25/09/2024

Data Mining:
Cluster Analysis: Basic
Concepts and Methods

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Cluster Analysis: Basic Concepts and

Methods

■ Cluster Analysis: Basic Concepts

■ Partitioning Methods

■ Hierarchical Methods

■ Density-Based Methods

■ Grid-Based Methods

■ Evaluation of Clustering
■ Summary
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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

Applications of Cluster Analysis

■ Data reduction
■ Summarization: Preprocessing for regression, PCA,

classification, and association analysis

■ Compression: Image processing: vector quantization
■ Hypothesis generation and testing
■ 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

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

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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Considerations for Cluster

Analysis
■ Partitioning criteria
■ Single level vs. hierarchical partitioning (often, multi-level
hierarchical partitioning is desirable)
■ Separation of clusters
■ Exclusive (e.g., one customer belongs to only one region) vs.
non-exclusive (e.g., one document may belong to more than
one class)
■ Similarity measure
■ Distance-based (e.g., Euclidian, road network, vector) vs.
connectivity-based (e.g., density or contiguity)
■ Clustering space
■ Full space (often when low dimensional) vs. subspaces (often
in high-dimensional clustering)
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Requirements and Challenges

■ Scalability
■ Clustering all the data instead of only on samples

■ Ability to deal with different types of attributes

■ Numerical, binary, categorical, ordinal, linked, and mixture of
these
■ Constraint-based clustering
■ User may give inputs on constraints
■ Use domain knowledge to determine input parameters
■ Interpretability and usability
■ Others
■ Discovery of clusters with arbitrary shape

■ Ability to deal with noisy data

■ Incremental clustering and insensitivity to input order

■ High dimensionality

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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 12

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Cluster Analysis: Basic Concepts and

Methods

■ Cluster Analysis: Basic Concepts

■ Partitioning Methods

■ Hierarchical Methods

■ Density-Based Methods

■ Grid-Based Methods

■ Evaluation of Clustering
■ Summary
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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)

■ 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:
■ Partition objects into k nonempty subsets
■ 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)
■ Assign each object to the cluster with the nearest
seed point
■ 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 1 0 1 2 3 4 5 6 7 8 9 1
0 0

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PAM: A Typical K-Medoids Algorithm

Total Cost = 20
1
0
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6
Arbitrary Assign
choose k each
5
remaining
4 object as
object to
3 initial nearest
medoids
2

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

K=2 Randomly select a

Total Cost = 26 nonmedoid object,Oramdom
1 1

Do loop
0 0
9 9
8 Compute 8
Swapping O 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 1 0 1 2 3 4 5 6 7 8 9 1
0 0

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Cluster Analysis: Basic Concepts and

Methods

■ Cluster Analysis: Basic Concepts

■ Partitioning Methods
■ Hierarchical Methods
■ Density-Based Methods
■ Grid-Based Methods
■ Evaluation of Clustering
■ Summary

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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

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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

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Distance between Clusters

X X

■ 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 X

Cluster (for numerical data sets)

■ Centroid: the “middle” of a cluster

■ Radius: square root of average distance from any

point of the cluster to its centroid

■ Diameter: square root of average mean squared

distance between all pairs of points in the cluster

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Cluster Analysis: Basic Concepts and

Methods

■ Cluster Analysis: Basic Concepts

■ Partitioning Methods
■ Hierarchical Methods
■ Density-Based Methods
■ Grid-Based Methods
■ Evaluation of Clustering
■ Summary

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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

Eps = 1 cm
■ core point condition:
q
|NEps (q)| ≥ MinPts
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Density-Reachable and Density-

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

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OPTICS: A Cluster-Ordering Method

(1999)
■ OPTICS: Ordering Points To Identify the Clustering Structure
■ Ankerst, Breunig, Kriegel, and Sander (SIGMOD’99)

■ Produces a special order of the database wrt its density-

based clustering structure
■ This cluster-ordering contains info equiv to the density-based
clusterings corresponding to a broad range of parameter
settings
■ Good for both automatic and interactive cluster analysis,
including finding intrinsic clustering structure
■ Can be represented graphically or using visualization
techniques

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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

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Grid-Based Clustering Method

■ Using multi-resolution grid data structure
■ Several interesting methods
■ STING (a STatistical INformation Grid approach) by
Wang, Yang and Muntz (1997)
■ CLIQUE: Agrawal, et al. (SIGMOD’98)
■ Both grid-based and subspace clustering

■ WaveCluster by Sheikholeslami, Chatterjee, and

Zhang (VLDB’98)
■ A multi-resolution clustering approach using

wavelet method

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STING: A Statistical Information Grid

Approach
■ Wang, Yang and Muntz (VLDB’97)
■ The spatial area is divided into rectangular cells
■ There are several levels of cells corresponding to
different levels of resolution

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The STING Clustering Method

■ Each cell at a high level is partitioned into a number of smaller
cells in the next lower level
■ Statistical info of each cell is calculated and stored beforehand
and is used to answer queries
■ Parameters of higher level cells can be easily calculated from
parameters of lower level cell
■ count, mean, s, min, max

■ type of distribution—normal, uniform, etc.

■ Use a top-down approach to answer spatial data queries

■ Start from a pre-selected layer—typically with a small number of
cells
■ For each cell in the current level compute the confidence interval

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STING Algorithm and Its Analysis

■ Remove the irrelevant cells from further consideration
■ When finish examining the current layer, proceed to
the next lower level
■ Repeat this process until the bottom layer is reached
■ Advantages:
■ Query-independent, easy to parallelize, incremental
update
■ O(K), where K is the number of grid cells at the
lowest level
■ Disadvantages:
■ All the cluster boundaries are either horizontal or
vertical, and no diagonal boundary is detected

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CLIQUE (Clustering In QUEst)

■ Agrawal, Gehrke, Gunopulos, Raghavan (SIGMOD’98)
■ Automatically identifying subspaces of a high dimensional data
space that allow better clustering than original space
■ CLIQUE can be considered as both density-based and grid-based
■ It partitions each dimension into the same number of equal
length interval
■ It partitions an m-dimensional data space into non-
overlapping rectangular units
■ A unit is dense if the fraction of total data points contained in
the unit exceeds the input model parameter
■ A cluster is a maximal set of connected dense units within a
subspace
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CLIQUE: The Major Steps

■ Partition the data space and find the number of points
that lie inside each cell of the partition.
■ Identify the subspaces that contain clusters using the
Apriori principle
■ Identify clusters
■ Determine dense units in all subspaces of interests
■ Determine connected dense units in all subspaces
of interests.
■ Generate minimal description for the clusters
■ Determine maximal regions that cover a cluster of
connected dense units for each cluster
■ Determination of minimal cover for each cluster

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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
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Determine the Number of Clusters

■ Empirical method
■ # of clusters: k ≈√n/2 for a dataset of n points, e.g., n = 200, k =
10
■ 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
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Measuring Clustering Quality

■ 3 kinds of measures: External, internal and relative
■ External: supervised, employ criteria not inherent to the dataset
■ Compare a clustering against prior or expert-specified
knowledge (i.e., the ground truth) using certain clustering
quality measure
■ Internal: unsupervised, criteria derived from data itself
■ Evaluate the goodness of a clustering by considering how
well the clusters are separated, and how compact the clusters
are, e.g., Silhouette coefficient
■ Relative: directly compare different clusterings, usually those
obtained via different parameter settings for the same algorithm

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Some Commonly Used External Measures

■ Matching-based measures
■ Purity, maximum matching, F-measure

■ Entropy-Based Measures Ground truth partitioning T1 T2

Cluster C Cluster C
1 2

■ Conditional entropy, normalized mutual information

(NMI), variation of information

■ Pair-wise measures
■ Four possibilities: True positive (TP), FN, FP, TN

■ Jaccard coefficient, Rand statistic, Fowlkes-Mallow

measure
■ Correlation measures
■ Discretized Huber static, normalized discretized

Huber static
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