OPTICS Clustering Algorithm

Introduction

This lab demonstrates the use of OPTICS clustering algorithm using scikit-learn library. OPTICS is an acronym for Ordering Points To Identify the Clustering Structure. It is a density-based clustering algorithm that finds core samples of high density and expands clusters from them. In this lab, we will generate sample data, plot the reachability plot, and use DBSCAN to cluster the data.

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Skills Graph

Import Libraries

We will begin by importing the necessary libraries for this lab - numpy, matplotlib.pyplot, and OPTICS and cluster_optics_dbscan from scikit-learn.

import numpy as np
import matplotlib.pyplot as plt
from sklearn.cluster import OPTICS, cluster_optics_dbscan

Generate Sample Data

We will generate sample data for clustering. In this example, we generate six clusters with different densities using numpy.

np.random.seed(0)
n_points_per_cluster = 250

C1 = [-5, -2] + 0.8 * np.random.randn(n_points_per_cluster, 2)
C2 = [4, -1] + 0.1 * np.random.randn(n_points_per_cluster, 2)
C3 = [1, -2] + 0.2 * np.random.randn(n_points_per_cluster, 2)
C4 = [-2, 3] + 0.3 * np.random.randn(n_points_per_cluster, 2)
C5 = [3, -2] + 1.6 * np.random.randn(n_points_per_cluster, 2)
C6 = [5, 6] + 2 * np.random.randn(n_points_per_cluster, 2)
X = np.vstack((C1, C2, C3, C4, C5, C6))

Run OPTICS Clustering Algorithm

We will now run OPTICS clustering algorithm on the generated data. In this example, we set min_samples=50, xi=0.05, and min_cluster_size=0.05.

clust = OPTICS(min_samples=50, xi=0.05, min_cluster_size=0.05)
clust.fit(X)

Cluster Data using DBSCAN

We will cluster the data using DBSCAN at different epsilon values. In this example, we set epsilon to 0.5 and 2.

labels_050 = cluster_optics_dbscan(
    reachability=clust.reachability_,
    core_distances=clust.core_distances_,
    ordering=clust.ordering_,
    eps=0.5,
)
labels_200 = cluster_optics_dbscan(
    reachability=clust.reachability_,
    core_distances=clust.core_distances_,
    ordering=clust.ordering_,
    eps=2,
)

Plot Reachability Plot and Clustering Results

We will plot the reachability plot and the clustering results for OPTICS and DBSCAN at different epsilon values.

space = np.arange(len(X))
reachability = clust.reachability_[clust.ordering_]
labels = clust.labels_[clust.ordering_]

plt.figure(figsize=(10, 7))
G = gridspec.GridSpec(2, 3)
ax1 = plt.subplot(G[0, :])
ax2 = plt.subplot(G[1, 0])
ax3 = plt.subplot(G[1, 1])
ax4 = plt.subplot(G[1, 2])

## Reachability plot
colors = ["g.", "r.", "b.", "y.", "c."]
for klass, color in zip(range(0, 5), colors):
    Xk = space[labels == klass]
    Rk = reachability[labels == klass]
    ax1.plot(Xk, Rk, color, alpha=0.3)
ax1.plot(space[labels == -1], reachability[labels == -1], "k.", alpha=0.3)
ax1.plot(space, np.full_like(space, 2.0, dtype=float), "k-", alpha=0.5)
ax1.plot(space, np.full_like(space, 0.5, dtype=float), "k-.", alpha=0.5)
ax1.set_ylabel("Reachability (epsilon distance)")
ax1.set_title("Reachability Plot")

## OPTICS
colors = ["g.", "r.", "b.", "y.", "c."]
for klass, color in zip(range(0, 5), colors):
    Xk = X[clust.labels_ == klass]
    ax2.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3)
ax2.plot(X[clust.labels_ == -1, 0], X[clust.labels_ == -1, 1], "k+", alpha=0.1)
ax2.set_title("Automatic Clustering\nOPTICS")

## DBSCAN at 0.5
colors = ["g.", "r.", "b.", "c."]
for klass, color in zip(range(0, 4), colors):
    Xk = X[labels_050 == klass]
    ax3.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3)
ax3.plot(X[labels_050 == -1, 0], X[labels_050 == -1, 1], "k+", alpha=0.1)
ax3.set_title("Clustering at 0.5 epsilon cut\nDBSCAN")

## DBSCAN at 2.
colors = ["g.", "m.", "y.", "c."]
for klass, color in zip(range(0, 4), colors):
    Xk = X[labels_200 == klass]
    ax4.plot(Xk[:, 0], Xk[:, 1], color, alpha=0.3)
ax4.plot(X[labels_200 == -1, 0], X[labels_200 == -1, 1], "k+", alpha=0.1)
ax4.set_title("Clustering at 2.0 epsilon cut\nDBSCAN")

plt.tight_layout()
plt.show()

Summary

In this lab, we learned how to use OPTICS clustering algorithm to cluster data and how to use DBSCAN to cluster the data at different epsilon values. We also learned how to plot the reachability plot and the clustering results.