Clustering

— Module 7 of CS8031 — Module 5 of CA532 —

Adapted from Data Mining: Concepts and Techniques ©2011

Han, Kamber & Pei.

1
Cluster Analysis: Basic Concepts and Methods

◼ 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
Clustering for Data Understanding and
Applications
◼ 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 research
4
 Clustering as a Preprocessing Tool (Utility)

◼ Summarization:
◼ Preprocessing for regression, PCA, classification, and
association analysis
◼ Compression:
◼ Image processing: vector quantization
◼ 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

5
 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 cluster-
(centers)
◼ 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

6
 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
7
Understanding Data

TYPES OF ATTRIBUTES AND

(DIS)SIMILARITY MEASURES
 Attributes

◼ Attribute (or dimensions, features, variables): a data

field, representing a characteristic or feature of a data
object.
◼ E.g., customer _ID, name, address
◼ Types:
◼ Categorical –

◼ Nominal
◼ Binary - Symmetric, Asymmetric
◼ Ordinal
◼ Numeric: quantitative
◼ Interval-scaled

◼ Ratio-scaled
9
 Categorical Attribute Types
◼ Nominal: categories, states, or “names of things”
◼ Hair_color = {auburn, black, blond, brown, grey, red, white}
◼ marital status, occupation, ID numbers, zip codes
◼ Binary
◼ Nominal attribute with only 2 states (0 and 1)
◼ Symmetric binary: both outcomes equally important
◼ e.g., gender
◼ Asymmetric binary: outcomes not equally important.
◼ e.g., medical test (positive vs. negative)
◼ Convention: assign 1 to most important outcome (e.g., HIV
positive)
◼ Ordinal
◼ Values have a meaningful order (ranking) but magnitude between
successive values is not known.
◼ Size = {small, medium, large}, grades, army rankings

10
 Numeric Attribute Types

◼ Quantity (integer or real-valued)

◼ Interval
◼ Measured on a scale of equal-sized units
◼ Values have order
◼ E.g., temperature in C˚or F˚, calendar dates
◼ No true zero-point
◼ Ratio
◼ Inherent zero-point
◼ We can speak of values as being an order of
magnitude larger than the unit of measurement (10
K˚ is twice as high as 5 K˚).
◼ e.g., temperature in Kelvin, length, counts,
monetary quantities
11
 Discrete vs. Continuous Attributes

◼ Discrete Attribute
◼ Has only a finite or countably infinite set of values

◼ E.g., zip codes, profession, or the set of words in a

collection of documents
◼ Sometimes, represented as integer variables

◼ Note: Binary attributes are a special case of discrete

attributes
◼ Continuous Attribute
◼ Has real numbers as attribute values

◼ E.g., temperature, height, or weight

◼ Practically, real values can only be measured and

represented using a finite number of digits
◼ Continuous attributes are typically represented as
floating-point variables
12
 Dissimilarity Measures – Numerical- Interval Scaled

Ecl(t1,t2)= {(22-20)^2+(1-0)^2+(42-36)^2+(10-8)^2}^(1/2) = 45^(1/2)

Mht(t1,t2) ={(22-20)+(1-0)+(42-36)+(10-8)} = 11
Mnks(t1,t2)[:p=4] ={(22-20)^4+(1-0)^4+(42-36)^4+(10-8)^4}^(1/4) = …
Dissimilarity Measures – Numerical (Ratio-Scaled)
-e.g. test3 here

Val Logn(Val)

445 2.65
22 1.34
164 2.21
1210 3.08
 Dissimilarity Measures – Categorical (Nominal)

m= No. of matches
p= Toal No. nominal
attributes

(p=1 here)
Dissimilarity Measures – Categorical (Ordinal)
-e.g. test2 here

Val (Mf=3) Rif Zif

Ex 3 1
F 1 0.0
G 2 0.5
Ex 3 1
 Dissimilarity Measures- Binary
Variables- Symmetric/ Asymmetric

Symmetric Binary – a variable whose difference of values (0/1) don’t

affect decision drastically. e.g. Gender (assuming that the application is
not affected otherwise).

Asymmetric Binary – a variable whose difference of values (0/1) affects

decision drastically. e.g. diagnostic tests. The the affective value e. g.
Positive in fever_test is set as 1.
(Dis)similarity Measures- Mixed Attribute types
 (Dis)similarity Measures- Mixed Attribute types
Name Gender Fever Cough Test1 Test2 Test3 Test4 Test5 Age Logn
(Test5)
Jack M (0) Y (1) N (0) P (1) N (0) N (0) CodeA 445 35 2.65

Marry F (1) Y (1) N (0) P(1) N (0) P (1) CodeA 25 45 1.31

Tim 1210 25 3.08

Attribute Type

Gender Bin-Symmetric 1 1 1

Fever Bin-Asymmetric 1 0 0

Cough Bin-Asymmetric 0 0 0

Test1 Bin-Asymmetric 1 0 0

Test2 Bin-Asymmetric 0 0 0

Test3 Bin-Asymmetric 1 1 1

Test4 Bin-Asymmetric 0 0 0

Test5 Ratio-scaled 1 0.75 0.75

(= (2.65-1.34)/(3.08-1.34))
Age Interval-scaled 1 0.5 (= (|35-45|)/(45-25)) 0.5

Sum 6 (A) 3.25 (B)

Dissimilarity B/A 0.54

 Practice Quiz

◼ Compute dissimilarity for any dataset of mixed

variable types

20
 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

22
 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

23
 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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 Illustration – capabilities of different approaches
https://machinelearningmastery.com/clustering-algorithms-with-python/

Synthetic Clustering Dataset Agglomerative (Hierarchical)

Clustering

DBSCAN Clustering K-Means Clustering

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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
26
 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 ( 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
27
 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

28
 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
29
 Numerical illustration of k-means
[https://towardsdatascience.com/k-means-clustering-one-rule-to-group-them-all-f47e00720ee7]

each point, based upon its distance

from the assumed centroids is
then assigned to a centroid

30
 Determining K : Cost Function, Elbow method

Likewise, the cost

can be calculated
for different
values of K

Elbow method to determine the optimum value of K - as

per the graph would be the one where it shows maximum
deflection (marked in red) or where the cost curve makes
an elbow.
Although the higher values of K reduce the cost further but
they lead to overfitting (extreme case would be N clusters
with N datapoints!!).

31
 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
32
 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

33
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

34
 A Typical K-Medoids Algorithm (PAM)
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

K
Swapping O
8 8

total cost of
Until no
7 7

and Oramdom 6
swapping 6

change R
5 5

If quality is 4 4
A
improved. 3 CA = d(A,P)- 3

d(A,R)
P
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

35
 Cost of swapping
◼ K=2, Initial Seed= A, C A B C D

A 0 5 3 4
◼ Iteration 1
B 5 0 7 4
◼ Clusters – {A, B} {C,D} C 3 7 0 2

◼ Swap- D 4 4 2 0

◼ A->D = {D,B} {C,A} :

◼ TC(A->D) = CostA +CostB +CostC +CostD= (new_dist-old_dist)
◼ =(d(A,C)-d(A,A)) + (d(B,D)-d(B,A))+ (d(C,C)-d(C,C)) + (d(D,D)-d(D,C))
◼ = (3-0) + (4-5) + (0-0) + (0-2) = 0
◼ TC ==0 => No Cost reduction on swapping A with D=> No Swap => {A,..}, {C,..}
◼ A->B
◼ C->D
◼ C->B
◼ Iteration 2…

36
 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
37
 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

38
 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)

39
 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

40
 CLARANS (“Randomized” CLARA) (1994)
◼ CLARANS (A Clustering Algorithm based on Randomized
Search) (Ng and Han’94)
◼ Draws sample of neighbors (Oi) for swap 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)

41
 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

42
Cluster Analysis: Basic Concepts and Methods

◼ Cluster Analysis: Basic Concepts

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

43
 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)
44
 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

45
 Bottom-Up-AGNES
◼ {2,3 ,5, 8, 10}
◼ Single-link: distance bw two groups is the distance bw the nearest
elements

◼ Complete-link: distance bw two groups is the distance bw the

farthest elements of the two groups
◼ Average-link: distance bw two groups is the distance bw the Means
of the respective elements of the two groups

46
 Bottom-Up-AGNES- Single-link
◼ {2,3 ,5, 8, 10}
◼ Single-link: distance bw two groups is the distance bw the nearest
elements
◼ {2},{3} ,{5}, {8}, {10} => distances= 1,2,3,2
◼ {2,3}, {5}, {8,10} => distances= 2,3
◼ {2,3,5}, {8,10} =>
◼ {2,3,5,8,10}=>

47
 Bottom-Up-AGNES- Complete-link
◼ {2,3 ,5, 8, 10}
◼ Complete-link: distance bw two groups is the distance bw the farthest
elements
◼ {2},{3} ,{5}, {8}, {10} => distances= 1,2,3,2

◼ {2,3}, {5}, {8,10} => distances= 3,5

◼ {2,3,5}, {8,10} => distances= 8

◼ {2,3,5,8,10}=>

48
 Bottom-Up-AGNES- Average-link
◼ {2,3 ,5, 8, 10}
◼ Average-link: distance bw two groups is the distance between the
means of the two groups
◼ {2},{3} ,{5}, {8}, {10} => distances= 1,2,3,2
◼ {2,3}, {5}, {8,10} => distances= {avg(5-2,5-3), avg(8-5,10-5)}= 2.5, 4
◼ {2,3,5}, {8,10} => distances= avg{8-2,8-3,8-5,10-2,10-3,10-5}= 34/6=5.67
◼ {2,3,5,8,10}=>

49
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

50
 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

51
 Top-Down- DIANA
◼ {2,3 ,5, 8, 10} => distances= 1,2,3,2
◼ {2,3 ,5}=> distances= 1,2

◼ {2}
◼ {3,5}
◼ {3}
◼ {5}

◼ {8, 10}
◼ {8}
◼ {10}

52
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
53
 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)

54
 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
55
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

56
 Clustering Feature Vector in BIRCH

Clustering Feature (CF): CF = (N, LS, SS)

N: Number of data points
N
LS: linear sum of N points:  X i
i =1

CF = (5, (16,30),(54,190))
SS: square sum of N points
N 2 10

(3,4)
 Xi
9

i =1
7

6
(2,6)
5

4 (4,5)
3

1
(4,7)
0
0 1 2 3 4 5 6 7 8 9 10
(3,8)

57
 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 to avoid overfitting

◼ Branching factor: max # of children

◼ Threshold: max diameter of sub-clusters stored at the leaf

nodes 58
 The CF Tree Structure
Root

B=7 CF1 CF2 CF3 CF6

child1 child2 child3 child6
L=6

Non-leaf node
CF1 CF2 CF3 CF5
child1 child2 child3 child5

Leaf node Leaf node

prev CF1 CF2 CF6 next prev CF1 CF2 CF4 next

59
 The Birch Algorithm
◼ Cluster Diameter 1
 ( xi − x j )
2

n( n − 1)

◼ 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
60
Cluster Analysis: Basic Concepts and Methods

◼ Cluster Analysis: Basic Concepts

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

61
 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)

62
 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(p): {q 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)
◼ core point condition: p MinPts = 5

|NEps (q)| ≥ MinPts Eps = 1 cm

q

63
 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 q o
are density-reachable from o w.r.t.
Eps and MinPts
64
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

65
 DBSCAN
[https://towardsdatascience.com/dbscan-make-density-based-clusters-by-
hand-2689dc335120]

66
 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

67
DBSCAN: Sensitive to Parameters

68
 Reachability
-distance

undefined


‘

Cluster-order
of the objects
69
Density-Based Clustering: OPTICS & Its Applications

70
Cluster Analysis: Basic Concepts and Methods

◼ Cluster Analysis: Basic Concepts

◼ Partitioning Methods

◼ Hierarchical Methods

◼ Density-Based Methods

◼ Grid-Based Methods

◼ Evaluation of Clustering

◼ Summary
71
 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 highly skewed, H is close to 0
72
 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
73
 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
◼ (intracluster distance/ intercluster distance)
◼ Ex. Silhouette coefficient 74
 Practice Quiz

◼ Answer the following …

75
 Outlir

◼ https://www.analyticsvidhya.com/blog/2018/03/int
roduction-k-neighbours-algorithm-clustering/

◼ https://www.kaggle.com/code/kimchanyoung/sim
ple-anomaly-detection-using-unsupervised-knn

76