5 Best Ways to Group a Set of Points into K Different Groups in Python

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πŸ’‘ Problem Formulation: Imagine you have a collection of points in a two-dimensional space and you want to divide them into ‘k’ distinct groups based on their proximity to each other. For instance, given the set of points [(1,2), (1,4), (3,5), (6,8), (7,7)] and k=2, the desired output could be either {(1,2), (1,4), (3,5)} and {(6,8), (7,7)} or any other optimal grouping based on the chosen method.

Method 1: K-Means Clustering

The K-Means clustering algorithm is aimed at partitioning n observations into k clusters in which each observation belongs to the cluster with the nearest mean. It is a popular method for vector quantization and is particularly well-suited for creating groups of points.

Here’s an example:

from sklearn.cluster import KMeans
import numpy as np

points = np.array([(1,2), (1,4), (3,5), (6,8), (7,7)])
kmeans = KMeans(n_clusters=2, random_state=0).fit(points)
print(kmeans.labels_)

Output:

[1 1 1 0 0]

This snippet uses the sklearn.cluster.KMeans class to perform clustering. It initializes the KMeans algorithm with two clusters and a fixed random state for reproducibility. The fit method computes the centroids and assigns each point in ‘points’ to one of the two clusters, as shown in the output labels.

Method 2: DBSCAN

Density-Based Spatial Clustering of Applications with Noise (DBSCAN) is an algorithm that groups together points that are closely packed together, marking as outliers points that lie alone in low-density regions. It doesn’t require one to specify the number of clusters in advance.

Here’s an example:

from sklearn.cluster import DBSCAN

points = [(1,2), (1,4), (3,5), (6,8), (7,7)]
clustering = DBSCAN(eps=3, min_samples=2).fit(points)
print(clustering.labels_)

Output:

[ 0  0  0  1  1]

This snippet uses the sklearn.cluster.DBSCAN class with an epsilon value of 3 and a minimum sample count of 2 to perform clustering. DBSCAN successfully identifies dense regions of points and assigns cluster labels accordingly.

Method 3: Agglomerative Hierarchical Clustering

Agglomerative Hierarchical Clustering starts with each point as a separate cluster and iteratively combines the closest pairs of clusters until all points have been merged into a single remaining cluster. This method is useful when the number of clusters is not predetermined.

Here’s an example:

from sklearn.cluster import AgglomerativeClustering

points = [(1,2), (1,4), (3,5), (6,8), (7,7)]
clustering = AgglomerativeClustering(n_clusters=2).fit(points)
print(clustering.labels_)

Output:

[1 1 1 0 0]

This code uses the sklearn.cluster.AgglomerativeClustering class to perform hierarchical clustering, specifying that we want to end up with 2 clusters. It fits the model to the points and outputs the labels that indicate cluster membership.

Method 4: Mean Shift Clustering

Mean Shift Clustering aims at discovering blobs in a smooth density of samples. It is a centroid-based algorithm, which works by updating candidates for centroids to be the mean of the points within a given region. These candidates are then filtered in a post-processing stage to eliminate near-duplicates.

Here’s an example:

from sklearn.cluster import MeanShift

points = [(1,2), (1,4), (3,5), (6,8), (7,7)]
clustering = MeanShift().fit(points)
print(clustering.labels_)

Output:

[1 1 1 0 0]

The example uses the Mean Shift algorithm implemented in sklearn.cluster.MeanShift. After fitting the points, it outputs labels indicating which points belong to which cluster. This method requires no specification of the number of clusters.

Bonus One-Liner Method 5: SciPy Hierarchical Clustering

For a hierarchical clustering approach that doesn’t require scikit-learn, SciPy library provides a method that computes a hierarchy of clusters and returns the labels accordingly.

Here’s an example:

from scipy.cluster.hierarchy import fcluster, linkage

points = [(1,2), (1,4), (3,5), (6,8), (7,7)]
Z = linkage(points, 'ward')
labels = fcluster(Z, 2, criterion='maxclust')
print(labels)

Output:

[2 2 2 1 1]

This snippet uses SciPy’s linkage and fcluster functions to perform agglomerative hierarchical clustering with Ward’s method and then assigns points to clusters, specifying a maximum number of clusters.

Summary/Discussion

  • Method 1: K-Means Clustering. Fast and efficient for large datasets. Requires specifying the number of clusters and may produce different results if the algorithm runs with different initializations.
  • Method 2: DBSCAN. Capable of finding arbitrarily shaped clusters and robust to outliers. Determining the optimal parameters can be difficult, and it doesn’t perform well with varying cluster densities.
  • Method 3: Agglomerative Hierarchical Clustering. Provides a tree of clusters which is informative. Computationally expensive and not suitable for large datasets. Number of clusters needs to be specified after the model is run.
  • Method 4: Mean Shift Clustering. Automatically determines the number of clusters. Computation can be expensive and it may not work well in high dimensional spaces.
  • Bonus One-Liner Method 5: SciPy Hierarchical Clustering. A simple one-liner for hierarchical clustering with SciPy. It’s a method good for visualizing dendrogram but can be computationally intensive.