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Clustering-based over-sampling¶
This example illustrates the data generation process and the performance of various over-samplers when clustering-based over-sampling is used.
# Author: Georgios Douzas <gdouzas@icloud.com>
# Licence: MIT
import matplotlib.pyplot as plt
import pandas as pd
from sklearn.base import clone
from sklearn.datasets import make_classification
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.cluster import KMeans, AgglomerativeClustering
from sklearn.model_selection import train_test_split
from sklearn.metrics import f1_score
from imblearn.over_sampling import RandomOverSampler, SMOTE, BorderlineSMOTE
from imblearn.pipeline import make_pipeline
from clover.over_sampling import ClusterOverSampler
print(__doc__)
RANDOM_STATE = 0
OVERSAMPLERS = [
RandomOverSampler(random_state=RANDOM_STATE),
SMOTE(random_state=RANDOM_STATE + 1),
BorderlineSMOTE(random_state=RANDOM_STATE + 2),
]
KMEANS = KMeans(random_state=RANDOM_STATE, n_clusters=100)
def generate_imbalanced_data():
"""Generate imbalanced data."""
X, y = make_classification(
n_classes=3,
class_sep=0.8,
weights=[0.01, 0.05, 0.94],
n_informative=2,
n_redundant=0,
n_repeated=0,
n_features=2,
n_clusters_per_class=1,
n_samples=2000,
random_state=RANDOM_STATE,
)
return X, y
def plot_data(X, y, oversampler, ax):
"""Plot original or resampled data."""
if oversampler is None:
X_res, y_res = X, y
title = 'Original data'
else:
oversampler = clone(oversampler)
X_res, y_res = oversampler.fit_resample(X, y)
if not isinstance(oversampler, ClusterOverSampler):
ovs_name = oversampler.__class__.__name__
title = f'Resampling using {ovs_name}'
else:
clusterer_name = oversampler.clusterer.__class__.__name__
ovs_name = oversampler.oversampler_.__class__.__name__
title = f'Resampling using {clusterer_name}-{ovs_name}'
ax.scatter(X_res[:, 0], X_res[:, 1], c=y_res, alpha=0.8, edgecolor='k')
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.get_xaxis().tick_bottom()
ax.get_yaxis().tick_left()
ax.spines['left'].set_position(('outward', 10))
ax.spines['bottom'].set_position(('outward', 10))
ax.set_title(title)
def compare_f1_scores(X_train, X_test, y_train, y_test, clf, oversampler, clusterer):
"""Compare F1 scores of oversamplers with and
without clustering."""
ovs_clf = make_pipeline(clone(oversampler), clf)
clr_ovs_clf = make_pipeline(ClusterOverSampler(clone(oversampler), clusterer), clf)
y_pred = ovs_clf.fit(X_train, y_train).predict(X_test)
y_pred_clr = clr_ovs_clf.fit(X_train, y_train).predict(X_test)
ovs_name = oversampler.__class__.__name__
clr_name = clusterer.__class__.__name__
ovs_score = f1_score(y_test, y_pred, average='macro')
clr_ovs_score = f1_score(y_test, y_pred_clr, average='macro')
return pd.DataFrame(
[[ovs_score, clr_ovs_score]],
columns=['No clustering', clr_name],
index=[ovs_name],
)
Generate imbalanced data¶
We are generating a highly imbalanced multi-class data set, using
make_classification
from scikit-learn.

Effect of clustering to over-samplers¶
Clustering based over-sampling allows to identify areas of the input space which are appropriate to generate artificial data. Therefore, the generation of noisy samples is avoided and the within-classes imbalanced issue is also addressed. The next plots show the resampled data when clustering is applied, comparing them to the resampled data of the initial over-samplers.
fig, axs = plt.subplots(3, 2, figsize=(15, 15))
for (ax1, ax2), oversampler in zip(axs, OVERSAMPLERS):
plot_data(X, y, clone(oversampler), ax1)
plot_data(X, y, ClusterOverSampler(oversampler, KMEANS), ax2)
fig.tight_layout()

Performance evaluation of clustering based over-sampling¶
We are evaluating various over-samplers using F1-score as evaluation metric on a test set. The scores with and without clustering are compared.
clf = GradientBoostingClassifier(random_state=RANDOM_STATE)
data = train_test_split(X, y, random_state=RANDOM_STATE)
scores = pd.DataFrame()
for oversampler in OVERSAMPLERS:
scores = scores.append(compare_f1_scores(*data, clf, oversampler, KMEANS))
print(scores)
Out:
No clustering KMeans
RandomOverSampler 0.755701 0.753091
SMOTE 0.611372 0.759189
BorderlineSMOTE 0.755701 0.763755
We repeat the process for AgglomerativeClustering instead of KMeans.
aff_prop = AgglomerativeClustering(n_clusters=100)
scores = pd.DataFrame()
for oversampler in OVERSAMPLERS:
scores = scores.append(compare_f1_scores(*data, clf, oversampler, aff_prop))
print(scores)
Out:
/Users/gdouzas/.pyenv/versions/miniconda3-latest/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: numpy.ufunc size changed, may indicate binary incompatibility. Expected 192 from C header, got 216 from PyObject
return f(*args, **kwds)
No clustering AgglomerativeClustering
RandomOverSampler 0.755701 0.746050
SMOTE 0.611372 0.757699
BorderlineSMOTE 0.755701 0.776927
Total running time of the script: ( 0 minutes 14.515 seconds)