KMedoids Demo

KMedoids clustering of data points. The goal is to find medoids than minimize the sum of absolute distance to the closest medoid. A medoid is a point of the dataset. Read more in the User Guide.

import matplotlib.pyplot as plt
import numpy as np

from sklearn_extra.cluster import KMedoids
from sklearn.datasets import make_blobs


print(__doc__)

# #############################################################################
# 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
)

# #############################################################################
# Compute Kmedoids clustering
cobj = KMedoids(n_clusters=3).fit(X)
labels = cobj.labels_

Plot results

unique_labels = set(labels)
colors = [
    plt.cm.Spectral(each) for each in np.linspace(0, 1, len(unique_labels))
]
for k, col in zip(unique_labels, colors):
    class_member_mask = labels == k

    xy = X[class_member_mask]
    plt.plot(
        xy[:, 0],
        xy[:, 1],
        "o",
        markerfacecolor=tuple(col),
        markeredgecolor="k",
        markersize=6,
    )

plt.plot(
    cobj.cluster_centers_[:, 0],
    cobj.cluster_centers_[:, 1],
    "o",
    markerfacecolor="cyan",
    markeredgecolor="k",
    markersize=6,
)

plt.title("KMedoids clustering. Medoids are represented in cyan.")

Text(0.5, 1.0, 'KMedoids clustering. Medoids are represented in cyan.')