What is Cluster Analysis?

• Cluster: a collection of data objects

– Similar to one another within the same cluster
– Dissimilar to the objects in other clusters
• Cluster analysis
– Grouping a set of data objects into clusters
• Clustering is unsupervised classification: no predefined
classes
• Typical applications
– As a stand-alone tool to get insight into data distribution
– As a preprocessing step for other algorithms
 Examples of Clustering
Applications
• Marketing: Help marketers discover distinct groups in their customer
bases, and then use this knowledge to develop targeted marketing
programs
• Land use: Identification of areas of similar land use in an earth
observation database
• Insurance: Identifying groups of motor insurance policy holders with a
high average claim cost
• City-planning: Identifying groups of houses according to their house
type, value, and geographical location
• Earth-quake studies: Observed earth quake epicenters should be
clustered along continent faults
 What Is Good Clustering?
• A good clustering method will produce high quality clusters with
– high intra-class similarity
– low inter-class similarity
• The quality of a clustering result depends on both the similarity
measure used by the method and its implementation.
• The quality of a clustering method is also measured by its ability to

discover some or all of the hidden patterns.

 Requirements of Clustering in
Data Mining
• Scalability
• Ability to deal with different types of attributes
• Discovery of clusters with arbitrary shape
• Minimal requirements for domain knowledge to determine input
parameters
• Able to deal with noise and outliers
• Insensitive to order of input records
• High dimensionality
• Incorporation of user-specified constraints
• Interpretability and usability
 Data Structures
• Data matrix  x11 ... x1f ... x1p 
 
– (two modes)  ... ... ... ... ... 
x ... xif ... xip 
 i1 
 ... ... ... ... ... 
x ... xnf ... xnp 
 n1 

 0 
 d(2,1) 
• Dissimilarity matrix  0 
 d(3,1) d ( 3,2) 0 
– (one mode)  
 : : : 
 d ( n,1) d ( n,2) ... ... 0
 Measure the Quality of
Clustering
• Dissimilarity/Similarity metric: Similarity is expressed in
terms of a distance function, which is typically metric:
d(i, j)
• There is a separate “quality” function that measures the
“goodness” of a cluster.
• The definitions of distance functions are usually very
different for interval-scaled, boolean, categorical, ordinal
and ratio variables.
• Weights should be associated with different variables
based on applications and data semantics.
• It is hard to define “similar enough” or “good enough”
– the answer is typically highly subjective.
 Major Clustering
Approaches
• Partitioning algorithms: Construct various partitions and
then evaluate them by some criterion
• Hierarchy algorithms: Create a hierarchical decomposition
of the set of data (or objects) using some criterion
• Density-based: based on connectivity and density functions
• Grid-based: based on a multiple-level granularity structure
• Model-based: A model is hypothesized for each of the
clusters and the idea is to find the best fit of that model to
each other
 Partitioning Algorithms: Basic
Concept
• Partitioning method: Construct a partition of a
database D of n objects into a set of k clusters
• Given a k, find a partition of k clusters that
optimizes the chosen partitioning criterion
– Global optimal: exhaustively enumerate all partitions
– Heuristic methods: k-means and k-medoids algorithms
– k-means (MacQueen’67): Each cluster is represented by
the center of the cluster
– k-medoids or PAM (Partition around medoids) (Kaufman
& Rousseeuw’87): Each cluster is represented by one of
the objects in the cluster
The K-Means Clustering Method

• Given k, the k-means algorithm is

implemented in four steps:
– Partition objects into k nonempty subsets
– Compute seed points as the centroids of the
clusters of the current partition (the centroid is the
center, i.e., mean point, of the cluster)
– Assign each object to the cluster with the nearest
seed point
– Go back to Step 2, stop when no more new
assignment
 The K-Means Clustering Method
• Example
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Assign 3 Update 3
3

2 each
2 the 2

1
objects
1

0
cluster 1

0
0
0 1 2 3 4 5 6 7 8 9 10 to
0 1 2 3 4 5 6 7 8 9 10 means 0 1 2 3 4 5 6 7 8 9 10

most
similar reassign reassign
center 10 10

K=2 9 9

8 8

Arbitrarily choose 7 7

6 6
K object as initial 5 5

cluster center 4 Update 4

2
the 3

1 cluster 1

0
0 1 2 3 4 5 6 7 8 9 10
means 0
0 1 2 3 4 5 6 7 8 9 10
 Comments on the K-Means
Method
• Strength: Relatively efficient: O(tkn), where n is #
objects, k is # clusters, and t is # iterations. Normally, k,
t << n.
• Comparing: PAM: O(k(n-k)2 ), CLARA: O(ks2 + k(n-k))
• 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
 Variations of the K-Means Method

• A few variants of the k-means which differ in

– Selection of the initial k means

– Dissimilarity calculations

– Strategies to calculate cluster means

• Handling categorical data: k-modes (Huang’98)

– Replacing means of clusters with modes

– Using new dissimilarity measures to deal with categorical objects

– Using a frequency-based method to update modes of clusters

– A mixture of categorical and numerical data: k-prototype method

 What is the problem of k-Means
Method?
• The k-means algorithm is sensitive to outliers !
– Since an object with an extremely large value may substantially distort the
distribution of the data.

• K-Medoids: Instead of taking the mean value of the object in a cluster as a

reference point, medoids can be used, which is the most centrally located
object in a cluster.

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The K-Medoids Clustering Method
• Find representative objects, called medoids, in clusters
• PAM (Partitioning Around Medoids, 1987)
– starts from an initial set of medoids and iteratively replaces one of the
medoids by one of the non-medoids if it improves the total distance of
the resulting clustering
– PAM works effectively for small data sets, but does not scale well for
large data sets

• CLARA (Kaufmann & Rousseeuw, 1990)

• CLARANS (Ng & Han, 1994): Randomized sampling
• Focusing + spatial data structure (Ester et al., 1995)
 Typical k-medoids algorithm (PAM)
Total Cost = 20
10 10 10

9 9 9

8 8 8

7 7 7

6
Arbitrar 6
Assign 6

5
y 5 each 5

4 choose 4 remaini 4

3
k object 3
ng 3

2
as 2
object 2

1 1
initial to
1

0 0 0
0 1 2 3 4 5 6 7 8 9 10
medoid 0 1 2 3 4 5 6 7 8 9 10
nearest 0 1 2 3 4 5 6 7 8 9 10

s medoid
K=2 s Randomly select a
Total Cost = 26 nonmedoid
object,Oramdom
10 10

Do loop 9

8
Compute
9

8
Swapping 7 total cost 7

Until no O and 6
of 6

Oramdom
change
5 5

4
swapping 4

If quality is 3

2
3

improved. 1 1

0 0
0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10
 PAM (Partitioning Around Medoids) (1987)
• PAM (Kaufman and Rousseeuw, 1987), built in Splus
• Use real object to represent the cluster
– Select k representative objects arbitrarily
– For each pair of non-selected object h and selected object i,
calculate the total swapping cost TCih
– For each pair of i and h,
• If TCih < 0, i is replaced by h
• Then assign each non-selected object to the most similar
representative object
– repeat steps 2-3 until there is no change
PAM Clustering: Total swapping cost
TCih=jCjih
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9 9
j
8
t 8
t
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5
j 6

4
i h 4
h
3

2
3

2
i
1 1

0 0
0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10

Cjih = d(j, h) - d(j, i) Cjih = 0

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10

9
9

8
h 8

j
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5
5 i
i h j
t
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4

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2
2

1
t
1
0
0
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0 1 2 3 4 5 6 7 8 9 10

Cjih = d(j, t) - d(j, i) Cjih = d(j, h) - d(j, t)

 What is the problem with PAM?
• 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 efficiently for small data sets but does not
scale well for large data sets.
– O(k(n-k)2 ) for each iteration

where n is # of data,k is # of clusters

 Sampling based method,

CLARA(Clustering LARge Applications)

 CLARA (Clustering Large Applications) (1990)

• CLARA (Kaufmann and Rousseeuw in 1990)

– Built in statistical analysis packages, such as S+
• It draws multiple samples of the data set, applies PAM on each
sample, and gives the best clustering as the output
• Strength: deals with larger data sets than PAM
• Weakness:
– Efficiency depends on the sample size
– A good clustering based on samples will not necessarily represent a
good clustering of the whole data set if the sample is biased
 K-Means Example
• Given: {2,4,10,12,3,20,30,11,25}, k=2
• Randomly assign means: m1=3,m2=4
• Solve for the rest ….
• Similarly try for k-medoids
 Clustering Approaches
Clustering

Hierarchical Partitional Categorical Large DB

Agglomerative Divisive Sampling Compression

Cluster Summary Parameters
 Distance Between Clusters
• Single Link: smallest distance between points
• Complete Link: largest distance between points
• Average Link: average distance between points
• Centroid: distance between centroids
 Hierarchical Clustering

• Use distance matrix as clustering criteria. This method does not

require the number of clusters k as an input, but needs a
termination condition
Step 0 Step 1 Step 2 Step 3 Step 4
agglomerative
(AGNES)
a ab
b abcde
c
cde
d
de
e
divisive
Step 4 Step 3 Step 2 Step 1 Step 0 (DIANA)
 Hierarchical Clustering
• Clusters are created in levels actually creating
sets of clusters at each level.
• Agglomerative
– Initially each item in its own cluster
– Iteratively clusters are merged together
– Bottom Up
• Divisive
– Initially all items in one cluster
– Large clusters are successively divided
– Top Down
 Hierarchical Algorithms
• Single Link
• MST Single Link
• Complete Link
• Average Link
 Dendrogram
• Dendrogram: a tree data
structure which illustrates
hierarchical clustering
techniques.
• Each level shows clusters for
that level.
– Leaf – individual clusters
– Root – one cluster
• A cluster at level i is the union
of its children clusters at level
i+1.
Levels of Clustering
 Agglomerative Example
A B C D E A B
A 0 1 2 2 3
B 1 0 2 4 3
C 2 2 0 1 5 E C
D 2 4 1 0 3
E 3 3 5 3 0
D

Threshold of

1 2 34 5

A B C D E
 MST Example

A B
A B C D E
A 0 1 2 2 3
B 1 0 2 4 3 E C
C 2 2 0 1 5
D 2 4 1 0 3
E 3 3 5 3 0 D
Agglomerative Algorithm
 Single Link
• View all items with links (distances) between them.
• Finds maximal connected components in this graph.
• Two clusters are merged if there is at least one edge
which connects them.
• Uses threshold distances at each level.
• Could be agglomerative or divisive.
MST Single Link Algorithm
Single Link Clustering
 AGNES (Agglomerative
Nesting)
• Introduced in Kaufmann and Rousseeuw (1990)
• Implemented in statistical analysis packages, e.g., Splus
• Use the Single-Link method and the dissimilarity matrix.
• Merge nodes that have the least dissimilarity
• Go on in a non-descending fashion
• Eventually all nodes belong to the same cluster

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4 4 4

3 3 3

2 2 2

1 1 1

0 0 0
0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10 0 1 2 3 4 5 6 7 8 9 10
 DIANA (Divisive Analysis)

• Introduced in Kaufmann and Rousseeuw (1990)

• Implemented in statistical analysis packages, e.g., Splus
• Inverse order of AGNES
• Eventually each node forms a cluster on its own

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 Readings
• CHAMELEON: A Hierarchical Clustering Algorithm Using Dynamic
Modeling. George Karypis, Eui-Hong Han, Vipin Kumar, IEEE Computer
32(8): 68-75, 1999 (http://glaros.dtc.umn.edu/gkhome/node/152)

• A Density-Based Algorithm for Discovering Clusters in Large Spatial

Databases with Noise. Martin Ester, Hans-Peter Kriegel, Jörg Sander,
Xiaowei Xu. Proceedings of 2nd International Conference on Knowledge
Discovery and Data Mining (KDD-96)

• BIRCH: A New Data Clustering Algorithm and Its Applications. Data Mining
and Knowledge Discovery Volume 1 , Issue 2 (1997)