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PARTITIONAL CLUSTERING. ACM Student Chapter, Heritage Institute of Technology 17 th February , 2012 SIGKDD Presentation by Megha Nangia J. M. Mansa Koustav Mullick. Why do we cluster? . Clustering results are used: As a stand-alone tool to get insight into data distribution

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Partitional clustering


ACM Student Chapter,

Heritage Institute of Technology

17th February, 2012

SIGKDD Presentation by


J. M. Mansa


Why do we cluster
Why do we cluster?

Clustering results are used:

As a stand-alone tool to get insight into data distribution

Visualization of clusters may unveil important information

As a preprocessing step for other algorithms

Efficient indexing or compression often relies on clustering

Partitional clustering

What is Cluster Analysis?

Cluster analysis or clustering is the task of assigning a set of objects into groups (called clusters) so that the objects in the same cluster are more “similar” (in some sense or another) to each other than to those in other clusters.

Cluster analysis itself is not one specific algorithm. But the general task to be solved is forming similar clusters. It can be achieved by various algorithms.

How do we define similarity
How do we define “similarity”?

Recall that the goal is to group together “similar” data – but what does this mean?

No single answer – it depends on what we want to find or emphasize in the data; this is one reason why clustering is an “art”

The similarity measure is often more important than the clustering algorithm used – don’t overlook this choice!

Partitional clustering


Minimize Intra-cluster distance

Maximize Inter-cluster distance

Partitional clustering


  • Clustering is a main task of explorative data mining to reduce the size of large data sets. Its a common technique for statistical data analysis used in many fields, including :

  • Machine learning

  • Pattern recognition

  • Image analysis

  • Information retrieval

  • Bioinformatics.

  • Web applications such as social network analysis, grouping of shopping items, search result grouping etc.

Requirements of clustering in data mining


Ability to deal with different types of attributes

Discovery of clusters with arbitrary shape

Able to deal with noise and outliers

Insensitive to order of input records

High dimensionality

Interpretability and usability

Notion of clustering
Notion of clustering:

How many clusters?

Six Clusters

Two Clusters

Four Clusters

Clustering algorithms
Clustering Algorithms:

Clustering algorithms can be categorized

Some of the major algorithms are:

Hierarchical or connectivity based clustering

Partitional clustering (K-means or centroid-based clustering)

Density based

Grid based

Model based

Partitional clustering1
Partitional Clustering:

  • In statistics and data mining, k-means clustering is a method of cluster analysis which aims to partition n observations into k clusters in which each observation belongs to the cluster with the nearest mean. This results into a partitioning of the data space into Voronoi cells.

    • A division data objects into non-overlapping subsets (clusters) such that each data object is in exactly one subset

Partitional clustering2
Partitional Clustering :

A Partitional Clustering

Original Points

Hierarchical clustering
Hierarchical Clustering:

Connectivity based clustering, also known as hierarchical clustering, is based on the core idea of objects being more related to nearby objects than to objects farther away.

As such, these algorithms connect "objects" to form "clusters" based on their distance. At different distances, different clusters will form, which can be represented using a dendrogram.

These algorithms do not provide a single partitioning of the data set, but instead provide an extensive hierarchy of clusters that merge with each other at certain distances.

A set of nested clusters organized as a hierarchical tree

Hierarchical clustering1
Hierarchical Clustering:

Traditional Hierarchical Clustering

Traditional Dendrogram

Non-traditional Hierarchical Clustering

Non-traditional Dendrogram

Partitional clustering

Hierarchical Clustering.

Partitional Clustering.

Partitional clustering

Partitioning Algorithms:

Partitioning method: Construct a partition of n objects into a set of Kclusters

Given: a set of objects and the number K

Find: a partition of K clusters that optimizes the chosen partitionin`g criterion

Effective heuristic methods: K-means and K-medoids algorithms

Partitional clustering

Common choices for Similarity/ Distance measures:

Euclidean distance:

City block or Manhattan distance:

Cosine similarity:

Jaccard similarity:

K means clustering
K-means Clustering:

Partitional clustering approach

Each cluster is associated with a centroid (center point)

Each point is assigned to the cluster with the closest centroid

Number of clusters, K, must be specified

The basic algorithm is very simple

Partitional clustering

K-Means Algorithm:


Choose K


Select K points as initial Centroids.


Form k clusters by assigning all points to their

respective closest centroid.

Re-compute the centroid for each cluster

5. Until: The centroids don`t change.

Form k clusters.







Time complexity
Time Complexity

Assume computing distance between two instances is O(m) where m is the dimensionality of the vectors.

Reassigning clusters: O(kn) distance computations, or O(knm).

Computing centroids: Each instance vector gets added once to some centroid: O(nm).

Assume these two steps are each done once for I iterations: O(Iknm).

Partitional clustering

K-means Clustering: Step 1

Algorithm: k-means, Distance Metric: Euclidean Distance

Partitional clustering

K-means Clustering: Step 2

Algorithm: k-means, Distance Metric: Euclidean Distance

Partitional clustering

K-means Clustering: Step 3

Algorithm: k-means, Distance Metric: Euclidean Distance

Partitional clustering

K-means Clustering: Step 4

Algorithm: k-means, Distance Metric: Euclidean Distance

Partitional clustering




K-means Clustering: Step 5

Algorithm: k-means, Distance Metric: Euclidean Distance

Two different k means clusterings
Two different K-means Clusterings

Optimal Clustering

Sub-optimal Clustering

Original Points

Solutions to initial centroids problem
Solutions to Initial Centroids Problem

Multiple runs

Helps, but probability is not on your side

Sample and use hierarchical clustering to determine initial centroids

Select more than k initial centroids and then select among these initial centroids

Select most widely separated


Bisecting K-means

Not as susceptible to initialization issues

Evaluating k means clusters

Most common measure is Sum of Squared Error (SSE)

For each point, the error is the distance to the nearest cluster

To get SSE, we square these errors and sum them.

x is a data point in cluster Ciand mi is the representative point for cluster Ci

can show that micorresponds to the center (mean) of the cluster

Given two clusters, we can choose the one with the smallest error

One easy way to reduce SSE is to increase K, the number of clusters

A good clustering with smaller K can have a lower SSE than a poor clustering with higher K

Partitional clustering

  • Strength

    • Relatively efficient: O(ikn), where n is # objects, k is # clusters, and iis # iterations. Normally, k, i << n.

    • Often terminates at a local optimum. The global optimum may be found using techniques such as: deterministic annealing and genetic algorithms

  • Weakness

    • Applicable only when mean is defined, then what about categorical data?

    • Need to specify k, the number of clusters, in advance

    • Unable to handle noisy data and outliers

    • Not suitable to discover clusters with non-convex shapes

    • Also may give rise to Empty-clusters.


Outliers are objects that do not belong to any cluster or form clusters of very small cardinality



Partitional clustering

Bisecting K-Means:

A variant of k-means, that can produce a partitional or heirarchical clustering.

Which cluster to be picked for bisection ?

Can pick the largest Cluster , or

The cluster With lowest average similarity, or

Cluster with the largest SSE.

Partitional clustering


Bisecting K-Means Algorithm:

Initialize clusters

Initialize the list of clusters.


Select a cluster from the list of clusters.

Fori=1 to number_of_iterations

Bisect the cluster using k-means algorithm

End for

Select two clusters having the lowest SSE

Add the two clusters from the bisection to

the list of clusters

9. Until: The list contains k clusters.

Select a cluster


i < no. of iterations


Bisect the cluster.


Add the two bisected clusters, having lowest SSE, to list of clusters


K clusters



Partitional clustering

Limitations of k means
Limitations of K-means:

K-means has problems when clusters are of differing



Non-globular shapes

K-means has problems when the data contains outliers.

Limitations of k means differing sizes
Limitations of K-means: Differing Sizes

Original Points

K-means (3 Clusters)

Partitional clustering

Limitations of K-means: Differing Density

Original Points

K-means (3 Clusters)

Limitations of k means non globular shapes
Limitations of K-means: Non-globular Shapes

Original Points

K-means (2 Clusters)

Overcoming k means limitations
Overcoming K-means Limitations

Original Points K-means Clusters

  • One solution is to use many clusters.

    • Find parts of clusters, but need to put together.

Overcoming k means limitations1
Overcoming K-means Limitations

Original Points K-means Clusters

Overcoming k means limitations2
Overcoming K-means Limitations

Original Points K-means Clusters

Partitional clustering

K-Medoids Algorithm

What is a medoid?

A medoid can be defined as the object of a cluster, whose average dissimilarity to all the objects in the cluster is minimal, i.e, it is a most centrally located point in the cluster.

In contrast to the k-means algorithm, k-medoids chooses datapoints as centers(medoids or exemplars)

The most common realisation of k-medoid clustering is the Partitioning Around Medoids (PAM) algorithm.

Partitional clustering

Partitioning around

medoids(PAM) algorithm

1. Initialize: randomly select k of the n data points as the medoids.

2. Associate each data point to the closest medoid.

3. For each medoid m

1. For each non-medoid data point o

1. Swap m and o and compute the total cost of the configuration.

4. Select the configuration with the lowest cost.

5. Repeat steps 2 to 5 until there is no change in the medoid.

Partitional clustering

Demonstration of PAM

Cluster the following set of ten objects into two clusters i.e. k=2.

Consider a data set of ten objects as follows:

Step 1
Step 1

Initialize k centres. Let us assume c1=(3,4) and c2=(7,4).

So here c1 and c2 are selected as medoids.

Calculating distance so as to associate each data object to its nearest medoid.

Partitional clustering

Then so the clusters become:


Cluster2={(7,4) (6,2)(6,4)(7,3)(8,5)(7,6)}

The total cost involved is 20

Cluster after step 1
Cluster after step 1

Next, we choose a non-medoid point for each medoid, swap it with the medoid and re-compute the cost. If the cost is optimized, we make it the new medoid and proceed similarly, until there is no change in the medoids.

Partitional clustering

Comments on PAM Algorithm

Pam is more robust than k-means in the presence of noise and outliers because a medoid is less influenced by outliers or other extreme values than a mean

Pam works well for small data sets but does not scale well for large data sets.

Partitional clustering


Partitional clustering is a very efficient and easy to implement clustering method.

It helps us find the global and local optimums.

Some of the heuristic approaches involve the K-means and K-medoid algorithms.

However partitional clustering also suffers from a number of shortcomings:

The performance of the algorithm depends on the initial centroids. So

the algorithm gives no guarantee for an optimal solution.

Choosing poor initial centroids may lead to the generation of empty clusters as well.

The number of clusters need to be determined beforehand.

Does not work well with non-globular clusters.

Some of the above stated drawbacks can be solved using the other popular Clustering approach, such as Hierarchical or density based clustering. Nevertheless the importance of partitional clustering cannot be denied.