Data Mining
Cluster Analysis: Basic Concepts
and Algorithms
Lecture Notes for Chapter 7
Introduction to Data Mining
by
Tan, Steinbach, Kumar
11/16/2020 Introduction to Data Mining, 2nd Edition
Tan, Steinbach, Karpatne, Kumar
What is Cluster Analysis?
Finding groups of objects such that the objects in a group
will be similar (or related) to one another and different
from (or unrelated to) the objects in other groups
Inter-cluster
Intra-cluster distances are
distances are maximized
minimized
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Applications of Cluster Analysis
Discovered Clusters Industry Group
Understanding Applied-Matl-DOWN,Bay-Network-Down,3-COM-DOWN,
– Group related documents
1 Cabletron-Sys-DOWN,CISCO-DOWN,HP-DOWN,
DSC-Comm-DOWN,INTEL-DOWN,LSI-Logic-DOWN,
Micron-Tech-DOWN,Texas-Inst-Down,Tellabs-Inc-Down,
Technology1-DOWN
Natl-Semiconduct-DOWN,Oracl-DOWN,SGI-DOWN,
for browsing, group genes Sun-DOWN
Apple-Comp-DOWN,Autodesk-DOWN,DEC-DOWN,
and proteins that have 2 ADV-Micro-Device-DOWN,Andrew-Corp-DOWN,
Computer-Assoc-DOWN,Circuit-City-DOWN,
Compaq-DOWN, EMC-Corp-DOWN, Gen-Inst-DOWN,
Technology2-DOWN
similar functionality, or Motorola-DOWN,Microsoft-DOWN,Scientific-Atl-DOWN
Fannie-Mae-DOWN,Fed-Home-Loan-DOWN,
group stocks with similar 3 MBNA-Corp-DOWN,Morgan-Stanley-DOWN Financial-DOWN
price fluctuations Baker-Hughes-UP,Dresser-Inds-UP,Halliburton-HLD-UP,
4 Louisiana-Land-UP,Phillips-Petro-UP,Unocal-UP,
Schlumberger-UP
Oil-UP
Summarization
– Reduce the size of large
data sets
Clustering precipitation
in Australia
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Notion of a Cluster can be Ambiguous
How many clusters? Six Clusters
Two Clusters Four Clusters
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Types of Clusterings
A clustering is a set of clusters
Important distinction between hierarchical and
partitional sets of clusters
– Partitional Clustering
◆ A division of data objects into non-overlapping subsets (clusters) such that
each data object is in exactly one subset
– Hierarchical clustering
◆ A set of nested clusters organized as a hierarchical tree
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Partitional Clustering
Original Points A Partitional Clustering
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Hierarchical Clustering
p1
p3 p4
p2
p1 p2 p3 p4
Traditional Hierarchical Clustering Traditional Dendrogram
p1
p3 p4
p2
p1 p2 p3 p4
Non-traditional Hierarchical Clustering Non-traditional Dendrogram
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Other Distinctions Between Sets of Clusters
Exclusive versus non-exclusive
– In non-exclusive clustering, points may belong to multiple
clusters.
◆ Can belong to multiple classes or could be ‘border’ points
Fuzzy clustering (one type of non-exclusive)
– In fuzzy clustering, a point belongs to every cluster with some
weight between 0 and 1
– Weights must sum to 1
– Probabilistic clustering has similar characteristics
Partial versus complete
– In some cases, we only want to cluster some of the data
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Types of Clusters
Well-separated clusters
Prototype-based clusters
Contiguity-based clusters
Density-based clusters
Described by an Objective Function
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Types of Clusters: Well-Separated
Well-Separated Clusters:
– A cluster is a set of points such that any point in a cluster is
closer (or more similar) to every other point in the cluster than
to any point not in the cluster.
3 well-separated clusters
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Types of Clusters: Prototype-Based
Prototype-based
– A cluster is a set of objects such that an object in a cluster is
closer (more similar) to the prototype or “center” of a cluster,
than to the center of any other cluster
– The center of a cluster is often a centroid, the average of all
the points in the cluster, or a medoid, the most “representative”
point of a cluster
4 center-based clusters
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Types of Clusters: Contiguity-Based
Contiguous Cluster (Nearest neighbor or
Transitive)
– A cluster is a set of points such that a point in a cluster is
closer (or more similar) to one or more other points in the
cluster than to any point not in the cluster.
8 contiguous clusters
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Types of Clusters: Density-Based
Density-based
– A cluster is a dense region of points, which is separated by
low-density regions, from other regions of high density.
– Used when the clusters are irregular or intertwined, and when
noise and outliers are present.
6 density-based clusters
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Types of Clusters: Objective Function
Clusters Defined by an Objective Function
– Finds clusters that minimize or maximize an objective function.
– Enumerate all possible ways of dividing the points into clusters and
evaluate the `goodness' of each potential set of clusters by using
the given objective function.
– Can have global or local objectives.
◆ Hierarchical clustering algorithms typically have local objectives
◆ Partitional algorithms typically have global objectives
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Clustering Algorithms
K-means clustering
Hierarchical clustering
Density-based clustering
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K-means Clustering
Partitional clustering approach
Number of clusters, K, must be specified
Each cluster is associated with a centroid (center point)
Each point is assigned to the cluster with the closest
centroid
The basic algorithm is very simple
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Example of K-means Clustering
Iteration 6
1
2
3
4
5
3
2.5
1.5
y
0.5
-2 -1.5 -1 -0.5 0 0.5 1 1.5 2
x
Pre-processing and Post-processing
Pre-processing
– Normalize the data
– Eliminate outliers
Post-processing
– Eliminate empty clusters and small clusters that may
represent outliers
– Split ‘loose’ clusters
– Merge clusters that are ‘close’
– These steps can be used multiple times during the
clustering process
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Empty Clusters
K-means can yield empty clusters
6.8 13 18
X X X
6.5 9 10 15 16 18.5
7.75 12.5 17.25
X X X
6.5 9 10 15 16 18.5
Empty
Cluster
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Limitations of K-means
K-means has problems when clusters are of
differing
– Sizes
– Densities
– Non-globular shapes
K-means has problems when the data contains
outliers.
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Hierarchical Clustering
Produces a set of nested clusters organized as a
hierarchical tree
Can be visualized as a dendrogram
– A tree like diagram that records the sequences of
merges or splits
6 5
0.2
4
3 4
0.15 2
5
2
0.1
1
0.05
3 1
0
1 3 2 5 4 6
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Strengths of Hierarchical Clustering
Do not have to assume any particular number of
clusters
– Any desired number of clusters can be obtained by
‘cutting’ the dendrogram at the proper level
They may correspond to meaningful taxonomies
– Example in biological sciences (e.g., animal kingdom)
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Hierarchical Clustering
Two main types of hierarchical clustering
– Agglomerative:
◆ Start with the points as individual clusters
◆ At each step, merge the closest pair of clusters until only one cluster
(or k clusters) left
– Divisive:
◆ Start with one, all-inclusive cluster
◆ At each step, split a cluster until each cluster contains an individual
point (or there are k clusters)
Traditional hierarchical algorithms use a similarity or
distance matrix
– Merge or split one cluster at a time
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Agglomerative Clustering Algorithm
Most popular hierarchical clustering technique
– Key Idea: Successively merge closest clusters
Basic algorithm is straightforward
1. Compute the proximity matrix
2. Let each data point be a cluster
3. Repeat
4. Merge the two closest clusters
5. Update the proximity matrix
6. Until only a single cluster remains
Key operation is the computation of the proximity of
two clusters
– Different approaches to defining the distance between
clusters distinguish the different algorithms
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Starting Situation
Start with clusters of individual points and a
proximity matrix p1 p2 p3 p4 p5 ...
p1
p2
p3
p4
p5
.
.
. Proximity Matrix
...
p1 p2 p3 p4 p9 p10 p11 p12
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Intermediate Situation
After some merging steps, we have some clusters
C1 C2 C3 C4 C5
C1
C2
C3
C3
C4
C4
C5
Proximity Matrix
C1
C2 C5
...
p1 p2 p3 p4 p9 p10 p11 p12
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Intermediate Situation
We want to merge the two closest clusters (C2 and C5) and
update the proximity matrix. C1 C2 C3 C4 C5
C1
C2
C3
C3
C4
C4
C5
Proximity Matrix
C1
C2 C5
...
p1 p2 p3 p4 p9 p10 p11 p12
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After Merging
The question is “How do we update the proximity matrix?”
C2
U
C1 C5 C3 C4
C1 ?
C2 U C5 ? ? ? ?
C3
C3 ?
C4
C4 ?
Proximity Matrix
C1
C2 U C5
...
p1 p2 p3 p4 p9 p10 p11 p12
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How to Define Inter-Cluster Distance
p1 p2 p3 p4 p5 ...
p1
Similarity?
p2
p3
p4
p5
MIN
.
MAX
.
Group Average .
Proximity Matrix
Distance Between Centroids
Other methods driven by an objective
function
– Ward’s Method uses squared error
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How to Define Inter-Cluster Similarity
p1 p2 p3 p4 p5 ...
p1
p2
p3
p4
p5
MIN
.
MAX
.
Group Average .
Proximity Matrix
Distance Between Centroids
Other methods driven by an objective
function
– Ward’s Method uses squared error
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How to Define Inter-Cluster Similarity
p1 p2 p3 p4 p5 ...
p1
p2
p3
p4
p5
MIN
.
MAX
.
Group Average .
Proximity Matrix
Distance Between Centroids
Other methods driven by an objective
function
– Ward’s Method uses squared error
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How to Define Inter-Cluster Similarity
p1 p2 p3 p4 p5 ...
p1
p2
p3
p4
p5
MIN
.
MAX
.
Group Average .
Proximity Matrix
Distance Between Centroids
Other methods driven by an objective
function
– Ward’s Method uses squared error
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How to Define Inter-Cluster Similarity
p1 p2 p3 p4 p5 ...
p1
p2
p3
p4
p5
MIN
.
MAX
.
Group Average .
Proximity Matrix
Distance Between Centroids
Other methods driven by an objective
function
– Ward’s Method uses squared error
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Density Based Clustering
Clusters are regions of high density that are
separated from one another by regions on low
density.
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DBSCAN
DBSCAN is a density-based algorithm.
– Density = number of points within a specified radius (Eps)
– A point is a core point if it has at least a specified number of
points (MinPts) within Eps
◆ These are points that are at the interior of a cluster
◆ Counts the point itself
– A border point is not a core point, but is in the neighborhood
of a core point
– A noise point is any point that is not a core point or a border
point
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DBSCAN: Core, Border, and Noise Points
MinPts = 7
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DBSCAN: Core, Border and Noise Points
Original Points Point types: core,
border and noise
Eps = 10, MinPts = 4
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