Clustering CIS 601 Fall 2004 Longin Jan Latecki Lecture slides taken/modified from: Jiawei Han (...

Clustering

CIS 601 Fall 2004

Longin Jan Latecki

Lecture slides taken/modified from:Jiawei Han (http://www-sal.cs.uiuc.edu/~hanj/DM_Book.html)

Vipin Kumar (http://www-users.cs.umn.edu/~kumar/csci5980/index.html)

http://www-users.cs.umn.edu/~kumar/csci5980/index.html

Clustering

• Cluster: a collection of data objects– Similar to one another within the same cluster– Dissimilar to the objects in other clusters

• Cluster analysis– Grouping a set of data objects into clusters

• Clustering is unsupervised classification: no predefined classes

• Typical applications– to get insight into data – as a preprocessing step– we will use it for image segmentation

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 distances are maximized

Intra-cluster distances are

minimized

Notion of a Cluster can be Ambiguous

How many clusters?

Four Clusters Two Clusters

Six Clusters

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

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

Euclidean Density – Cell-based

• Simplest approach is to divide region into a number of rectangular cells of equal volume and define density as # of points the cell contains

Euclidean Density – Center-based

• Euclidean density is the number of points within a specified radius of the point

Data Structures in Clustering

• Data matrix– (two modes)

• Dissimilarity matrix– (one mode)

npx...nfx...n1x

...............ipx...ifx...i1x

...............1px...1fx...11x

0...)2,()1,(

:::

)2,3()

...ndnd

0dd(3,1

0d(2,1)

0

Interval-valued variables

• Standardize data

– Calculate the mean squared deviation:

where

– Calculate the standardized measurement (z-score)

• Using mean absolute deviation could be more robust

than using standard deviation

.)...21

1nffff

xx(xn m

)2||...2||2|(|121 fnffffff

mxmxmxns

f

fifif s

mx z

• Euclidean distance:

– Properties

• d(i,j) 0

• d(i,j) = 0 iff i=j

• d(i,j) = d(j,i)

• d(i,j) d(i,k) + d(k,j)

• Also one can use weighted distance, parametric Pearson product moment correlation, or other disimilarity measures.

)||...|||(|),( 22

22

2

11 pp jx

ix

jx

ix

jx

ixjid

Similarity and Dissimilarity Between Objects

The set of 5 observations, measuring 3 variables, can be described by its mean vector and covariance matrix. The three variables, from left to right are length, width, and height of a certain object, for example.Each row vector Xrow is another observation

of the three variables (or components) for row=1, …, 5.

Covariance Matrix

The mean vector consists of the means of each variable. The covariance matrix consists of the variances of the variables along the main diagonal and the covariances between each pair of variables in the other matrix positions.

0.025 is the variance of the length variable, 0.0075 is the covariance between the length and the width variables, 0.00175 is the covariance between the length and the height variables, 0.007 is the variance of the width variable.

where n = 5 for this example

n

row

krowkjrowjjk

n

rowrowrow

xXxXn

s

xXxXn

XXn

S

1

1

))((1

1

)')((1

1'

1

1

Mahalanobis Distance

Tqpqpqpsmahalanobi )()(),( 1

For red points, the Euclidean distance is 14.7, Mahalanobis distance is 6.

is the covariance matrix of the input data X

n

i

kikjijkj XXXXn 1

, ))((1

1

Mahalanobis Distance

Covariance Matrix:

3.02.0

2.03.0

B

A

C

A: (0.5, 0.5)

B: (0, 1)

C: (1.5, 1.5)

Mahal(A,B) = 5

Mahal(A,C) = 4

Cosine Similarity

• If x1 and x2 are two document vectors, then

cos( x1, x2 ) = (x1 x2) / ||x1|| ||x2|| , where indicates vector dot product and || d || is the length of vector d.

• Example:

x1 = 3 2 0 5 0 0 0 2 0 0

x2 = 1 0 0 0 0 0 0 1 0 2

x1 x2= 3*1 + 2*0 + 0*0 + 5*0 + 0*0 + 0*0 + 0*0 + 2*1 + 0*0 + 0*2 = 5

||x1|| = (3*3+2*2+0*0+5*5+0*0+0*0+0*0+2*2+0*0+0*0)0.5 = (42) 0.5 = 6.481

||x2|| = (1*1+0*0+0*0+0*0+0*0+0*0+0*0+1*1+0*0+2*2) 0.5 = (6) 0.5 = 2.245

cos( x1, x2 ) = .3150

Correlation• Correlation measures the linear

relationship between objects

• To compute correlation, we standardize data objects, p and q, and then take their dot product

)(/))(( pstdpmeanpp kk

)(/))(( qstdqmeanqq kk

qpqpncorrelatio ),(

Visually Evaluating Correlation

Scatter plots showing the similarity from –1 to 1.

K-means Clustering

• Partitional clustering approach • Each cluster is associated with a centroid (center point) • Each point is assigned to the cluster with the closest centroid• Number of clusters, K, must be specified• The basic algorithm is very simple

k-means Clustering

• An algorithm for partitioning (or clustering) N data points into K disjoint subsets Sj containing Nj data points so as to minimize the sum-of-squares criterion

2

1

|| j

K

j Snn

j

xJ

where xn is a vector representing the nth data point and j is

the geometric centroid of the data points in SSjj

K-means Clustering – Details• Initial centroids are often chosen randomly.

– Clusters produced vary from one run to another.

• The centroid is (typically) the mean of the points in the cluster.• ‘Closeness’ is measured by Euclidean distance, cosine similarity, correlation, etc.• K-means will converge for common distance functions.• Most of the convergence happens in the first few iterations.

– Often the stopping condition is changed to ‘Until relatively few points change clusters’

• Complexity is O( n * K * I * d )– n = number of points, K = number of clusters,

I = number of iterations, d = number of attributes

Two different K-means Clusterings

-2 -1.5 -1 -0.5 0 0.5 1 1.5 2

0

0.5

1

1.5

2

2.5

3

x

y

-2 -1.5 -1 -0.5 0 0.5 1 1.5 2

0

0.5

1

1.5

2

2.5

3

x

y

Sub-optimal Clustering

-2 -1.5 -1 -0.5 0 0.5 1 1.5 2

0

0.5

1

1.5

2

2.5

3

x

y

Optimal Clustering

Original Points

• Importance of choosing initial centroids

Evaluating K-means Clusters

• Most common measure is Sum of Squared Error (SSE)– For each point, the error is the distance to the nearest cluster– To get SSE, we square these errors and sum them.

– x is a data point in cluster Ci and mi is the representative point for cluster Ci

• can show that mi corresponds to the center (mean) of the cluster

– Given two clusters, we can choose the one with the smallest error– One easy way to reduce SSE is to increase K, the number of

clusters• A good clustering with smaller K can have a lower SSE than a poor

clustering with higher K

K

i Cxi

i

xmdistSSE1

2 ),(

Solutions to Initial Centroids Problem

• Multiple runs– Helps, but probability is not on your side

• Sample and use hierarchical clustering to determine initial centroids

• Select more than k initial centroids and then select among these initial centroids– Select most widely separated

• Postprocessing• Bisecting K-means

– Not as susceptible to initialization issues

Basic K-means algorithm can yield empty clusters

Handling Empty Clusters

Pre-processing and Post-processing

• Pre-processing– Normalize the data– Eliminate outliers

• Post-processing– Eliminate small clusters that may represent outliers– Split ‘loose’ clusters, i.e., clusters with relatively high

SSE– Merge clusters that are ‘close’ and that have relatively

low SSE

Bisecting K-means

• Bisecting K-means algorithm– Variant of K-means that can produce a partitional or a hierarchical clustering

Bisecting K-means Example

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.

Limitations of K-means: Differing Sizes

Original Points K-means (3 Clusters)

Limitations of K-means: Differing Density


Limitations of K-means: Non-globular Shapes


Overcoming K-means Limitations

Original Points K-means Clusters

One solution is to use many clusters.Find parts of clusters, but need to put together.

Overcoming K-means Limitations

Original Points K-means Clusters

Variations of the K-Means Method

• A few 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 (Huang’98)– 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

• Handling a mixture of categorical and numerical data: k-prototype method

The K-Medoids Clustering Method

• Find representative objects, called medoids, in clusters

• PAM (Partitioning Around Medoids, 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

• CLARA (Kaufmann & Rousseeuw, 1990)– draws multiple samples of the data set, applies PAM on each

sample, and gives the best clustering as the output

• CLARANS (Ng & Han, 1994): Randomized sampling

• Focusing + spatial data structure (Ester et al., 1995)

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

1 3 2 5 4 60

0.05

0.1

0.15

0.2

1

2

3

4

5

6

1

23 4

5

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 dendogram at the proper level

• They may correspond to meaningful taxonomies– Example in biological sciences (e.g., animal kingdom,

phylogeny reconstruction, …)

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

Matlab: Statistics Toolbox: clusterdata,

which performs all these steps: pdist, linkage, cluster

– Divisive: • Start with one, all-inclusive cluster

• At each step, split a cluster until each cluster contains a point (or there are k clusters)

• Traditional hierarchical algorithms use a similarity or distance matrix– Merge or split one cluster at a time– Image segmentation mostly uses simultaneous merge/split

Agglomerative Clustering Algorithm

• More popular hierarchical clustering technique

• Basic algorithm is straightforward1. Compute the proximity matrix2. Let each data point be a cluster3. Repeat4. Merge the two closest clusters5. Update the proximity matrix6. 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

Starting Situation

• Start with clusters of individual points and a proximity matrix

p1

p3

p5

p4

p2

p1 p2 p3 p4 p5 . . .

.

.

. Proximity Matrix

...p1 p2 p3 p4 p9 p10 p11 p12

Intermediate Situation

• After some merging steps, we have some clusters

C1

C4

C2 C5

C3

C2C1

C1

C3

C5

C4

C2

C3 C4 C5

Proximity Matrix

...p1 p2 p3 p4 p9 p10 p11 p12

Intermediate Situation

• We want to merge the two closest clusters (C2 and C5) and update the proximity matrix.

C1

C4

C2 C5

C3

C2C1

C1

C3

C5

C4

C2

C3 C4 C5

Proximity Matrix

...p1 p2 p3 p4 p9 p10 p11 p12

After Merging• The question is “How do we update the proximity matrix?”

C1

C4

C2 U C5

C3? ? ? ?

?

?

?

C2 U C5C1

C1

C3

C4

C2 U C5

C3 C4

Proximity Matrix

...p1 p2 p3 p4 p9 p10 p11 p12

How to Define Inter-Cluster Similarity

p1

p3

p5

p4

p2

p1 p2 p3 p4 p5 . . .

.

.

.

Similarity?

• MIN• MAX• Group Average• Distance Between Centroids• Other methods driven by an

objective function– Ward’s Method uses squared error

Proximity Matrix

How to Define Inter-Cluster Similarity

p1

p3

p5

p4

p2

p1 p2 p3 p4 p5 . . .

.

.

.Proximity Matrix

• MIN• MAX• Group Average• Distance Between Centroids• Other methods driven by an

objective function– Ward’s Method uses squared error

Hierarchical Clustering: Comparison

Group Average

Ward’s Method

1

2

3

4

5

61

2

5

3

4

MIN MAX

1

2

3

4

5

61

2

5

34

1

2

3

4

5

61

2 5

3

41

2

3

4

5

6

12

3

4

5

Hierarchical Clustering: Time and Space requirements

• O(N2) space since it uses the proximity matrix. – N is the number of points.

• O(N3) time in many cases– There are N steps and at each step the size, N2,

proximity matrix must be updated and searched– Complexity can be reduced to O(N2 log(N) ) time for

some approaches

Hierarchical Clustering: Problems and Limitations

• Once a decision is made to combine two clusters, it cannot be undone

Therefore, we use merge/split to segment images!

• No objective function is directly minimized• Different schemes have problems with one or

more of the following:– Sensitivity to noise and outliers– Difficulty handling different sized clusters and convex

shapes– Breaking large clusters

MST: Divisive Hierarchical Clustering

• Build MST (Minimum Spanning Tree)– Start with a tree that consists of any point– In successive steps, look for the closest pair of points (p, q)

such that one point (p) is in the current tree but the other (q) is not

– Add q to the tree and put an edge between p and q

MST: Divisive Hierarchical Clustering

• Use MST for constructing hierarchy of clusters

More on Hierarchical Clustering Methods

• Major weakness of agglomerative clustering methods– do not scale well: time complexity of at least O(n2), where n is the

number of total objects– can never undo what was done previously

• Integration of hierarchical with distance-based clustering– BIRCH (1996): uses CF-tree and incrementally adjusts the quality

of sub-clusters– CURE (1998): selects well-scattered points from the cluster and

then shrinks them towards the center of the cluster by a specified fraction

– CHAMELEON (1999): hierarchical clustering using dynamic modeling

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)

Graph-Based Clustering

• Graph-Based clustering uses the proximity graph– Start with the proximity matrix– Consider each point as a node in a graph– Each edge between two nodes has a weight which is

the proximity between the two points– Initially the proximity graph is fully connected – MIN (single-link) and MAX (complete-link) can be

viewed as starting with this graph

• In the simplest case, clusters are connected components in the graph.

Graph-Based Clustering: Sparsification

• Clustering may work better– Sparsification techniques keep the connections to the most

similar (nearest) neighbors of a point while breaking the connections to less similar points.

– The nearest neighbors of a point tend to belong to the same class as the point itself.

– This reduces the impact of noise and outliers and sharpens the distinction between clusters.

• Sparsification facilitates the use of graph partitioning algorithms (or algorithms based on graph partitioning algorithms.

– Chameleon and Hypergraph-based Clustering

Sparsification in the Clustering Process

Cluster Validity

• For supervised classification we have a variety of measures to evaluate how good our model is– Accuracy, precision, recall

• For cluster analysis, the analogous question is how to evaluate the “goodness” of the resulting clusters?

• Then why do we want to evaluate them?– To avoid finding patterns in noise– To compare clustering algorithms– To compare two sets of clusters– To compare two clusters

Clusters found in Random Data

0 0.2 0.4 0.6 0.8 10

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

x

y

Random Points

0 0.2 0.4 0.6 0.8 10

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

x

y

K-means

0 0.2 0.4 0.6 0.8 10

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

x

y

DBSCAN

0 0.2 0.4 0.6 0.8 10

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0.9

1

x

y

Complete Link

• Numerical measures that are applied to judge various aspects of cluster validity, are classified into the following three types.– External Index: Used to measure the extent to which cluster labels

match externally supplied class labels.• Entropy

– Internal Index: Used to measure the goodness of a clustering structure without respect to external information.

• Sum of Squared Error (SSE)

– Relative Index: Used to compare two different clusterings or clusters.

• Often an external or internal index is used for this function, e.g., SSE or entropy

• Sometimes these are referred to as criteria instead of indices– However, sometimes criterion is the general strategy and index is the

numerical measure that implements the criterion.

Measures of Cluster Validity

• Cluster Cohesion: Measures how closely related are objects in a cluster– Example: SSE

• Cluster Separation: Measure how distinct or well-separated a cluster is from other clusters

• Example: Squared Error– Cohesion is measured by the within cluster sum of squares (SSE)

– Separation is measured by the between cluster sum of squares

• Where |Ci| is the size of cluster i

Internal Measures: Cohesion and Separation

i Cx

ii

mxWSS 2)(

i

ii mmCBSS 2)(


• Example:

1 2 3 4 5 m1 m2

m

1091

9)35.4(2)5.13(2

1)5.45()5.44()5.12()5.11(22

2222

Total

BSS

WSSK=2 clusters:

10010

0)33(4

10)35()34()32()31(2

2222

Total

BSS

WSSK=1 cluster:

• A proximity graph based approach can also be used for cohesion and separation.– Cluster cohesion is the sum of the weight of all links within a

cluster.– Cluster separation is the sum of the weights between nodes in the

cluster and nodes outside the cluster.


cohesion separation

Clustering CIS 601 Fall 2004 Longin Jan Latecki Lecture slides taken/modified from: Jiawei Han (...

Documents

Transcript of Clustering CIS 601 Fall 2004 Longin Jan Latecki Lecture slides taken/modified from: Jiawei Han (...