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DBSCAN Clustering

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Home » Python • Unsupervised Machine Learning » How to create clusters using DBSCAN in Python

How to create clusters using DBSCAN in


Python
Python, Unsupervised Machine Learning / 2 Comments / By Farukh Hashmi

Density Based Spatial Clustering of Applications with Noise(DBSCAN) is one of the clustering
algorithms which can find clusters in noisy data. It works even on those datasets where K-
Means fail to find meaningful clusters. More information about it can be found here.

You can learn more about the DBSCAN algorithm in the below video.

How DBSCAN clustering works? | AI ML tutorials by a Data Scientist | …

The below code snippet will help to create clusters in data using DBSCAN.

Creating data for clustering

1 # importing plotting library


2 import matplotlib.pyplot as plt
3 # Create Sample data
4 from sklearn.datasets import make_moons
5 X, y= make_moons(n_samples=500, shuffle=True, noise=0.1, random_state=20)
6 plt.scatter(x= X[:,0], y= X[:,1])

Sample Output:

Moons clustering data for DBCAN

Finding Best hyperparameters for DBSCAN using Silhouette


Coefficient

The Silhouette Coefficient is calculated using the mean intra-cluster distance (a) and the
mean nearest-cluster distance (b) for each sample. The Silhouette Coefficient for a sample is
(b – a) / max(a, b). To clarify, b is the distance between a sample and the nearest cluster that
the sample is not a part of. Note that Silhouette Coefficient is only defined if number of labels
is 2 <= n_labels <= n_samples – 1.

The best value of the Silhouette Coefficient is 1 and the worst value is -1. Values near 0 indicate
overlapping clusters. Negative values generally indicate that a sample has been assigned to
the wrong cluster

1 ## Finding best values of eps and min_samples


2 import numpy as np
3 import pandas as pd
4 from sklearn.metrics import silhouette_score
5 from sklearn.cluster import DBSCAN
6
7 # Defining the list of hyperparameters to try
8 eps_list=np.arange(start=0.1, stop=0.9, step=0.01)
9 min_sample_list=np.arange(start=2, stop=5, step=1)
10
11 # Creating empty data frame to store the silhouette scores for each trials
12 silhouette_scores_data=pd.DataFrame()
13
14 for eps_trial in eps_list:
15 for min_sample_trial in min_sample_list:
16
17 # Generating DBSAN clusters
18 db = DBSCAN(eps=eps_trial, min_samples=min_sample_trial)
19
20 if(len(np.unique(db.fit_predict(X)))&gt;1):
21 sil_score=silhouette_score(X, db.fit_predict(X))
22 else:
23 continue
24 trial_parameters="eps:" + str(eps_trial.round(1)) +" min_sample :" + str(min_
25
26 silhouette_scores_data=silhouette_scores_data.append(pd.DataFrame(data=[[sil_
27
28 # Finding out the best hyperparameters with highest Score
29 silhouette_scores_data.sort_values(by='score', ascending=False).head(1)

Sample Output

Finding best hyperparameters for


DBSCAN

Creating clusters using the best hyperparameters

1 # DBSCAN Clustering
2 from sklearn.cluster import DBSCAN
3 db = DBSCAN(eps=0.18, min_samples=2)
4 # Plotting the clusters
5 plt.scatter(x= X[:,0], y= X[:,1], c=db.fit_predict(X))

DBSCAN clustering in python


AUTHOR DETAILS

Farukh Hashmi

Lead Data Scientist

Farukh is an innovator in solving industry problems using


Artificial intelligence. His expertise is backed with 10 years
of industry experience. Being a senior data scientist he is
responsible for designing the AI/ML solution to provide
maximum gains for the clients. As a thought leader, his
focus is on solving the key business problems of the CPG
Industry. He has worked across different domains like
Telecom, Insurance, and Logistics. He has worked with
global tech leaders including Infosys, IBM, and Persistent
systems. His passion to teach inspired him to create this
website!

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2 thoughts on “How to create clusters using DBSCAN in Python”

REBECCA V.
AUGUST 2, 2022 AT 6:02 PM

Hi! Thanks for the code snippet. Just a heads up it appears there may be a rendering error in
line 20:

if(len(np.unique(db.fit_predict(X)))>1):

Reply
REBECCA V.
AUGUST 2, 2022 AT 6:03 PM

Of course it’s rendering properly in my comment lololol. Anyway, thanks again!

Reply

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