Demo of DBSCAN clustering algorithm

Finds core samples of high density and expands clusters from them.

Script output:

Estimated number of clusters: 3
Homogeneity: 0.945
Completeness: 0.876
V-measure: 0.909
Adjusted Rand Index: 0.948
Adjusted Mutual Information: 0.875
Silhouette Coefficient: 0.626

Python source code: plot_dbscan.py

print(__doc__)

import numpy as np

from sklearn.cluster import DBSCAN
from sklearn import metrics
from sklearn.datasets.samples_generator import make_blobs
from sklearn.preprocessing import StandardScaler


##############################################################################
# Generate sample data
centers = [[1, 1], [-1, -1], [1, -1]]
X, labels_true = make_blobs(n_samples=750, centers=centers, cluster_std=0.4,
                            random_state=0)

X = StandardScaler().fit_transform(X)

##############################################################################
# Compute DBSCAN
db = DBSCAN(eps=0.3, min_samples=10).fit(X)
core_samples = db.core_sample_indices_
labels = db.labels_

# Number of clusters in labels, ignoring noise if present.
n_clusters_ = len(set(labels)) - (1 if -1 in labels else 0)

print('Estimated number of clusters: %d' % n_clusters_)
print("Homogeneity: %0.3f" % metrics.homogeneity_score(labels_true, labels))
print("Completeness: %0.3f" % metrics.completeness_score(labels_true, labels))
print("V-measure: %0.3f" % metrics.v_measure_score(labels_true, labels))
print("Adjusted Rand Index: %0.3f"
      % metrics.adjusted_rand_score(labels_true, labels))
print("Adjusted Mutual Information: %0.3f"
      % metrics.adjusted_mutual_info_score(labels_true, labels))
print("Silhouette Coefficient: %0.3f"
      % metrics.silhouette_score(X, labels))

##############################################################################
# Plot result
import pylab as pl

# Black removed and is used for noise instead.
unique_labels = set(labels)
colors = pl.cm.Spectral(np.linspace(0, 1, len(unique_labels)))
for k, col in zip(unique_labels, colors):
    if k == -1:
        # Black used for noise.
        col = 'k'
        markersize = 6
    class_members = [index[0] for index in np.argwhere(labels == k)]
    cluster_core_samples = [index for index in core_samples
                            if labels[index] == k]
    for index in class_members:
        x = X[index]
        if index in core_samples and k != -1:
            markersize = 14
        else:
            markersize = 6
        pl.plot(x[0], x[1], 'o', markerfacecolor=col,
                markeredgecolor='k', markersize=markersize)

pl.title('Estimated number of clusters: %d' % n_clusters_)
pl.show()

Total running time of the example: 0.98 seconds