ML | OPTICS Clustering Implementing using Sklearn

Last Updated : 14 Jul, 2019

Prerequisites: OPTICS Clustering

This article will demonstrate how to implement OPTICS Clustering technique using Sklearn in Python. The dataset used for the demonstration is the Mall Customer Segmentation Data which can be downloaded from Kaggle.

Step 1: Importing the required libraries

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from matplotlib import gridspec
from sklearn.cluster import OPTICS, cluster_optics_dbscan
from sklearn.preprocessing import normalize, StandardScaler

Step 2: Loading the Data

# Changing the working location to the location of the data
cd C:\Users\Dev\Desktop\Kaggle\Customer Segmentation
  
X = pd.read_csv('Mall_Customers.csv')
  
# Dropping irrelevant columns
drop_features = ['CustomerID', 'Gender']
X = X.drop(drop_features, axis = 1)
  
# Handling the missing values if any
X.fillna(method ='ffill', inplace = True)
  
X.head()

Step 3: Preprocessing the Data

# Scaling the data to bring all the attributes to a comparable level
scaler = StandardScaler()
X_scaled = scaler.fit_transform(X)
  
# Normalizing the data so that the data
# approximately follows a Gaussian distribution
X_normalized = normalize(X_scaled)
  
# Converting the numpy array into a pandas DataFrame
X_normalized = pd.DataFrame(X_normalized)
  
# Renaming the columns
X_normalized.columns = X.columns
  
X_normalized.head()

Step 4: Building the Clustering Model

# Building the OPTICS Clustering model
optics_model = OPTICS(min_samples = 10, xi = 0.05, min_cluster_size = 0.05)
  
# Training the model
optics_model.fit(X_normalized)

Step 5: Storing the results of the training

# Producing the labels according to the DBSCAN technique with eps = 0.5
labels1 = cluster_optics_dbscan(reachability = optics_model.reachability_,
                                   core_distances = optics_model.core_distances_,
                                   ordering = optics_model.ordering_, eps = 0.5)
  
# Producing the labels according to the DBSCAN technique with eps = 2.0
labels2 = cluster_optics_dbscan(reachability = optics_model.reachability_,
                                   core_distances = optics_model.core_distances_,
                                   ordering = optics_model.ordering_, eps = 2)
  
# Creating a numpy array with numbers at equal spaces till
# the specified range
space = np.arange(len(X_normalized))
  
# Storing the reachability distance of each point
reachability = optics_model.reachability_[optics_model.ordering_]
  
# Storing the cluster labels of each point
labels = optics_model.labels_[optics_model.ordering_]
  
print(labels)

Step 6: Visualizing the results

# Defining the framework of the visualization
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])
  
# Plotting the Reachability-Distance Plot
colors = ['c.', 'b.', 'r.', 'y.', 'g.']
for Class, colour in zip(range(0, 5), colors):
    Xk = space[labels == Class]
    Rk = reachability[labels == Class]
    ax1.plot(Xk, Rk, colour, alpha = 0.3)
ax1.plot(space[labels == -1], reachability[labels == -1], 'k.', alpha = 0.3)
ax1.plot(space, np.full_like(space, 2., 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 Distance')
ax1.set_title('Reachability Plot')
  
# Plotting the OPTICS Clustering
colors = ['c.', 'b.', 'r.', 'y.', 'g.']
for Class, colour in zip(range(0, 5), colors):
    Xk = X_normalized[optics_model.labels_ == Class]
    ax2.plot(Xk.iloc[:, 0], Xk.iloc[:, 1], colour, alpha = 0.3)
      
ax2.plot(X_normalized.iloc[optics_model.labels_ == -1, 0],
        X_normalized.iloc[optics_model.labels_ == -1, 1],
       'k+', alpha = 0.1)
ax2.set_title('OPTICS Clustering')
  
# Plotting the DBSCAN Clustering with eps = 0.5
colors = ['c', 'b', 'r', 'y', 'g', 'greenyellow']
for Class, colour in zip(range(0, 6), colors):
    Xk = X_normalized[labels1 == Class]
    ax3.plot(Xk.iloc[:, 0], Xk.iloc[:, 1], colour, alpha = 0.3, marker ='.')
        
ax3.plot(X_normalized.iloc[labels1 == -1, 0],
        X_normalized.iloc[labels1 == -1, 1],
       'k+', alpha = 0.1)
ax3.set_title('DBSCAN clustering with eps = 0.5')
  
# Plotting the DBSCAN Clustering with eps = 2.0
colors = ['c.', 'y.', 'm.', 'g.']
for Class, colour in zip(range(0, 4), colors):
    Xk = X_normalized.iloc[labels2 == Class]
    ax4.plot(Xk.iloc[:, 0], Xk.iloc[:, 1], colour, alpha = 0.3)
          
ax4.plot(X_normalized.iloc[labels2 == -1, 0],
        X_normalized.iloc[labels2 == -1, 1],
       'k+', alpha = 0.1)
ax4.set_title('DBSCAN Clustering with eps = 2.0')
  
  
plt.tight_layout()
plt.show()

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