Data Mining:

Concepts and Techniques

(3rd ed.)

— Chapter 10 —

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 Chapter 10. Cluster Analysis: Basic
Concepts and Methods

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Evaluation of Clustering

 Summary

2
 What is Cluster Analysis?
 Cluster: A collection of data objects
 similar (or related) to one another within the same group

 dissimilar (or unrelated) to the objects in other groups

 Cluster analysis (or clustering, data segmentation, …)

 Finding similarities between data according to the

characteristics found in the data and grouping similar

data objects into clusters
 Unsupervised learning: no predefined classes (i.e., learning
by observations vs. learning by examples: supervised)
 Typical applications
 As a stand-alone tool to get insight into data distribution

 As a preprocessing step for other algorithms

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 Applications of Cluster Analysis
 Data reduction
 Summarization: Preprocessing for regression, PCA,

classification, and association analysis

 Compression: Image processing: vector quantization
 Prediction based on groups
 Cluster & find characteristics/patterns for each group

 Finding K-nearest Neighbors

 Localizing search to one or a small number of clusters
 Outlier detection: Outliers are often viewed as those “far
away” from any cluster

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 Clustering: Application Examples
 Biology: taxonomy of living things: kingdom, phylum, class, order,
family, genus and species
 Information retrieval: document clustering
 Land use: Identification of areas of similar land use in an earth
observation database
 Marketing: Help marketers discover distinct groups in their customer
bases, and then use this knowledge to develop targeted marketing
programs
 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
 Climate: understanding earth climate, find patterns of atmospheric
and ocean
 Economic Science: market resarch
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Basic Steps to Develop a Clustering Task
 Feature selection
 Select info concerning the task of interest

 Minimal information redundancy

 Proximity measure
 Similarity of two feature vectors

 Clustering criterion
 Expressed via a cost function or some rules

 Clustering algorithms
 Choice of algorithms

 Validation of the results

 Validation test (also, clustering tendency test)

 Interpretation of the results

 Integration with applications

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 Quality: What Is Good Clustering?

 A good clustering method will produce high quality

clusters
 high intra-class similarity: cohesive within clusters
 low inter-class similarity: distinctive between clusters
 The quality of a clustering method depends on
 the similarity measure used by the method
 its implementation, and
 Its ability to discover some or all of the hidden
patterns

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 Measure the Quality of Clustering
 Dissimilarity/Similarity metric
 Similarity is expressed in terms of a distance function,
typically metric: d(i, j)
 The definitions of distance functions are usually rather
different for interval-scaled, boolean, categorical,
ordinal ratio, and vector variables
 Weights should be associated with different variables
based on applications and data semantics
 Quality of clustering:
 There is usually a separate “quality” function that
measures the “goodness” of a cluster.
 It is hard to define “similar enough” or “good enough”
 The answer is typically highly subjective
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 Major Clustering Approaches (I)

 Partitioning approach:
 Construct various partitions and then evaluate them by some

criterion, e.g., minimizing the sum of square errors

 Typical methods: k-means, k-medoids, CLARANS

 Hierarchical approach:
 Create a hierarchical decomposition of the set of data (or objects)

using some criterion

 Typical methods: Diana, Agnes, BIRCH, CAMELEON

 Density-based approach:
 Based on connectivity and density functions

 Typical methods: DBSACN, OPTICS, DenClue

 Grid-based approach:
 based on a multiple-level granularity structure

 Typical methods: STING, WaveCluster, CLIQUE

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 Major Clustering Approaches (II)
 Model-based:
 A model is hypothesized for each of the clusters and tries to find

the best fit of that model to each other

 Typical methods: EM, SOM, COBWEB

 Frequent pattern-based:
 Based on the analysis of frequent patterns

 Typical methods: p-Cluster

 User-guided or constraint-based:
 Clustering by considering user-specified or application-specific

constraints
 Typical methods: COD (obstacles), constrained clustering

 Link-based clustering:
 Objects are often linked together in various ways

 Massive links can be used to cluster objects: SimRank, LinkClus

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 Chapter 10. Cluster Analysis: Basic
Concepts and Methods

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Evaluation of Clustering

 Summary

11
 Partitioning Algorithms: Basic Concept

 Partitioning method: Partitioning a database D of n objects into a set

of k clusters, such that the sum of squared distances is minimized
(where ci is the centroid or medoid of cluster Ci)

E   ik1 pCi (d ( p, ci )) 2

 Given 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, Lloyd’57/’82): 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
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 The K-Means Clustering Method

 Given k, the k-means algorithm is implemented in

four steps:
1. Partition objects into k nonempty subsets
2. Compute seed points as the centroids of the
clusters of the current partitioning (the centroid
is the center, i.e., mean point, of the cluster)
3. Assign each object to the cluster with the nearest
seed point
4. Go back to Step 2, stop when the assignment
does not change

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 An Example of K-Means Clustering

K=2

Arbitrarily Update the

partition cluster
objects into centroids
k groups

The initial data set Loop if Reassign objects

needed
 Partition objects into k nonempty
subsets
 Repeat
 Compute centroid (i.e., mean Update the
cluster
point) for each partition
centroids
 Assign each object to the
cluster of its nearest centroid
 Until no change
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 Comments on the K-Means Method

 Strength: 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))
 Comment: Often terminates at a local optimal
 Weakness
 Applicable only to objects in a continuous n-dimensional space
 Using the k-modes method for categorical data
 In comparison, k-medoids can be applied to a wide range of
data
 Need to specify k, the number of clusters, in advance (there are
ways to automatically determine the best k (see Hastie et al., 2009)
 Sensitive to noisy data and outliers
 Not suitable to discover clusters with non-convex shapes
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 Variations of the K-Means Method

 Most of the 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

 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

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What Is the Problem of the 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

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

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 PAM: A Typical K-Medoids Algorithm
Total Cost = 20
10 10 10

9 9 9

8 8 8

Arbitrary Assign
7 7 7

6 6 6

5
choose k 5 each 5

4 object as 4 remainin 4

3
initial 3
g object 3

2
medoids 2
to 2

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

K=2 Randomly select a

Total Cost = 26 nonmedoid object,Oramdom
10 10

Do loop 9
Compute
9

Swapping O
8 8

total cost of
Until no
7 7

and Oramdom 6
swapping 6

change
5 5

If quality is 4 4

improved. 3 3

2 2

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

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 The K-Medoid Clustering Method

 K-Medoids Clustering: Find representative objects (medoids) in clusters

 PAM (Partitioning Around Medoids, Kaufmann & Rousseeuw 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 (due to the computational complexity)

 Efficiency improvement on PAM

 CLARA (Kaufmann & Rousseeuw, 1990): PAM on samples

 CLARANS (Ng & Han, 1994): Randomized re-sampling

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 Chapter 10. Cluster Analysis: Basic
Concepts and Methods
 Cluster Analysis: Basic Concepts
 Partitioning Methods
 Hierarchical Methods
 Density-Based Methods
 Grid-Based Methods
 Evaluation of Clustering
 Summary

20
 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
(DIANA)
Step 4 Step 3 Step 2 Step 1 Step 0

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 AGNES (Agglomerative Nesting)
 Introduced in Kaufmann and Rousseeuw (1990)
 Implemented in statistical 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
10 10 10

9 9 9

8 8 8

7 7 7

6 6 6

5 5 5

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

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Dendrogram: Shows How Clusters are Merged

Decompose data objects into a several levels of nested partitioning (tree of

clusters), called a dendrogram

A clustering of the data objects is obtained by cutting the dendrogram at

the desired level, then each connected component forms a cluster

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 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

10 10
10

9 9
9

8 8
8

7 7
7

6 6
6

5 5
5

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

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 Distance between X X

Clusters
 Single link: smallest distance between an element in one cluster
and an element in the other, i.e., dist(Ki, Kj) = min(tip, tjq)

 Complete link: largest distance between an element in one cluster

and an element in the other, i.e., dist(Ki, Kj) = max(tip, tjq)

 Average: avg distance between an element in one cluster and an

element in the other, i.e., dist(Ki, Kj) = avg(tip, tjq)

 Centroid: distance between the centroids of two clusters, i.e.,

dist(Ki, Kj) = dist(Ci, Cj)

 Medoid: distance between the medoids of two clusters, i.e., dist(Ki,

Kj) = dist(Mi, Mj)
 Medoid: a chosen, centrally located object in the cluster
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Centroid, Radius and Diameter of a Cluster
(for numerical data sets)
 Centroid: the “middle” of a cluster iN 1(t
Cm  ip )
N

 Radius: square root of average distance from any point

of the cluster to its centroid  N (t  cm ) 2
Rm  i 1 ip
N
 Diameter: square root of average mean squared
distance between all pairs of points in the cluster

 N  N (t  t ) 2
Dm  i 1 i 1 ip iq
N ( N 1)

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Extensions to Hierarchical Clustering
 Major weakness of agglomerative clustering methods

 Can never undo what was done previously

 Do not scale well: time complexity of at least O(n2),

where n is the number of total objects

 Integration of hierarchical & distance-based clustering

 BIRCH (1996): uses CF-tree and incrementally adjusts

the quality of sub-clusters

 CHAMELEON (1999): hierarchical clustering using

dynamic modeling
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 Chapter 10. Cluster Analysis: Basic
Concepts and Methods
 Cluster Analysis: Basic Concepts
 Partitioning Methods
 Hierarchical Methods
 Density-Based Methods
 Evaluation of Clustering
 Summary

28
 Density-Based Clustering Methods

 Clustering based on density (local cluster criterion), such

as density-connected points
 Major features:
 Discover clusters of arbitrary shape

 Handle noise

 One scan

 Need density parameters as termination condition

 Several interesting studies:

 DBSCAN: Ester, et al. (KDD’96)

 OPTICS: Ankerst, et al (SIGMOD’99).

 DENCLUE: Hinneburg & D. Keim (KDD’98)

 CLIQUE: Agrawal, et al. (SIGMOD’98) (more grid-based)

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 Density-Based Clustering: Basic
Concepts
 Two parameters:
 Eps: Maximum radius of the neighbourhood
 MinPts: Minimum number of points in an Eps-
neighbourhood of that point
 NEps(q): {p belongs to D | dist(p,q) ≤ Eps}
 Directly density-reachable: A point p is directly
density-reachable from a point q w.r.t. Eps, MinPts if

 p belongs to NEps(q) p MinPts = 5

 core point condition: Eps = 1 cm

q
|NEps (q)| ≥ MinPts
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Density-Reachable and Density-Connected

 Density-reachable:
 A point p is density-reachable from p
a point q w.r.t. Eps, MinPts if there p1
is a chain of points p1, …, pn, p1 = q
q, pn = p such that pi+1 is directly
density-reachable from pi
 Density-connected
 A point p is density-connected to a p q

point q w.r.t. Eps, MinPts if there

is a point o such that both, p and o

q are density-reachable from o

w.r.t. Eps and MinPts
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 DBSCAN: Density-Based Spatial
Clustering of Applications with Noise
 Relies on a density-based notion of cluster: A cluster is
defined as a maximal set of density-connected points
 Discovers clusters of arbitrary shape in spatial databases
with noise

Outlier

Border
Eps = 1cm

Core MinPts = 5

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 DBSCAN: The Algorithm
 Arbitrary select a point p

 Retrieve all points density-reachable from p w.r.t. Eps

and MinPts

 If p is a core point, a cluster is formed

 If p is a border point, no points are density-reachable

from p and DBSCAN visits the next point of the database

 Continue the process until all of the points have been

processed
 If a spatial index is used, the computational complexity of DBSCAN is
O(nlogn), where n is the number of database objects. Otherwise, the
complexity is O(n2)
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 DBSCAN: Sensitive to Parameters

DBSCAN online Demo:

http://webdocs.cs.ualberta.ca/~yaling/Cluster/Applet/Code/Cluster.html
34
 Chapter 10. Cluster Analysis: Basic
Concepts and Methods

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Evaluation of Clustering

 Summary

35
 Assessing Clustering Tendency
 Assess if non-random structure exists in the data by measuring the
probability that the data is generated by a uniform data distribution
 Test spatial randomness by statistic test: Hopkins Static
 Given a dataset D regarded as a sample of a random variable o,

determine how far away o is from being uniformly distributed in

the data space
 Sample n points, p1, …, pn, uniformly from D. For each pi, find its

nearest neighbor in D: xi = min{dist (pi, v)} where v in D

 Sample n points, q1, …, qn, uniformly from D. For each qi, find its

nearest neighbor in D – {qi}: yi = min{dist (qi, v)} where v in D

and v ≠ qi
 Calculate the Hopkins Statistic:

 If D is uniformly distributed, ∑ xi and ∑ yi will be close to each

other and H is close to 0.5. If D is clustered, H is close to 1
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 Determine the Number of Clusters
 Empirical method
 # of clusters ≈√n/2 for a dataset of n points

 Elbow method
 Use the turning point in the curve of sum of within cluster variance

w.r.t the # of clusters

 Cross validation method
 Divide a given data set into m parts

 Use m – 1 parts to obtain a clustering model

 Use the remaining part to test the quality of the clustering

 E.g., For each point in the test set, find the closest centroid, and

use the sum of squared distance between all points in the test
set and the closest centroids to measure how well the model fits
the test set
 For any k > 0, repeat it m times, compare the overall quality

measure w.r.t. different k’s, and find # of clusters that fits the data
the best 37
 Measuring Clustering Quality

 Two methods: extrinsic vs. intrinsic

 Extrinsic: supervised, i.e., the ground truth is available
 Compare a clustering against the ground truth using
certain clustering quality measure
 Ex. BCubed precision and recall metrics
 Intrinsic: unsupervised, i.e., the ground truth is unavailable
 Evaluate the goodness of a clustering by considering
how well the clusters are separated, and how compact
the clusters are
 Ex. Silhouette coefficient

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Measuring Clustering Quality: Extrinsic Methods

 Clustering quality measure: Q(C, Cg), for a clustering C

given the ground truth Cg.
 Q is good if it satisfies the following 4 essential criteria
 Cluster homogeneity: the purer, the better

 Cluster completeness: should assign objects belong to

the same category in the ground truth to the same

cluster
 Rag bag: putting a heterogeneous object into a pure

cluster should be penalized more than putting it into a

rag bag (i.e., “miscellaneous” or “other” category)
 Small cluster preservation: splitting a small category

into pieces is more harmful than splitting a large

category into pieces
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 Chapter 10. Cluster Analysis: Basic
Concepts and Methods

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary
40
 Summary
 Cluster analysis groups objects based on their similarity and has
wide applications
 Measure of similarity can be computed for various types of data
 Clustering algorithms can be categorized into partitioning methods,
hierarchical methods, density-based methods, grid-based methods,
and model-based methods
 K-means and K-medoids algorithms are popular partitioning-based
clustering algorithms
 Birch and Chameleon are interesting hierarchical clustering algorithms,
and there are also probabilistic hierarchical clustering algorithms
 DBSCAN, OPTICS, and DENCLU are interesting density-based
algorithms
 STING and CLIQUE are grid-based methods, where CLIQUE is also a
subspace clustering algorithm
 Quality of clustering results can be evaluated in various ways
41