call to this function.
For more general information about parallel computing, see Run MATLAB Functions with Automatic Parallel Support (Parallel Computing Toolbox).
GPU Arrays
Accelerate code by running on a graphics processing unit (GPU) using Parallel Computing Toolbox™.
Usage notes and limitations:
This function fully supports GPU arrays for the following regression and classification models:
LinearModel
andCompactLinearModel
objectsGeneralizedLinearModel
andCompactGeneralizedLinearModel
objectsRegressionSVM
andCompactRegressionSVM
objectsRegressionLinear
objectsClassificationLinear
objects
This function supports GPU arrays with limitations for the regression and classification models described in this table.
Full or Compact Model Object Limitations ClassificationECOC
orCompactClassificationECOC
Surrogate splits are not supported for decision tree learners.
For KNN learners, you cannot set the following options to the values shown:
"NSMethod","kdtree"
"Distance"
,function handle"IncludeTies",true
ClassificationEnsemble
orCompactClassificationEnsemble
Surrogate splits are not supported for decision tree learners.
ClassificationKNN
You cannot set the following options to the values shown:
"NSMethod","kdtree"
"Distance"
,function handle"IncludeTies",true
ClassificationSVM
orCompactClassificationSVM
Oneclass classification is not supported
Data
cannot contain infinite valuesNamevalue arguments have the following limitations:
You cannot specify the
KernelFunction
namevalue argument as a custom kernel function.You can specify the
Solver
namevalue argument as "SMO
" only.You cannot specify the
OutlierFraction
orShrinkagePeriod
namevalue argument.
ClassificationTree
orCompactClassificationTree
Surrogate splits are not supported for decision trees.
RegressionEnsemble
orCompactRegressionEnsemble
Surrogate splits are not supported for decision tree learners.
RegressionTree
orCompactRegressionTree
Surrogate splits are not supported for decision trees.
This function fully supports GPU arrays for a custom function if the custom function supports GPU arrays.
For more information, see Run MATLAB Functions on a GPU (Parallel Computing Toolbox).
Version History
Introduced in R2020bR2024a: Support for observations with missing predictor values
If RegressionMdl
is a Gaussian process regression, kernel, linear,
neural network, or support vector machine model, you can now use observations with missing
predictor values in partial dependence computations. Specify the
PredictionForMissingValue
namevalue argument.
A value of
"median"
is consistent with the behavior in R2023b.A value of
NaN
is consistent with the behavior in R2023a, where the regression models do not support using observations with missing predictor values for prediction.
R2024a: Specify GPU arrays for RegressionLinear
models
partialDependence
fully supports GPU arrays for
RegressionLinear
models.
R2024a: GPU array support for ClassificationLinear
Starting in R2024a, partialDependence
fully supports GPU arrays for
ClassificationLinear
models.
R2023a: GPU array support for RegressionSVM
and CompactRegressionSVM
models
Starting in R2023a, partialDependence
fully supports GPU arrays for
RegressionSVM
and
CompactRegressionSVM
models.
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