Based on slides from Han J., et. al.

2013

1
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-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
3
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
4
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

5
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

6
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

7
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

8
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)

9
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

10
 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
11
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
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

13
 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 c i 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

14
 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
15
 An Example of K-Means Clustering

K=2

Arbitrarily Update
partition the
objects cluster
into k centroids
groups
The initial data Loop if
set Reassign objects
needed
 Partition objects into k nonempty
subsets
 Repeat
 Compute centroid (i.e., mean Update
the
point) for each partition cluster
 Assign each object to the centroids
cluster of its nearest centroid
 Until no change
16
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
17
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

18
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

19
 PAM: A Typical K-Medoids Algorithm
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

20
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

21
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

22
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

Ste Ste Ste Ste Ste agglomerative

p0 p1 p2 p3 p4 (AGNES)
a ab
b abcde
c
cde
d de
e
divisive
Ste Ste Ste Ste Ste (DIANA)
p4 p3 p2 p1 p0 23
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

24
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

25
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

26
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(K i, Kj) =
dist(Ci, Cj)
Medoid: distance between the medoids of two clusters, i.e., dist(K i, Kj) =
dist(Mi, Mj)
 Medoid: a chosen, centrally located object in the cluster

27
 Centroid, Radius and Diameter of a Cluster (for X

numerical data sets)

Centroid: the “middle” of a cluster iN1(t )

Cm  N ip

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)

28
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
29
BIRCH (Balanced Iterative Reducing and
Clustering Using Hierarchies)
 Zhang, Ramakrishnan & Livny, SIGMOD’96

 Incrementally construct a CF (Clustering Feature) tree, a hierarchical data

structure for multiphase clustering
 Phase 1: scan DB to build an initial in-memory CF tree (a multi-level
compression of the data that tries to preserve the inherent clustering
structure of the data)
 Phase 2: use an arbitrary clustering algorithm to cluster the leaf nodes of the
CF-tree
 Scales linearly: finds a good clustering with a single scan and improves the
quality with a few additional scans
 Weakness: handles only numeric data, and sensitive to the order of the data
record
30
 Clustering Feature Vector in BIRCH

Clustering Feature (CF): CF = (N,

LS, SS)
N
N: Number of data points
 Xi
i 1
LS: linear sum of N points:
CF = (5, (16,30),
(54,190))
N 2 10

(3,4)
 Xi 9

SS: squarei 1sum of N points

8

5
(2,6)
4

2
(4,5)
(4,7)
1

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

(3,8)
31
CF-Tree in BIRCH
Clustering feature:
Summary of the statistics for a given subcluster: the 0-th, 1st,
and 2nd moments of the subcluster from the statistical point of
view
Registers crucial measurements for computing cluster and
utilizes storage efficiently
A CF tree is a height-balanced tree that stores the clustering
features for a hierarchical clustering
A nonleaf node in a tree has descendants or “children”
The nonleaf nodes store sums of the CFs of their children
A CF tree has two parameters
Branching factor: max # of children
Threshold: max diameter of sub-clusters stored at the leaf nodes
32
The CF Tree Structure
Root
The Birch Algorithm
 Cluster Diameter 1 2
 (x  x )
n( n  1) i j

 For each point in the input

 Find closest leaf entry
 Add point to leaf entry and update CF
 If entry diameter > max_diameter, then split leaf, and possibly parents
 Algorithm is O(n)
 Concerns
 Sensitive to insertion order of data points
 Since we fix the size of leaf nodes, so clusters may not be so natural
 Clusters tend to be spherical given the radius and diameter measures

34
CHAMELEON: Hierarchical Clustering Using
Dynamic Modeling (1999)
 CHAMELEON: G. Karypis, E. H. Han, and V. Kumar, 1999
 Measures the similarity based on a dynamic model
 Two clusters are merged only if the interconnectivity and
closeness (proximity) between two clusters are high relative
to the internal interconnectivity of the clusters and closeness
of items within the clusters
 Graph-based, and a two-phase algorithm
1. Use a graph-partitioning algorithm: cluster objects into a
large number of relatively small sub-clusters
2. Use an agglomerative hierarchical clustering algorithm: find
the genuine clusters by repeatedly combining these sub-
clusters 35
KNN Graphs & Interconnectivity
k-nearest graphs from an original data in 2D:

EC{Ci ,Cj } :The absolute inter-connectivity between Ci and Cj: the

sum of the weight of the edges that connect vertices in Ci to
vertices in Cj
Internal inter-connectivity of a cluster Ci : the size of its min-cut
bisector ECCi (i.e., the weighted sum of edges that partition the
graph into two roughly equal parts)
Relative Inter-connectivity (RI):
36
Relative Closeness & Merge of Sub-Clusters
Relative closeness between a pair of clusters Ci and Cj : the
absolute closeness between Ci and Cj normalized w.r.t. the
internal closeness of the two clusters Ci and Cj

 and are the average weights of the edges that belong in the
min-cut bisector of clusters Ci and Cj , respectively, and is the
average weight of the edges that connect vertices in Ci to vertices in Cj
Merge Sub-Clusters:
 Merges only those pairs of clusters whose RI and RC are both above
some user-specified thresholds
 Merge those maximizing the function that combines RI and RC

37
 Overall Framework of CHAMELEON
Construct (K-NN)
Sparse Graph Partition the Graph

Data Set

K-NN Graph
Merge Partition
P and q are
connected if q is Relative interconnectivity:
connectivity of c1 and c2
among the top k over internal connectivity
closest Final Clusters
Relative closeness:
neighbors of p closeness of c1 and c2 over
internal closeness
CHAMELEON (Clustering Complex Objects)

39
Probabilistic Hierarchical Clustering
 Algorithmic hierarchical clustering
 Nontrivial to choose a good distance measure
 Hard to handle missing attribute values
 Optimization goal not clear: heuristic, local search
 Probabilistic hierarchical clustering
 Use probabilistic models to measure distances between clusters
 Generative model: Regard the set of data objects to be clustered as a
sample of the underlying data generation mechanism to be analyzed
 Easy to understand, same efficiency as algorithmic agglomerative
clustering method, can handle partially observed data
 In practice, assume the generative models adopt common distribution
functions, e.g., Gaussian distribution or Bernoulli distribution, governed by
parameters

40
Generative Model
 Given a set of 1-D points X = {x1, …, xn} for clustering
analysis & assuming they are generated by a Gaussian
distribution:

 The probability that a point xi ∈ X is generated by the model

 The likelihood that X is generated by the model:

 The task of learning the generative model: find the

parameters μ and σ2 such that the maximum likelihood

41
Gaussian Distribution
Bean
machine: drop
ball with pins

1-d 2-d
Gaussia Gaussia
n From wikipedia and n
http://home.dei.polimi.it
42
A Probabilistic Hierarchical Clustering Algorithm
 For a set of objects partitioned into m clusters C1, . . . ,Cm, the quality can be
measured by,

where P() is the maximum likelihood

 If we merge two clusters Cj1 and Cj2 into a cluster Cj1∪Cj2, then, the change in
quality of the overall clustering is

 Distance between clusters C1 and C2:

 If dist(Ci, Cj) < 0, merge Ci and Cj

43
Chapter 10. Cluster Analysis
 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

44
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)
45
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 N (q)
Eps

core point condition:

p MinPts = 5

|NEps (q)| ≥ MinPts q Eps = 1 cm

46
Density-Reachable and Density-Connected
Density-reachable:
A point p is density-reachable from a
p
point q w.r.t. Eps, MinPts if there is a
chain of points p1, …, pn, p1 = q, pn = p
p1
q
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 q are
o
density-reachable from o w.r.t. Eps
and MinPts 47
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

Outlie
r
Borde Eps = 1cm
r
MinPts = 5
Cor
e
48
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)

49
 DBSCAN: Sensitive to Parameters

BSCAN online Demo:

http://webdocs.cs.ualberta.ca/~yaling/Cluster/Applet/Code/Cluster.htm 50
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

51
OPTICS: Some Extension from DBSCAN
Index-based: k = # of dimensions, N: # of points
Complexity: O(N*logN)
Core Distance of an object p: the smallest value ε such that the ε-
neighborhood of p has at least MinPts objects
Let Nε(p): ε-neighborhood of p, ε is a distance value
Core-distanceε, MinPts(p) = Undefined if card(Nε(p)) < MinPts
MinPts-distance(p), otherwise
Reachability Distance of object p from core object q is the min
radius value that makes p density-reachable from q
Reachability-distanceε, MinPts(p, q) =
Undefined if q is not a core object
max(core-distance(q), distance (q, p)), otherwise

52
Core Distance & Reachability Distance

53
Reachability-
distance

undefined


 ‘

Cluster-order of
the objects
54
Density-Based Clustering: OPTICS & Applications
demo: http://www.dbs.informatik.uni-muenchen.de/Forschung/KDD/Clustering/OPTICS/Demo

55
DENCLUE: Using Statistical Density Functions
 DENsity-based CLUstEring by Hinneburg & Keim (KDD’98)
total influence
 Using statistical density functions: on x

d ( x , xi ) 2
d ( x , y )2 
( x )  i 1 e
D N
2 2
f Gaussian ( x , y ) e

2 2 f Gaussian

d ( x , xi ) 2
influence of 
( x, xi )  i 1 ( xi  x) e
D N
2 2
y on x f
 Major features Gaussian

gradient of x
 Solid mathematical foundation in the
direction of xi
 Good for data sets with large amounts of noise
 Allows a compact mathematical description of arbitrarily shaped clusters
in high-dimensional data sets
 Significant faster than existing algorithm (e.g., DBSCAN)
 But needs a large number of parameters
56
Denclue: Technical Essence
 Uses grid cells but only keeps information about grid cells that do actually
contain data points and manages these cells in a tree-based access structure
 Influence function: describes the impact of a data point within its
neighborhood
 Overall density of the data space can be calculated as the sum of the influence
function of all data points
 Clusters can be determined mathematically by identifying density attractors
 Density attractors are local maximal of the overall density function
 Center defined clusters: assign to each density attractor the points density
attracted to it
 Arbitrary shaped cluster: merge density attractors that are connected through
paths of high density (> threshold)

57
Density Attractor

58
Center-Defined and Arbitrary

59
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

60
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

61
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
1st layer

(i-1) st layer

i-th layer

62
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
63
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

64
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

65
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

66
67
Strength and Weakness of CLIQUE
Strength
automatically finds subspaces of the highest dimensionality
such that high density clusters exist in those subspaces
insensitive to the order of records in input and does not
presume some canonical data distribution
scales linearly with the size of input and has good scalability
as the number of dimensions in the data increases
Weakness
The accuracy of the clustering result may be degraded at the
expense of simplicity of the method

68
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

69
 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 the best

70
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

71
Measuring Clustering Quality: External Methods

Clustering quality measure: Q(C, T), for a clustering C given the

ground truth T
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

72
Some Commonly Used External Measures
Matching-based measures
Purity, maximum matching, F-measure
Entropy-Based Measures
Ground truth partitioning T1 T2
Conditional entropy, normalized mutual information
Cluster Cluster
C2
(NMI), variation of information C 1

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
73
Entropy-Based Measure (I): Conditional Entropy
 Entropy of clustering C:
 Entropy of partitioning T:
 Entropy of T w.r.t. cluster Ci:

 Conditional entropy of T
w.r.t. clustering C:

The more a cluster’s members are split into different partitions, the
higher the conditional entropy
For a perfect clustering, the conditional entropy value is 0, where the
worst possible conditional entropy value is log k

74
Entropy-Based Measure (II): Normalized mutual
information (NMI)
Mutual information: quantify the amount of shared info between the
clustering C and partitioning T:

It measures the dependency between the observed joint probability p ij of C and

T, and the expected joint probability pCi * pTj under the independence
assumption
When C and T are independent, pij = pCi * pTj, I(C, T) = 0. However, there is no
upper bound on the mutual information
Normalized mutual information (NMI)

Value range of NMI: [0,1]. Value close to 1 indicates a good clustering

75
Chapter 10. Cluster Analysis

 Cluster Analysis: Basic Concepts

 Partitioning Methods

 Hierarchical Methods

 Density-Based Methods

 Grid-Based Methods

 Evaluation of Clustering

 Summary

76
 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

77
78
CS512-Spring 2011: An Introduction
 Coverage
 Cluster Analysis: Chapter 11
 Outlier Detection: Chapter 12
 Mining Sequence Data: BK2: Chapter 8
 Mining Graphs Data: BK2: Chapter 9
 Social and Information Network Analysis
 BK2: Chapter 9
 Partial coverage: Mark Newman: “Networks: An Introduction”, Oxford U., 2010

 Scattered coverage: Easley and Kleinberg, “Networks, Crowds, and Markets: Reasoning

About a Highly Connected World”, Cambridge U., 2010

 Recent research papers

 Mining Data Streams: BK2: Chapter 8

 Requirements
 One research project
 One class presentation (15 minutes)
 Two homeworks (no programming assignment)
 Two midterm exams (no final exam)

79
References (1)
 R. Agrawal, J. Gehrke, D. Gunopulos, and P. Raghavan. Automatic subspace clustering
of high dimensional data for data mining applications. SIGMOD'98
 M. R. Anderberg. Cluster Analysis for Applications. Academic Press, 1973.
 M. Ankerst, M. Breunig, H.-P. Kriegel, and J. Sander. Optics: Ordering points to
identify the clustering structure, SIGMOD’99.
 Beil F., Ester M., Xu X.: "Frequent Term-Based Text Clustering", KDD'02
 M. M. Breunig, H.-P. Kriegel, R. Ng, J. Sander. LOF: Identifying Density-Based Local
Outliers. SIGMOD 2000.
 M. Ester, H.-P. Kriegel, J. Sander, and X. Xu. A density-based algorithm for
discovering clusters in large spatial databases. KDD'96.
 M. Ester, H.-P. Kriegel, and X. Xu. Knowledge discovery in large spatial databases:
Focusing techniques for efficient class identification. SSD'95.
 D. Fisher. Knowledge acquisition via incremental conceptual clustering. Machine
Learning, 2:139-172, 1987.
 D. Gibson, J. Kleinberg, and P. Raghavan. Clustering categorical data: An approach
based on dynamic systems. VLDB’98.
 V. Ganti, J. Gehrke, R. Ramakrishan. CACTUS Clustering Categorical Data Using
Summaries. KDD'99.
80
References (2)

 D. Gibson, J. Kleinberg, and P. Raghavan. Clustering categorical data: An approach

based on dynamic systems. In Proc. VLDB’98.
 S. Guha, R. Rastogi, and K. Shim. Cure: An efficient clustering algorithm for large
databases. SIGMOD'98.
 S. Guha, R. Rastogi, and K. Shim. ROCK: A robust clustering algorithm for
categorical attributes. In ICDE'99, pp. 512-521, Sydney, Australia, March 1999.
 A. Hinneburg, D.l A. Keim: An Efficient Approach to Clustering in Large
Multimedia Databases with Noise. KDD’98.
 A. K. Jain and R. C. Dubes. Algorithms for Clustering Data. Printice Hall, 1988.
 G. Karypis, E.-H. Han, and V. Kumar. CHAMELEON: A Hierarchical Clustering
Algorithm Using Dynamic Modeling. COMPUTER, 32(8): 68-75, 1999.
 L. Kaufman and P. J. Rousseeuw. Finding Groups in Data: an Introduction to
Cluster Analysis. John Wiley & Sons, 1990.
 E. Knorr and R. Ng. Algorithms for mining distance-based outliers in large datasets.
VLDB’98.

81
References (3)
 G. J. McLachlan and K.E. Bkasford. Mixture Models: Inference and Applications to
Clustering. John Wiley and Sons, 1988.
 R. Ng and J. Han. Efficient and effective clustering method for spatial data mining. VLDB'94.
 L. Parsons, E. Haque and H. Liu, Subspace Clustering for High Dimensional Data: A Review,
SIGKDD Explorations, 6(1), June 2004
 E. Schikuta. Grid clustering: An efficient hierarchical clustering method for very large data
sets. Proc. 1996 Int. Conf. on Pattern Recognition,.
 G. Sheikholeslami, S. Chatterjee, and A. Zhang. WaveCluster: A multi-resolution clustering
approach for very large spatial databases. VLDB’98.
 A. K. H. Tung, J. Han, L. V. S. Lakshmanan, and R. T. Ng. Constraint-Based Clustering in
Large Databases, ICDT'01.
 A. K. H. Tung, J. Hou, and J. Han. Spatial Clustering in the Presence of Obstacles, ICDE'01
 H. Wang, W. Wang, J. Yang, and P.S. Yu. Clustering by pattern similarity in large data sets,
SIGMOD’ 02.
 W. Wang, Yang, R. Muntz, STING: A Statistical Information grid Approach to Spatial Data
Mining, VLDB’97.
 T. Zhang, R. Ramakrishnan, and M. Livny. BIRCH : An efficient data clustering method for
very large databases. SIGMOD'96.
 Xiaoxin Yin, Jiawei Han, and Philip Yu, “
LinkClus: Efficient Clustering via Heterogeneous Semantic Links”, in Proc. 2006 Int. Conf. on
Very Large Data Bases (VLDB'06), Seoul, Korea, Sept. 2006.

82
Chapter 10. Cluster Analysis
 Cluster Analysis: Basic Concepts
 What Is Cluster Analysis?
 What is Good Clustering? Measuring the Quality of Clustering
 Major categories of clustering methods
 Clustering structures
 Calculating Distance between Clusters
 Partitioning Methods
 k-Means: A Classical Partitioning Method
 Alternative Methods: k-Medoids, k-Median, and its Variations
 Hierarchical Methods
 Agglomerative and Divisive Hierarchical Clustering
 BIRCH: A Hierarchical, Micro-Clustering Approach
 Chameleon: A Hierarchical Clustering Algorithm Using Dynamic Modeling
 Density-Based Methods
 DBSCAN and OPTICS: Density-Based Clustering Based on Connected Regions
 DENCLUE: Clustering Based on Density Distribution Functions
 Link-Based Cluster Analysis
 SimRank: Exploring Links in Cluster Analysis
 LinkClus: Scalability in Link-Based Cluster Analysis
 Grid-Based Methods
 STING: STatistical INformation Grid
 WaveCluster: Clustering Using Wavelet Transformation
 CLIQUE: A Dimension-Growth Subspace Clustering Method
 Summary
83 83
Slides unused in class

84
 A 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

85
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
86
PAM Clustering: Finding the Best Cluster Center

 Case 1: p currently belongs to oj. If oj is replaced by orandom as a

representative object and p is the closest to one of the other representative
object oi, then p is reassigned to oi

87
 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)

88
CLARA (Clustering Large Applications) (1990)

CLARA (Kaufmann and Rousseeuw in 1990)

Built in statistical analysis packages, such as SPlus

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
89
 CLARANS (“Randomized” CLARA) (1994)
CLARANS (A Clustering Algorithm based on Randomized
Search) (Ng and Han’94)
Draws sample of neighbors dynamically
The clustering process can be presented as searching a graph
where every node is a potential solution, that is, a set of k
medoids
If the local optimum is found, it starts with new randomly
selected node in search for a new local optimum
Advantages: More efficient and scalable than both PAM and
CLARA
Further improvement: Focusing techniques and spatial access
structures (Ester et al.’95)
90
ROCK: Clustering Categorical Data

ROCK: RObust Clustering using linKs

S. Guha, R. Rastogi & K. Shim, ICDE’99
Major ideas
Use links to measure similarity/proximity
Not distance-based
Algorithm: sampling-based clustering
Draw random sample
Cluster with links
Label data in disk
Experiments
Congressional voting, mushroom data

91
Similarity Measure in ROCK
 Traditional measures for categorical data may not work well, e.g., Jaccard
coefficient
 Example: Two groups (clusters) of transactions
 C1. <a, b, c, d, e>: {a, b, c}, {a, b, d}, {a, b, e}, {a, c, d}, {a, c, e}, {a,
d, e}, {b, c, d}, {b, c, e}, {b, d, e}, {c, d, e}
 C2. <a, b, f, g>: {a, b, f}, {a, b, g}, {a, f, g}, {b, f, g}
 Jaccard co-efficient may lead to wrong clustering result
 C1: 0.2 ({a, b, c}, {b, d, e}} to 0.5 ({a, b, c}, {a, b, d})
 C1 & C2: could be as high as 0.5 ({a, b, c}, {a, b, f})
 Jaccard co-efficient-based similarity function: T1  T2
Sim( T1 , T2 ) 
T1  T2
 Ex. Let T1 = {a, b, c}, T2 = {c, d, e}
{c} 1
Sim (T 1, T 2)   0.2
{a, b, c, d , e} 5
92
Link Measure in ROCK
 Clusters
 C :<a, b, c, d, e>: {a, b, c}, {a, b, d}, {a, b, e}, {a, c, d}, {a, c, e}, {a, d, e}, {b, c,
1
d}, {b, c, e}, {b, d, e}, {c, d, e}
 C : <a, b, f, g>: {a, b, f}, {a, b, g}, {a, f, g}, {b, f, g}
2
 Neighbors
 Two transactions are neighbors if sim(T ,T ) > threshold
1 2

 Let T1 = {a, b, c}, T2 = {c, d, e}, T3 = {a, b, f}

T1 connected to: {a,b,d}, {a,b,e}, {a,c,d}, {a,c,e}, {b,c,d}, {b,c,e}, {a,b,f},
{a,b,g}
 T connected to: {a,c,d}, {a,c,e}, {a,d,e}, {b,c,e}, {b,d,e}, {b,c,d}
2
 T connected to: {a,b,c}, {a,b,d}, {a,b,e}, {a,b,g}, {a,f,g}, {b,f,g}
3
 Link Similarity
 Link similarity between two transactions is the # of common neighbors

 link(T1, T2) = 4, since they have 4 common neighbors

 {a, c, d}, {a, c, e}, {b, c, d}, {b, c, e}

 link(T1, T3) = 3, since they have 3 common neighbors

 {a, b, d}, {a, b, e}, {a, b, g} 93

Measuring Clustering Quality: External 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

95
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

96