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Plot Grid Search Stats

================================================== Statistical comparison of models using grid search

This example illustrates how to statistically compare the performance of models trained and evaluated using :class:~sklearn.model_selection.GridSearchCV.

Imports for Statistical Comparison of Grid Search Models

Why naive score comparison is insufficient: GridSearchCV ranks models by mean_test_score, but small differences may not be statistically significant – they could arise from random variation in the CV splits rather than genuine performance differences. Since all models are evaluated on the same data partitions, their scores are correlated (a fold that is easy for one model tends to be easy for others), and standard statistical tests that assume independence will underestimate variance, inflating false positive rates. RepeatedStratifiedKFold with 10 repeats of 10-fold CV produces 100 score samples per model, providing enough data for rigorous statistical testing.

Frequentist and Bayesian approaches: The Nadeau-Bengio corrected t-test adjusts the variance estimate by the ratio n_test/n_train to account for the overlap between training sets across folds, yielding more calibrated p-values than a standard paired t-test. For pairwise comparison of all models, Bonferroni correction multiplies p-values by the number of comparisons to control the family-wise error rate. The Bayesian alternative models the mean score difference as a Student’s t-distribution (conjugate posterior under a Normal-Gamma prior), enabling direct probability statements like “there is a 43% chance these models are practically equivalent” within a Region of Practical Equivalence (ROPE). Unlike the frequentist approach, Bayesian estimation does not require multiple-comparison corrections.

# Authors: The scikit-learn developers
# SPDX-License-Identifier: BSD-3-Clause

# %%
# We will start by simulating moon shaped data (where the ideal separation
# between classes is non-linear), adding to it a moderate degree of noise.
# Datapoints will belong to one of two possible classes to be predicted by two
# features. We will simulate 50 samples for each class:

import matplotlib.pyplot as plt
import seaborn as sns

from sklearn.datasets import make_moons

X, y = make_moons(noise=0.352, random_state=1, n_samples=100)

sns.scatterplot(
    x=X[:, 0], y=X[:, 1], hue=y, marker="o", s=25, edgecolor="k", legend=False
).set_title("Data")
plt.show()

# %%
# We will compare the performance of :class:`~sklearn.svm.SVC` estimators that
# vary on their `kernel` parameter, to decide which choice of this
# hyper-parameter predicts our simulated data best.
# We will evaluate the performance of the models using
# :class:`~sklearn.model_selection.RepeatedStratifiedKFold`, repeating 10 times
# a 10-fold stratified cross validation using a different randomization of the
# data in each repetition. The performance will be evaluated using
# :class:`~sklearn.metrics.roc_auc_score`.

from sklearn.model_selection import GridSearchCV, RepeatedStratifiedKFold
from sklearn.svm import SVC

param_grid = [
    {"kernel": ["linear"]},
    {"kernel": ["poly"], "degree": [2, 3]},
    {"kernel": ["rbf"]},
]

svc = SVC(random_state=0)

cv = RepeatedStratifiedKFold(n_splits=10, n_repeats=10, random_state=0)

search = GridSearchCV(estimator=svc, param_grid=param_grid, scoring="roc_auc", cv=cv)
search.fit(X, y)

# %%
# We can now inspect the results of our search, sorted by their
# `mean_test_score`:

import pandas as pd

results_df = pd.DataFrame(search.cv_results_)
results_df = results_df.sort_values(by=["rank_test_score"])
results_df = results_df.set_index(
    results_df["params"].apply(lambda x: "_".join(str(val) for val in x.values()))
).rename_axis("kernel")
results_df[["params", "rank_test_score", "mean_test_score", "std_test_score"]]

# %%
# We can see that the estimator using the `'rbf'` kernel performed best,
# closely followed by `'linear'`. Both estimators with a `'poly'` kernel
# performed worse, with the one using a two-degree polynomial achieving a much
# lower performance than all other models.
#
# Usually, the analysis just ends here, but half the story is missing. The
# output of :class:`~sklearn.model_selection.GridSearchCV` does not provide
# information on the certainty of the differences between the models.
# We don't know if these are **statistically** significant.
# To evaluate this, we need to conduct a statistical test.
# Specifically, to contrast the performance of two models we should
# statistically compare their AUC scores. There are 100 samples (AUC
# scores) for each model as we repreated 10 times a 10-fold cross-validation.
#
# However, the scores of the models are not independent: all models are
# evaluated on the **same** 100 partitions, increasing the correlation
# between the performance of the models.
# Since some partitions of the data can make the distinction of the classes
# particularly easy or hard to find for all models, the models scores will
# co-vary.
#
# Let's inspect this partition effect by plotting the performance of all models
# in each fold, and calculating the correlation between models across folds:

# create df of model scores ordered by performance
model_scores = results_df.filter(regex=r"split\d*_test_score")

# plot 30 examples of dependency between cv fold and AUC scores
fig, ax = plt.subplots()
sns.lineplot(
    data=model_scores.transpose().iloc[:30],
    dashes=False,
    palette="Set1",
    marker="o",
    alpha=0.5,
    ax=ax,
)
ax.set_xlabel("CV test fold", size=12, labelpad=10)
ax.set_ylabel("Model AUC", size=12)
ax.tick_params(bottom=True, labelbottom=False)
plt.show()

# print correlation of AUC scores across folds
print(f"Correlation of models:\n {model_scores.transpose().corr()}")

# %%
# We can observe that the performance of the models highly depends on the fold.
#
# As a consequence, if we assume independence between samples we will be
# underestimating the variance computed in our statistical tests, increasing
# the number of false positive errors (i.e. detecting a significant difference
# between models when such does not exist) [1]_.
#
# Several variance-corrected statistical tests have been developed for these
# cases. In this example we will show how to implement one of them (the so
# called Nadeau and Bengio's corrected t-test) under two different statistical
# frameworks: frequentist and Bayesian.

# %%
# Comparing two models: frequentist approach
# ------------------------------------------
#
# We can start by asking: "Is the first model significantly better than the
# second model (when ranked by `mean_test_score`)?"
#
# To answer this question using a frequentist approach we could
# run a paired t-test and compute the p-value. This is also known as
# Diebold-Mariano test in the forecast literature [5]_.
# Many variants of such a t-test have been developed to account for the
# 'non-independence of samples problem'
# described in the previous section. We will use the one proven to obtain the
# highest replicability scores (which rate how similar the performance of a
# model is when evaluating it on different random partitions of the same
# dataset) while maintaining a low rate of false positives and false negatives:
# the Nadeau and Bengio's corrected t-test [2]_ that uses a 10 times repeated
# 10-fold cross validation [3]_.
#
# This corrected paired t-test is computed as:
#
# .. math::
#    t=\frac{\frac{1}{k \cdot r}\sum_{i=1}^{k}\sum_{j=1}^{r}x_{ij}}
#    {\sqrt{(\frac{1}{k \cdot r}+\frac{n_{test}}{n_{train}})\hat{\sigma}^2}}
#
# where :math:`k` is the number of folds,
# :math:`r` the number of repetitions in the cross-validation,
# :math:`x` is the difference in performance of the models,
# :math:`n_{test}` is the number of samples used for testing,
# :math:`n_{train}` is the number of samples used for training,
# and :math:`\hat{\sigma}^2` represents the variance of the observed
# differences.
#
# Let's implement a corrected right-tailed paired t-test to evaluate if the
# performance of the first model is significantly better than that of the
# second model. Our null hypothesis is that the second model performs at least
# as good as the first model.

import numpy as np
from scipy.stats import t

Nadeau-Bengio Corrected Standard Deviation

Variance correction for dependent CV scores: The corrected_std function implements the Nadeau-Bengio variance correction, which inflates the sample variance by a factor of (1/kr + n_test/n_train) instead of the naive 1/kr. The n_test/n_train term accounts for the overlap between training sets across different CV folds – since each pair of training sets shares most of their samples, the resulting score differences are positively correlated, and ignoring this correlation leads to underestimated standard errors and spuriously small p-values.

def corrected_std(differences, n_train, n_test):
    """Corrects standard deviation using Nadeau and Bengio's approach.

    Parameters
    ----------
    differences : ndarray of shape (n_samples,)
        Vector containing the differences in the score metrics of two models.
    n_train : int
        Number of samples in the training set.
    n_test : int
        Number of samples in the testing set.

    Returns
    -------
    corrected_std : float
        Variance-corrected standard deviation of the set of differences.
    """
    # kr = k times r, r times repeated k-fold crossvalidation,
    # kr equals the number of times the model was evaluated
    kr = len(differences)
    corrected_var = np.var(differences, ddof=1) * (1 / kr + n_test / n_train)
    corrected_std = np.sqrt(corrected_var)
    return corrected_std

Corrected Paired t-Test for Model Comparison

Right-tailed hypothesis testing with variance correction: The compute_corrected_ttest function computes the t-statistic as the mean score difference divided by the corrected standard deviation, then obtains the one-sided p-value from the survival function t.sf. A right-tailed test evaluates the null hypothesis that the second model performs at least as well as the first. The degrees of freedom equal kr - 1 where kr is the total number of score pairs (folds times repeats). This corrected test has been shown to achieve the highest replicability scores while maintaining controlled false positive and false negative rates compared to alternative approaches.

def compute_corrected_ttest(differences, df, n_train, n_test):
    """Computes right-tailed paired t-test with corrected variance.

    Parameters
    ----------
    differences : array-like of shape (n_samples,)
        Vector containing the differences in the score metrics of two models.
    df : int
        Degrees of freedom.
    n_train : int
        Number of samples in the training set.
    n_test : int
        Number of samples in the testing set.

    Returns
    -------
    t_stat : float
        Variance-corrected t-statistic.
    p_val : float
        Variance-corrected p-value.
    """
    mean = np.mean(differences)
    std = corrected_std(differences, n_train, n_test)
    t_stat = mean / std
    p_val = t.sf(np.abs(t_stat), df)  # right-tailed t-test
    return t_stat, p_val


# %%
model_1_scores = model_scores.iloc[0].values  # scores of the best model
model_2_scores = model_scores.iloc[1].values  # scores of the second-best model

differences = model_1_scores - model_2_scores

n = differences.shape[0]  # number of test sets
df = n - 1
n_train = len(next(iter(cv.split(X, y)))[0])
n_test = len(next(iter(cv.split(X, y)))[1])

t_stat, p_val = compute_corrected_ttest(differences, df, n_train, n_test)
print(f"Corrected t-value: {t_stat:.3f}\nCorrected p-value: {p_val:.3f}")

# %%
# We can compare the corrected t- and p-values with the uncorrected ones:

t_stat_uncorrected = np.mean(differences) / np.sqrt(np.var(differences, ddof=1) / n)
p_val_uncorrected = t.sf(np.abs(t_stat_uncorrected), df)

print(
    f"Uncorrected t-value: {t_stat_uncorrected:.3f}\n"
    f"Uncorrected p-value: {p_val_uncorrected:.3f}"
)

# %%
# Using the conventional significance alpha level at `p=0.05`, we observe that
# the uncorrected t-test concludes that the first model is significantly better
# than the second.
#
# With the corrected approach, in contrast, we fail to detect this difference.
#
# In the latter case, however, the frequentist approach does not let us
# conclude that the first and second model have an equivalent performance. If
# we wanted to make this assertion we need to use a Bayesian approach.

# %%
# Comparing two models: Bayesian approach
# ---------------------------------------
# We can use Bayesian estimation to calculate the probability that the first
# model is better than the second. Bayesian estimation will output a
# distribution followed by the mean :math:`\mu` of the differences in the
# performance of two models.
#
# To obtain the posterior distribution we need to define a prior that models
# our beliefs of how the mean is distributed before looking at the data,
# and multiply it by a likelihood function that computes how likely our
# observed differences are, given the values that the mean of differences
# could take.
#
# Bayesian estimation can be carried out in many forms to answer our question,
# but in this example we will implement the approach suggested by Benavoli and
# colleagues [4]_.
#
# One way of defining our posterior using a closed-form expression is to select
# a prior conjugate to the likelihood function. Benavoli and colleagues [4]_
# show that when comparing the performance of two classifiers we can model the
# prior as a Normal-Gamma distribution (with both mean and variance unknown)
# conjugate to a normal likelihood, to thus express the posterior as a normal
# distribution.
# Marginalizing out the variance from this normal posterior, we can define the
# posterior of the mean parameter as a Student's t-distribution. Specifically:
#
# .. math::
#    St(\mu;n-1,\overline{x},(\frac{1}{n}+\frac{n_{test}}{n_{train}})
#    \hat{\sigma}^2)
#
# where :math:`n` is the total number of samples,
# :math:`\overline{x}` represents the mean difference in the scores,
# :math:`n_{test}` is the number of samples used for testing,
# :math:`n_{train}` is the number of samples used for training,
# and :math:`\hat{\sigma}^2` represents the variance of the observed
# differences.
#
# Notice that we are using Nadeau and Bengio's corrected variance in our
# Bayesian approach as well.
#
# Let's compute and plot the posterior:

# initialize random variable
t_post = t(
    df, loc=np.mean(differences), scale=corrected_std(differences, n_train, n_test)
)

# %%
# Let's plot the posterior distribution:

x = np.linspace(t_post.ppf(0.001), t_post.ppf(0.999), 100)

plt.plot(x, t_post.pdf(x))
plt.xticks(np.arange(-0.04, 0.06, 0.01))
plt.fill_between(x, t_post.pdf(x), 0, facecolor="blue", alpha=0.2)
plt.ylabel("Probability density")
plt.xlabel(r"Mean difference ($\mu$)")
plt.title("Posterior distribution")
plt.show()

# %%
# We can calculate the probability that the first model is better than the
# second by computing the area under the curve of the posterior distribution
# from zero to infinity. And also the reverse: we can calculate the probability
# that the second model is better than the first by computing the area under
# the curve from minus infinity to zero.

better_prob = 1 - t_post.cdf(0)

print(
    f"Probability of {model_scores.index[0]} being more accurate than "
    f"{model_scores.index[1]}: {better_prob:.3f}"
)
print(
    f"Probability of {model_scores.index[1]} being more accurate than "
    f"{model_scores.index[0]}: {1 - better_prob:.3f}"
)

# %%
# In contrast with the frequentist approach, we can compute the probability
# that one model is better than the other.
#
# Note that we obtained similar results as those in the frequentist approach.
# Given our choice of priors, we are essentially performing the same
# computations, but we are allowed to make different assertions.

# %%
# Region of Practical Equivalence
# ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
# Sometimes we are interested in determining the probabilities that our models
# have an equivalent performance, where "equivalent" is defined in a practical
# way. A naive approach [4]_ would be to define estimators as practically
# equivalent when they differ by less than 1% in their accuracy. But we could
# also define this practical equivalence taking into account the problem we are
# trying to solve. For example, a difference of 5% in accuracy would mean an
# increase of $1000 in sales, and we consider any quantity above that as
# relevant for our business.
#
# In this example we are going to define the
# Region of Practical Equivalence (ROPE) to be :math:`[-0.01, 0.01]`. That is,
# we will consider two models as practically equivalent if they differ by less
# than 1% in their performance.
#
# To compute the probabilities of the classifiers being practically equivalent,
# we calculate the area under the curve of the posterior over the ROPE
# interval:

rope_interval = [-0.01, 0.01]
rope_prob = t_post.cdf(rope_interval[1]) - t_post.cdf(rope_interval[0])

print(
    f"Probability of {model_scores.index[0]} and {model_scores.index[1]} "
    f"being practically equivalent: {rope_prob:.3f}"
)

# %%
# We can plot how the posterior is distributed over the ROPE interval:

x_rope = np.linspace(rope_interval[0], rope_interval[1], 100)

plt.plot(x, t_post.pdf(x))
plt.xticks(np.arange(-0.04, 0.06, 0.01))
plt.vlines([-0.01, 0.01], ymin=0, ymax=(np.max(t_post.pdf(x)) + 1))
plt.fill_between(x_rope, t_post.pdf(x_rope), 0, facecolor="blue", alpha=0.2)
plt.ylabel("Probability density")
plt.xlabel(r"Mean difference ($\mu$)")
plt.title("Posterior distribution under the ROPE")
plt.show()

# %%
# As suggested in [4]_, we can further interpret these probabilities using the
# same criteria as the frequentist approach: is the probability of falling
# inside the ROPE bigger than 95% (alpha value of 5%)?  In that case we can
# conclude that both models are practically equivalent.

# %%
# The Bayesian estimation approach also allows us to compute how uncertain we
# are about our estimation of the difference. This can be calculated using
# credible intervals. For a given probability, they show the range of values
# that the estimated quantity, in our case the mean difference in
# performance, can take.
# For example, a 50% credible interval [x, y] tells us that there is a 50%
# probability that the true (mean) difference of performance between models is
# between x and y.
#
# Let's determine the credible intervals of our data using 50%, 75% and 95%:

cred_intervals = []
intervals = [0.5, 0.75, 0.95]

for interval in intervals:
    cred_interval = list(t_post.interval(interval))
    cred_intervals.append([interval, cred_interval[0], cred_interval[1]])

cred_int_df = pd.DataFrame(
    cred_intervals, columns=["interval", "lower value", "upper value"]
).set_index("interval")
cred_int_df

# %%
# As shown in the table, there is a 50% probability that the true mean
# difference between models will be between 0.000977 and 0.019023, 70%
# probability that it will be between -0.005422 and 0.025422, and 95%
# probability that it will be between -0.016445 and 0.036445.

# %%
# Pairwise comparison of all models: frequentist approach
# -------------------------------------------------------
#
# We could also be interested in comparing the performance of all our models
# evaluated with :class:`~sklearn.model_selection.GridSearchCV`. In this case
# we would be running our statistical test multiple times, which leads us to
# the `multiple comparisons problem
# <https://en.wikipedia.org/wiki/Multiple_comparisons_problem>`_.
#
# There are many possible ways to tackle this problem, but a standard approach
# is to apply a `Bonferroni correction
# <https://en.wikipedia.org/wiki/Bonferroni_correction>`_. Bonferroni can be
# computed by multiplying the p-value by the number of comparisons we are
# testing.
#
# Let's compare the performance of the models using the corrected t-test:

from itertools import combinations
from math import factorial

n_comparisons = factorial(len(model_scores)) / (
    factorial(2) * factorial(len(model_scores) - 2)
)
pairwise_t_test = []

for model_i, model_k in combinations(range(len(model_scores)), 2):
    model_i_scores = model_scores.iloc[model_i].values
    model_k_scores = model_scores.iloc[model_k].values
    differences = model_i_scores - model_k_scores
    t_stat, p_val = compute_corrected_ttest(differences, df, n_train, n_test)
    p_val *= n_comparisons  # implement Bonferroni correction
    # Bonferroni can output p-values higher than 1
    p_val = 1 if p_val > 1 else p_val
    pairwise_t_test.append(
        [model_scores.index[model_i], model_scores.index[model_k], t_stat, p_val]
    )

pairwise_comp_df = pd.DataFrame(
    pairwise_t_test, columns=["model_1", "model_2", "t_stat", "p_val"]
).round(3)
pairwise_comp_df

# %%
# We observe that after correcting for multiple comparisons, the only model
# that significantly differs from the others is `'2_poly'`.
# `'rbf'`, the model ranked first by
# :class:`~sklearn.model_selection.GridSearchCV`, does not significantly
# differ from `'linear'` or `'3_poly'`.

# %%
# Pairwise comparison of all models: Bayesian approach
# ----------------------------------------------------
#
# When using Bayesian estimation to compare multiple models, we don't need to
# correct for multiple comparisons (for reasons why see [4]_).
#
# We can carry out our pairwise comparisons the same way as in the first
# section:

pairwise_bayesian = []

for model_i, model_k in combinations(range(len(model_scores)), 2):
    model_i_scores = model_scores.iloc[model_i].values
    model_k_scores = model_scores.iloc[model_k].values
    differences = model_i_scores - model_k_scores
    t_post = t(
        df, loc=np.mean(differences), scale=corrected_std(differences, n_train, n_test)
    )
    worse_prob = t_post.cdf(rope_interval[0])
    better_prob = 1 - t_post.cdf(rope_interval[1])
    rope_prob = t_post.cdf(rope_interval[1]) - t_post.cdf(rope_interval[0])

    pairwise_bayesian.append([worse_prob, better_prob, rope_prob])

pairwise_bayesian_df = pd.DataFrame(
    pairwise_bayesian, columns=["worse_prob", "better_prob", "rope_prob"]
).round(3)

pairwise_comp_df = pairwise_comp_df.join(pairwise_bayesian_df)
pairwise_comp_df

# %%
# Using the Bayesian approach we can compute the probability that a model
# performs better, worse or practically equivalent to another.
#
# Results show that the model ranked first by
# :class:`~sklearn.model_selection.GridSearchCV` `'rbf'`, has approximately a
# 6.8% chance of being worse than `'linear'`, and a 1.8% chance of being worse
# than `'3_poly'`.
# `'rbf'` and `'linear'` have a 43% probability of being practically
# equivalent, while `'rbf'` and `'3_poly'` have a 10% chance of being so.
#
# Similarly to the conclusions obtained using the frequentist approach, all
# models have a 100% probability of being better than `'2_poly'`, and none have
# a practically equivalent performance with the latter.

# %%
# Take-home messages
# ------------------
# - Small differences in performance measures might easily turn out to be
#   merely by chance, but not because one model predicts systematically better
#   than the other. As shown in this example, statistics can tell you how
#   likely that is.
# - When statistically comparing the performance of two models evaluated in
#   GridSearchCV, it is necessary to correct the calculated variance which
#   could be underestimated since the scores of the models are not independent
#   from each other.
# - A frequentist approach that uses a (variance-corrected) paired t-test can
#   tell us if the performance of one model is better than another with a
#   degree of certainty above chance.
# - A Bayesian approach can provide the probabilities of one model being
#   better, worse or practically equivalent than another. It can also tell us
#   how confident we are of knowing that the true differences of our models
#   fall under a certain range of values.
# - If multiple models are statistically compared, a multiple comparisons
#   correction is needed when using the frequentist approach.

# %%
# .. rubric:: References
#
# .. [1] Dietterich, T. G. (1998). `Approximate statistical tests for
#        comparing supervised classification learning algorithms
#        <http://web.cs.iastate.edu/~jtian/cs573/Papers/Dietterich-98.pdf>`_.
#        Neural computation, 10(7).
# .. [2] Nadeau, C., & Bengio, Y. (2000). `Inference for the generalization
#        error
#        <https://papers.nips.cc/paper/1661-inference-for-the-generalization-error.pdf>`_.
#        In Advances in neural information processing systems.
# .. [3] Bouckaert, R. R., & Frank, E. (2004). `Evaluating the replicability
#        of significance tests for comparing learning algorithms
#        <https://www.cms.waikato.ac.nz/~ml/publications/2004/bouckaert-frank.pdf>`_.
#        In Pacific-Asia Conference on Knowledge Discovery and Data Mining.
# .. [4] Benavoli, A., Corani, G., Demšar, J., & Zaffalon, M. (2017). `Time
#        for a change: a tutorial for comparing multiple classifiers through
#        Bayesian analysis
#        <http://www.jmlr.org/papers/volume18/16-305/16-305.pdf>`_.
#        The Journal of Machine Learning Research, 18(1). See the Python
#        library that accompanies this paper `here
#        <https://github.com/janezd/baycomp>`_.
# .. [5] Diebold, F.X. & Mariano R.S. (1995). `Comparing predictive accuracy
#        <http://www.est.uc3m.es/esp/nueva_docencia/comp_col_get/lade/tecnicas_prediccion/Practicas0708/Comparing%20Predictive%20Accuracy%20(Dielbold).pdf>`_
#        Journal of Business & economic statistics, 20(1), 134-144.