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Clustering: K-Means

K-Means: Inertia

Inertia measures how well a dataset was clustered by K-Means. It is calculated by measuring the distance between each data point and its centroid, squaring this distance, and summing these squares across one cluster.

A good model is one with low inertia AND a low number of clusters (K). However, this is a tradeoff because as K increases, inertia decreases.

To find the optimal K for a dataset, use the Elbow method; find the point where the decrease in inertia begins to slow. K=3 is the “elbow” of this graph.

A line graph plotting the optimal number of clusters.

 At the top of the graph there is a label 'Optimal Number of Clusters'. The x-axis of the graph is labeled 'Number of Clusters (k)'. The y-axis of the graph is labeled 'Inertia'. The x-axis ranges from 1 to 7 with increments of 1 marked with the numbers 1 through 7. The y-axis ranges from 100 to 700 and is marked at increments of 100.

The first plot point number of clusters is 1 and inertia is about 650. When the number of clusters is 2 the inertia is about 225. When the number of clusters is 3 the inertia is about 150. When the number of clusters is 4 the inertia is about 130. When the number of clusters is 5 the inertia is about 115. When the number of clusters is 6 the inertia is about 105. Finally when the number of clusters is 7 the inertia is about 100.

Unsupervised Learning Basics

Patterns and structure can be found in unlabeled data using unsupervised learning, an important branch of machine learning. Clustering is the most popular unsupervised learning algorithm; it groups data points into clusters based on their similarity. Because most datasets in the world are unlabeled, unsupervised learning algorithms are very applicable.

Possible applications of clustering include:

  • Search engines: grouping news topics and search results
  • Market segmentation: grouping customers based on geography, demographics, and behaviors

K-Means Algorithm: Intro

K-Means is the most popular clustering algorithm. It uses an iterative technique to group unlabeled data into K clusters based on cluster centers (centroids). The data in each cluster are chosen such that their average distance to their respective centroid is minimized.

  1. Randomly place K centroids for the initial clusters.
  2. Assign each data point to their nearest centroid.
  3. Update centroid locations based on the locations of the data points.

Repeat Steps 2 and 3 until points don’t move between clusters and centroids stabilize.

An animated gif of how the k- means algorithm works. 

To start there is a graph with the numbers 0 through 8 on the x-axis and the numbers 0 through 8 on the y-axis. There are many points plotted and each of the points starts out as blue.

Next centroids are placed. A green centroid in the shape of the letter 'X' is placed at an x value of 1 and a y value of 6. A red centroid in the shape of the letter 'X' is placed at an x value of about 5 and a y value of 3. The data points are then assigned to their nearest centroid and color coded as such. 

The centroids are updated based on the new data points that were assigned to the centroids. The green centroid moves to an x value of 2 and a y value of 5. The red centroid moves to an x value of 3.5 and a y value of about 2.5. Again, the data points are reassigned based on the closest centroid and then the centroids are updated based on their newly assigned data points. The centroids move for the third time, the green centroid  is at an x value of 3.5 and a y value of 5.5. the third position of the red centroid is an x value of 3 and a y value of 1.5. The data samples are assigned to the nearest centroid again and the centroids are updated based on the newly assigned data samples. The centroids move to their final positions. The green centroid is at an x value of 4.5 and a y value of 6.5. The red centroid is at an x value of 2 and a y value of 1.5.

K-Means Algorithm: 2nd Step

After randomly choosing centroid locations for K-Means, each data sample is allocated to its closest centroid to start creating more precise clusters.

The distance between each data sample and every centroid is calculated, the minimum distance is selected, and each data sample is assigned a label that indicates its closest cluster.

The distance formula is implemented as .distance()and used for each data point.

np.argmin() is used to find the minimum distance and find the cluster at that distance.

# distance formula
def distance(a, b):
one = (a[0] - b[0]) **2
two = (a[1] - b[1]) **2
distance = (one+two) ** 0.5
return distance

Scikit-Learn Datasets

The scikit-learn library contains built-in datasets in its datasets module that are often used in machine learning problems like classification or regression.


  • Iris dataset (classification)
  • Boston house-prices dataset (regression)

The format of these datasets are important to their use with algorithms. For example, each piece of data in the Iris dataset is a sample (flower type), and each element within a sample is a feature (i.e. petal width).

K-Means Using Scikit-Learn

Scikit-Learn, or sklearn, is a machine learning library for Python that has a K-Means algorithm implementation that can be used instead of creating one from scratch.

To use it:

  • Import the KMeans() method from the sklearn.cluster library to build a model with n_clusters

  • Fit the model to the data samples using .fit()

  • Predict the cluster that each data sample belongs to using .predict() and store these as labels

from sklearn.cluster import KMeans
model = KMeans(n_clusters=3)
labels = model.predict(data_samples)

Cross Tabulation Overview

Cross-tabulations involve grouping pieces of data together in order to examine their relationship in a different way. Sometimes correlations within data can be seen better when not just looking at total responses.

This technique is often performed in Python after running K-Means; the Pandas method .crosstab() allows for comparison between resulting cluster labels and user-defined labels for each data sample. In order to validate the results of a K-Means model with this technique, there must be user-defined labels for all data samples.

import pandas as pd
cross_tab = pd.crosstab(df['pred_labels'], df['user_labels'])

K-Means: Reaching Convergence

In K-Means, after placing K random centroids, the data samples are repeatedly assigned to the nearest centroid and then centroid locations are updated. This continues until each of the centroids’ coordinates converge, or stop changing.

This sequence of events can be implemented in Python using a while loop. The loop continues until the difference between each element of the updated centroids and each element of the past centroids_old is 0. This will mean the centroids have converged and the clusters are complete!

K-Means Algorithm: 3rd Step

The third step of K-Means updates centroid locations. After the data are assigned to their respectively closest centroid in step 2, each cluster center location is adjusted to be the average of its assigned data points.

The NumPy .mean() function is used to find the average x and y-coordinates of all data points for each cluster and store these as the new centroid locations.

K-Means Algorithm: 1st Step

The first step of the K-Means clustering algorithm requires placing K random centroids which will become the centers of the K initial clusters. This step can be implemented in Python using the Numpy random.uniform() function; the x and y-coordinates are randomly chosen within the x and y ranges of the data points.