K-Means Clustering Algorithm

K-Means Clustering is an unsupervised learning algorithm that is used to

solve the clustering problems in machine learning or data science. In this
topic, we will learn what is K-means clustering algorithm, how the algorithm
works, along with the Python implementation of k-means clustering.

What is K-Means Algorithm?

K-Means Clustering is an Unsupervised Learning algorithm, which groups

the unlabeled dataset into different clusters. Here K defines the number of
pre-defined clusters that need to be created in the process, as if K=2, there
will be two clusters, and for K=3, there will be three clusters, and so on.

It is an iterative algorithm that divides the unlabeled dataset into k different

clusters in such a way that each dataset belongs only one group that has
similar properties.

It allows us to cluster the data into different groups and a convenient way
to discover the categories of groups in the unlabeled dataset on its own
without the need for any training.

It is a centroid-based algorithm, where each cluster is associated with a

centroid. The main aim of this algorithm is to minimize the sum of distances
between the data point and their corresponding clusters.

The algorithm takes the unlabeled dataset as input, divides the dataset into
k-number of clusters, and repeats the process until it does not find the best
clusters. The value of k should be predetermined in this algorithm.

The k-means clustering algorithm mainly performs two tasks:

o Determines the best value for K center points or centroids by an

iterative process.
o Assigns each data point to its closest k-center. Those data points
which are near to the particular k-center, create a cluster.
Hence each cluster has datapoints with some commonalities, and it is away
from other clusters.

The below diagram explains the working of the K-means Clustering

Algorithm:

How does the K-Means Algorithm Work?

The working of the K-Means algorithm is explained in the below steps:

Step-1: Select the number K to decide the number of clusters.

Step-2: Select random K points or centroids. (It can be other from the input
dataset).

Step-3: Assign each data point to their closest centroid, which will form the
predefined K clusters.

Step-4: Calculate the variance and place a new centroid of each cluster.

Step-5: Repeat the third steps, which means reassign each datapoint to the
new closest centroid of each cluster.

Step-6: If any reassignment occurs, then go to step-4 else go to FINISH.

Step-7: The model is ready

Suppose we have two variables M1 and M2. The x-y axis scatter plot of
these two variables is given below:

o Let's take number k of clusters, i.e., K=2, to identify the dataset and to
put them into different clusters. It means here we will try to group
these datasets into two different clusters.
o We need to choose some random k points or centroid to form the
cluster. These points can be either the points from the dataset or any
other point. So, here we are selecting the below two points as k
points, which are not the part of our dataset. Consider the below
 image:

o Now we will assign each data point of the scatter plot to its closest K-
point or centroid. We will compute it by applying some mathematics
that we have studied to calculate the distance between two points.
So, we will draw a median between both the centroids. Consider the
 below image:

From the above image, it is clear that points left side of the line is near to
the K1 or blue centroid, and points to the right of the line are close to the
yellow centroid. Let's color them as blue and yellow for clear visualization.
o As we need to find the closest cluster, so we will repeat the process
by choosing a new centroid. To choose the new centroids, we will
compute the center of gravity of these centroids, and will find new
 centroids as below:

o Next, we will reassign each datapoint to the new centroid. For this, we
will repeat the same process of finding a median line. The median will
 be like below image:

From the above image, we can see, one yellow point is on the left side of
the line, and two blue points are right to the line. So, these three points will
be assigned to new centroids.
As reassignment has taken place, so we will again go to the step-4, which is
finding new centroids or K-points.
o We will repeat the process by finding the center of gravity of
centroids, so the new centroids will be as shown in the below image:
o As we got the new centroids so again will draw the median line and
reassign the data points. So, the image will be:

o We can see in the above image; there are no dissimilar data points on
either side of the line, which means our model is formed. Consider
 the below image:

As our model is ready, so we can now remove the assumed centroids, and
the two final clusters will be as shown in the below image:

K-Medoids clustering-Theoretical Explanation

K-Medoids and K-Means are two types of clustering mechanisms in
Partition Clustering. First, Clustering is the process of breaking down an
abstract group of data points/ objects into classes of similar objects such
that all the objects in one cluster have similar traits. , a group of n objects is
broken down into k number of clusters based on their similarities.

Two statisticians, Leonard Kaufman, and Peter J. Rousseeuw came up with

this method. This tutorial explains what K-Medoids do, their applications,
and the difference between K-Means and K-Medoids.

K-medoids is an unsupervised method with unlabelled data to be clustered.

It is an improvised version of the K-Means algorithm mainly designed to
deal with outlier data sensitivity. Compared to other partitioning
algorithms, the algorithm is simple, fast, and easy to implement.

1. Each cluster must have at least one object

2. An object must belong to only one cluster

Here is a small recap on K-Means clustering:

In the K-Means algorithm, given the value of k and unlabelled data:

1. Choose k number of random points (Data point from the data set or
some other points). These points are also called "Centroids" or
"Means".
2. Assign all the data points in the data set to the closest centroid by
applying any distance formula like Euclidian distance, Manhattan
distance, etc.
3. Now, choose new centroids by calculating the mean of all the data
points in the clusters and goto step 2
4. Continue step 3 until no data point changes classification between
two iterations.

The problem with the K-Means algorithm is that the algorithm needs to
handle outlier data. An outlier is a point different from the rest of the
points. All the outlier data points show up in a different cluster and will
attract other clusters to merge with it. Outlier data increases the mean of a
cluster by up to 10 units. Hence, K-Means clustering is highly affected by
outlier data.

K-Medoids:

Medoid: A Medoid is a point in the cluster from which the sum of distances
to other data points is minimal.

(or)

A Medoid is a point in the cluster from which dissimilarities with all the
other points in the clusters are minimal.

Instead of centroids as reference points in K-Means algorithms, the K-

Medoids algorithm takes a Medoid as a reference point.

There are three types of algorithms for K-Medoids Clustering:

1. PAM (Partitioning Around Clustering)

2. CLARA (Clustering Large Applications)
3. CLARANS (Randomized Clustering Large Applications)

PAM is the most powerful algorithm of the three algorithms but has the
disadvantage of time complexity. The following K-Medoids are performed
using PAM. In the further parts, we'll see what CLARA and CLARANS are.

Algorithm:

Given the value of k and unlabelled data:

1. Choose k number of random points from the data and assign these k
points to k number of clusters. These are the initial medoids.
2. For all the remaining data points, calculate the distance from each
medoid and assign it to the cluster with the nearest medoid.
3. Calculate the total cost (Sum of all the distances from all the data
points to the medoids)
 4. Select a random point as the new medoid and swap it with the
previous medoid. Repeat 2 and 3 steps.
5. If the total cost of the new medoid is less than that of the previous
medoid, make the new medoid permanent and repeat step 4.
6. If the total cost of the new medoid is greater than the cost of the
previous medoid, undo the swap and repeat step 4.
7. The Repetitions have to continue until no change is encountered with
new medoids to classify data points.

Here is an example to make the theory clear:

Data set:

x y

0 5 4

1 7 7

2 1 3

3 8 6

4 4 9

Scatter plot:
If k is given as 2, we need to break down the data points into 2 clusters.

1. Initial medoids: M1(1, 3) and M2(4, 9)

2. Calculation of distances

Manhattan Distance: |x1 - x2| + |y1 - y2|

x< y From M1(1, 3) From M2(4, 9)

0 5 4 5 6

1 7 7 10 5

2 1 3 - -
3 8 6 10 7

4 4 9 - -

Cluster 1: 0

Cluster 2: 1, 3

1. Calculation of total cost:

(5) + (5 + 7) = 17
2. Random medoid: (5, 4)

M1(5, 4) and M2(4, 9):

x y From M1(5, 4) From M2(4, 9)

0 5 4 - -

1 7 7 5 5

2 1 3 5 9

3 8 6 5 7

4 4 9 - -

Cluster 1: 2, 3

Cluster 2: 1

1. Calculation of total cost:

(5 + 5) + 5 = 15
 Less than the previous cost
New medoid: (5, 4).
2. Random medoid: (7, 7)

M1(5, 4) and M2(7, 7)

x y From M1(5, 4) From M2(7, 7)

0 5 4 - -

1 7 7 - -

2 1 3 5 10

3 8 6 5 2

4 4 9 6 5

Cluster 1: 2

Cluster 2: 3, 4

1. Calculation of total cost:

(5) + (2 + 5) = 12
Less than the previous cost
New medoid: (7, 7).
2. Random medoid: (8, 6)

M1(7, 7) and M2(8, 6)

x y From M1(7, 7) From M2(8, 6)

0 5 4 5 5

1 7 7 - -

2 1 3 10 10

3 8 6 - -

4 4 9 5 7

Cluster 1: 4

Cluster 2: 0, 2

1. Calculation of total cost:

(5) + (5 + 10) = 20
Greater than the previous cost
UNDO
Hence, the final medoids: M1(5, 4) and M2(7, 7)
Cluster 1: 2
Cluster 2: 3, 4
Total cost: 12
Clusters:
Limitation of PAM:
Time complexity: O(k * (n - k)2)

Possible combinations for every node: k*(n - k)

Cost for each computation: (n - k)

Total cost: k*(n - k)2

Hence, PAM is suitable and recommended to be used for small data sets.

CLARA:

It is an extension to PAM to support Medoid clustering for large data sets.

This algorithm selects data samples from the data set, applies Pam on
each sample, and outputs the best Clustering out of these samples. This
is more effective than PAM. We should ensure that the selected samples
aren't biased as they affect the Clustering of the whole data.

CLARANS:

This algorithm selects a sample of neighbors to examine instead of

selecting samples from the data set. In every step, it examines the
neighbors of every node. The time complexity of this algorithm is O(n 2), and
this is the best and most efficient Medoids algorithm of all.

Advantages of using K-Medoids:

1. Deals with noise and outlier data effectively
2. Easily implementable and simple to understand
3. Faster compared to other partitioning algorithms

Disadvantages:
1. Not suitable for Clustering arbitrarily shaped groups of data points.
2. As the initial medoids are chosen randomly, the results might vary
based on the choice in different runs.

K-Means and K-Medoids:

K-Means K-Medoids

Both methods are types of Partition Clustering.

Unsupervised iterative algorithms

Have to deal with unlabelled data

Both algorithms group n objects into k clusters based on similar

traits where k is pre-defined.

Inputs: Unlabelled data and the value of k

Metric of similarity: Euclidian Metric of
Distance similarity: Manhattan
Distance

Clustering is done based on Clustering is done based on

distance from centroids. distance from medoids.

A centroid can be a data point A medoid is always a data

or some other point in the point in the cluster.
cluster

Can't cope with outlier data Can manage outlier data too

Sometimes, outlier sensitivity Tendency to ignore

can turn out to be useful meaningful clusters in outlier
data

Hierarchical Clustering in Machine Learning

Hierarchical clustering is another unsupervised machine learning algorithm,

which is used to group the unlabeled datasets into a cluster and also known
as hierarchical cluster analysis or HCA.

In this algorithm, we develop the hierarchy of clusters in the form of a tree,

and this tree-shaped structure is known as the dendrogram.

Sometimes the results of K-means clustering and hierarchical clustering

may look similar, but they both differ depending on how they work. As
there is no requirement to predetermine the number of clusters as we did
in the K-Means algorithm.

The hierarchical clustering technique has two approaches:

 1. Agglomerative: Agglomerative is a bottom-up approach, in which
the algorithm starts with taking all data points as single clusters and
merging them until one cluster is left.
2. Divisive: Divisive algorithm is the reverse of the agglomerative
algorithm as it is a top-down approach.

Why hierarchical clustering?

As we already have other clustering algorithms such as K-Means

Clustering, then why we need hierarchical clustering? So, as we have seen
in the K-means clustering that there are some challenges with this
algorithm, which are a predetermined number of clusters, and it always tries
to create the clusters of the same size. To solve these two challenges, we
can opt for the hierarchical clustering algorithm because, in this algorithm,
we don't need to have knowledge about the predefined number of clusters.

In this topic, we will discuss the Agglomerative Hierarchical clustering

algorithm.

Agglomerative Hierarchical clustering

The agglomerative hierarchical clustering algorithm is a popular example of

HCA. To group the datasets into clusters, it follows the bottom-up
approach. It means, this algorithm considers each dataset as a single
cluster at the beginning, and then start combining the closest pair of
clusters together. It does this until all the clusters are merged into a single
cluster that contains all the datasets.

This hierarchy of clusters is represented in the form of the dendrogram.

How the Agglomerative Hierarchical clustering Work?

The working of the AHC algorithm can be explained using the below steps:
o Step-1: Create each data point as a single cluster. Let's say there are
N data points, so the number of clusters will also be N.

o Step-2: Take two closest data points or clusters and merge them to
form one cluster. So, there will now be N-1 clusters.
o Step-3: Again, take the two closest clusters and merge them together
to form one cluster. There will be N-2 clusters.

o Step-4: Repeat Step 3 until only one cluster left. So, we will get the
following clusters. Consider the below images:
 o Step-5: Once all the clusters are combined into one big cluster,
develop the dendrogram to divide the clusters as per the problem.

Measure for the distance between two clusters

As we have seen, the closest distance between the two clusters is crucial
for the hierarchical clustering. There are various ways to calculate the
distance between two clusters, and these ways decide the rule for
clustering. These measures are called Linkage methods. Some of the
popular linkage methods are given below:

1. Single Linkage: It is the Shortest Distance between the closest points

of the clusters. Consider the below image:

2. Complete Linkage: It is the farthest distance between the two points

of two different clusters. It is one of the popular linkage methods as it
forms tighter clusters than single-linkage.
 3. Average Linkage: It is the linkage method in which the distance
between each pair of datasets is added up and then divided by the
total number of datasets to calculate the average distance between
two clusters. It is also one of the most popular linkage methods.
4. Centroid Linkage: It is the linkage method in which the distance
between the centroid of the clusters is calculated. Consider the below
image:

From the above-given approaches, we can apply any of them according to

the type of problem or business requirement.

Woking of Dendrogram in Hierarchical clustering

The dendrogram is a tree-like structure that is mainly used to store each

step as a memory that the HC algorithm performs. In the dendrogram plot,
the Y-axis shows the Euclidean distances between the data points, and the
x-axis shows all the data points of the given dataset.

The working of the dendrogram can be explained using the below diagram:
In the above diagram, the left part is showing how clusters are created in
agglomerative clustering, and the right part is showing the corresponding
dendrogram.

o As we have discussed above, firstly, the datapoints P2 and P3

combine together and form a cluster, correspondingly a dendrogram
is created, which connects P2 and P3 with a rectangular shape. The
hight is decided according to the Euclidean distance between the
data points.
o In the next step, P5 and P6 form a cluster, and the corresponding
dendrogram is created. It is higher than of previous, as the Euclidean
distance between P5 and P6 is a little bit greater than the P2 and P3.
o Again, two new dendrograms are created that combine P1, P2, and P3
in one dendrogram, and P4, P5, and P6, in another dendrogram.
o At last, the final dendrogram is created that combines all the data
points together.