I noticed there's a difference in partial dependence calculated by R package gbm and Python's scikit-learn.

Here's gbm's partial dependence of median value on median income of the California housing dataset:

enter image description here

And here's scikit-learn': enter image description here

It's easy to see that R's partial dependence ranges from 1.5 to 4.5, whereas scikit-learn's from -0.5 to 1.5, but the shape of the lines is nearly the same. I don't get why it's like that.

Relevant code:


X <- calHousing[ ,!(colnames(calHousing) == "medianValue")]
y <- calHousing$medianValue / 100000
gbm.model <- gbm.fit(X, y, distribution="gaussian", n.trees=100, interaction.depth=12, shrinkage=0.15)
plot(gbm.model, i.var="medianIncome")

Python code is a copy-paste from scikit-learn' example page.


import numpy as np
import matplotlib.pyplot as plt

from mpl_toolkits.mplot3d import Axes3D

from sklearn.cross_validation import train_test_split
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble.partial_dependence import plot_partial_dependence
from sklearn.ensemble.partial_dependence import partial_dependence
from sklearn.datasets.california_housing import fetch_california_housing

def main():
    cal_housing = fetch_california_housing()
    # import ipdb; ipdb.set_trace()
    # split 80/20 train-test
    X_train, X_test, y_train, y_test = train_test_split(cal_housing.data,
    names = cal_housing.feature_names

    print('_' * 80)
    print("Training GBRT...")
    clf = GradientBoostingRegressor(n_estimators=100, max_depth=12, min_samples_split=10,
                                    learning_rate=0.15, loss='ls', subsample=0.5,
    clf.fit(X_train, y_train)

    print('_' * 80)
    print('Convenience plot with ``partial_dependence_plots``')

    features = [0, 5, 1, 2, (5, 1)]
    fig, axs = plot_partial_dependence(clf, X_train, features,
                                       n_jobs=3, grid_resolution=100)
    fig.suptitle('Partial dependence of house value on nonlocation features\n'
                 'for the California housing dataset')
    plt.subplots_adjust(top=0.9)  # tight_layout causes overlap with suptitle

# Needed on Windows because plot_partial_dependence uses multiprocessing
if __name__ == '__main__':
  • 1
    $\begingroup$ My guess is some sort of standardization took place for the outcome variable for scikit-learn (either in the underlying data or for the plotting function) that didn't take place in the R example. $\endgroup$
    – dmartin
    Commented Apr 2, 2016 at 20:40
  • $\begingroup$ Max depth and interaction depth do not mean the same thing. $\endgroup$ Commented Aug 27, 2016 at 18:54

1 Answer 1


Scikit-learn center the partial dependence with the mean of the target value, R does not.

Here is an example using diabetes dataset.


data(diabetes, package="lars")

y        <- diabetes$y
x        <- diabetes$x
class(x) <- "matrix"
data     <- data.frame(y, as.data.frame(x))

model <- gbm::gbm(formula = y ~ . , data = data, distribution = "gaussian", 
                  shrinkage = 1, bag.fraction = 1, n.trees = 100,
                  interaction.depth = 2, verbose = T, keep.data = F)

partial <- plot.gbm(dgbm, i.var = 1, return.grid = T)
plot(partial[, 2] - mean(y), type = "l")

R partial plot


import numpy as np
import sklearn
import matplotlib.pyplot as plt
import sklearn.datasets
import sklearn.ensemble
from sklearn.ensemble.partial_dependence import partial_dependence

diabetes = sklearn.datasets.load_diabetes()
X= diabetes.data
y= diabetes.target

gbm = sklearn.ensemble.GradientBoostingRegressor(loss='ls', learning_rate=1, max_leaf_nodes=3, min_samples_leaf=10,
                                             n_estimators=100, verbose=True)
model_gbm = gbm.fit(X, y)

partial, axe = partial_dependence(gbrt=model_gbm, X=X, target_variables=(0))


enter image description here

  • $\begingroup$ Great answer, I wish I could upvote it twice. Any idea why Scikit-learn would subtract off the mean of the target variable? Isn't is nice to see, for a given independent variable, what the predicted target variable is after averaging over your data? $\endgroup$
    – Chris A.
    Commented Aug 25, 2016 at 15:49
  • $\begingroup$ @EtienneKintzler, how would the scale on y-axis get affected in case of classification. $\endgroup$ Commented Apr 21, 2022 at 10:12

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