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Uses of cluster analysis Clustering methods Hierarchical Partitioned Additive trees Cluster distance metrics. Chinese wolf. Cuon. Dingo. Pre-dog. Modern dog. Golden jackal. 0. 1. 2. 3. 4. Distance. Lecture 10: Cluster analysis.

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lecture 10 cluster analysis
Uses of cluster analysis

Clustering methods

Hierarchical

Partitioned

Additive trees

Cluster distance metrics

Chinese wolf

Cuon

Dingo

Pre-dog

Modern dog

Golden jackal

0

1

2

3

4

Distance

Lecture 10: Cluster analysis

Bio 8102A Applied Multivariate Biostatistics

cluster analysis i grouping objects
Given a set of p variables X1, X2,…, Xp, and a set of N objects, the task is to group the objects into classes so that objects within classes are more similar to one another than to members of other classes.

Questions of interest: does the set of objects fall into a smaller set of “natural” groups? What are the relationships among different objects?

Note: in most cases, clusters are not defined a priori.

Cluster analysis I: grouping objects

Bio 8102A Applied Multivariate Biostatistics

cluster analysis ii grouping variables
Given a set of p variables X1, X2,…, Xp, and a set of N objects, the task is to group the variables into classes so that variables within classes are more highly correlated with one another than to members of other classes.

Questions of interest: does the set of variables fall into a smaller set of “natural” groups? What are the relationships among different variables?

Cluster analysis II: grouping variables

Bio 8102A Applied Multivariate Biostatistics

cluster analysis iii grouping objects and variables
Given a set of p variables X1, X2,…, Xp, and a set of N objects, the task is to group the objects andvariables into classes so that variables and objects within classes are more highly correlated with/more similar to one another than to members of other classes.

Questions of interest: does the set of variables/objects combinations fall into a smaller set of “natural” groups? What are the relationships among the different combinations?

Cluster analysis III: grouping objects and variables

Bio 8102A Applied Multivariate Biostatistics

the basic principle
The basic principle
  • Objects that are similar to/highly correlated with one another should be in the same group, whereas objects that are dissimilar/uncorrelated should be in different groups.
  • Thus, all cluster analyses begin with measures of similarity/dissimilarity among objects (distance matrices) or correlation matrices.

Bio 8102A Applied Multivariate Biostatistics

clustering objects
Clustering objects
  • Objects that are closer together based on pairwise multivariate distances or pairwise correlations are assigned to the same cluster, whereas those farther apart or having low pairwise correlations are assigned to different clusters.

Bio 8102A Applied Multivariate Biostatistics

clustering variables
Clustering variables
  • Variables that have high pairwise correlations are assigned to the same cluster, whereas those having low pairwise correlations are assigned to different clusters.

Bio 8102A Applied Multivariate Biostatistics

clustering objects and variables
Clustering objects and variables
  • Object/variable combinations are classified into discrete categories determined by the magnitude of the corresponding entries in the original data matrix
  • Allows for easier visualization of object/variable combinations.

Bio 8102A Applied Multivariate Biostatistics

types of clusters
Types of clusters
  • Exclusive: each object/variable belongs to one and only one cluster.
  • Overlapping: an object or variable may belong to more than one cluster.

Exclusive

clusters

Overlapping

clusters

Bio 8102A Applied Multivariate Biostatistics

scale considerations
Scale considerations
  • In general, correlation measures are not influenced by differences in scale, but distance measures (e.g. Euclidean distance) are affected.
  • So, use distance measures when variables are measured on common scales, or compute distance measures based on standardized values when variables are not on the same scale.

Bio 8102A Applied Multivariate Biostatistics

exclusive clustering methods i hierarchical clustering of objects

Chinese wolf

Cuon

Dingo

Pre-dog

Modern dog

Golden jackal

0

1

2

3

4

Distance

Exclusive clustering methods I. Hierarchical clustering of objects
  • Begins with calculation of distances / correlations among all pairs of objects…
  • … with groups being formed by agglomeration (lumping of objects)
  • The end result is a dendogram (tree) which shows the distances between pairs of objects.

Bio 8102A Applied Multivariate Biostatistics

exclusive clustering methods i hierarchical clustering of variables
Exclusive clustering methods I. Hierarchical clustering of variables
  • Begins with calculation of correlations/distances between all pairs of variables…
  • … with groups being formed lumping of highly correlated variables.
  • The end result is a dendogram or tree which shows the distances between pairs of variables.

MOLARBR

MANDBRTH

MOLARL

MANDHT

MOLARS

MOLARS2

0

5

10

15

Distance

Bio 8102A Applied Multivariate Biostatistics

hierarchical clustering of objects and variables
Hierarchical clustering of objects and variables
  • Standardized data matrix is used to produce a two-dimensional colour/shading graph with colour codes/shading intensities determined by the magnitude of the values in the original data matrix…
  • …which allows one to pick out “similar” objects and variables at a glance.

Bio 8102A Applied Multivariate Biostatistics

hierarchical joining algorithms
Single (nearest-neighbour): distance between two clusters = distance between two closest members of the two clusters.

Complete (furthest neighbour): distance between two clusters = distance between two most distant cluster members.

Centroid : distance between two clusters = distance between multivariate means of each cluster.

Hierarchical joining algorithms

Centroid

Cluster 1

Single

Cluster 2

Cluster 3

Complete

Bio 8102A Applied Multivariate Biostatistics

hierarchical joining algorithms cont d
Average: distance between two clusters = average distance between all members of the two clusters.

Median: distance between two clusters = median distance between all members of the two clusters.

Ward: distance between two clusters = average distance between all members of the two clusters with adjustment for covariances.

Hierarchical joining algorithms (cont’d)

Cluster 1

Cluster 2

Cluster 3

Mean/median/adjusted mean

of all pairwise distances

Bio 8102A Applied Multivariate Biostatistics

simple joining nearest neighbour
Simple joining (nearest neighbour)

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

complete joining furthest neighbour
Complete joining (furthest neighbour)

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

average joining
Average joining

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

median joining
Median joining

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

centroid joining
Centroid joining

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

ward joining
Ward joining

Distance matrix

Bio 8102A Applied Multivariate Biostatistics

important note

1

2

3

4

5

1

2

3

?

4

5

Important note!
  • Centroid, average, median and Ward joining need not produce a strictly hierarchical tree with increasing lumping distances, resulting in “unattached” branches.
  • If you encounter this problem, try another method!

Cluster Tree

Bio 8102A Applied Multivariate Biostatistics

exclusive hierarchical clustering ii partitioned clustering
Exclusive hierarchical clustering II. Partitioned clustering
  • In partitioned clustering, the object is to partition a set of N objects into a number kpredetermined clusters by maximizing the distance between cluster centers while minimizing the within-cluster variation.

Bio 8102A Applied Multivariate Biostatistics

partitioned clustering the procedure

Objects

Seeds

Object

center

Partitioned clustering: the procedure

X1

  • Choose k “seed” cases which are spread apart from center of all objects as much as possible.
  • Assign all remaining objects to nearest seed.
  • Reassign objects so that within-group sum of squares is reduced…
  • …and continue to do so until SSwithin is minimized.

Seed 1

Seed 2

Seed 3

X2

Bio 8102A Applied Multivariate Biostatistics

k means clustering
K-means clustering
  • Because k-means clustering does not search though every possible partitioning, it is always possible that there are other solutions yielding smaller SSwithin.
  • A method of partitioned clustering whereby a set of k clusters is produced by minimizing the SSwithin based on Euclidean distances.
  • This is very much like a single-classification MANOVA with k groups, except that groups are not known a priori.

Bio 8102A Applied Multivariate Biostatistics

k means partitioning example
K-means partitioning: example

k =2 clustering of 6 dog species

  • Cluster profile plots give z-scores for each variable used in clustering objects, with variables ordered by univariate F ratios
  • Zero indicates mean of all objects.
  • The more similar the profiles for objects within a cluster, the smaller the within-cluster heterogeneity.

Bio 8102A Applied Multivariate Biostatistics

k means partitioning example1
K-means partitioning: example

k =2 clustering of 6 dog species

  • Cluster means plots give means for each variable used in clustering objects, with variables ordered by univariate F ratios
  • Dashed indicates mean of all objects .
  • The greater the difference in group means, the greater the discriminating ability of the variable in question

Bio 8102A Applied Multivariate Biostatistics

some clustering distances
Some clustering distances

Bio 8102A Applied Multivariate Biostatistics

exclusive non hierarchical clustering additive trees
Exclusive non-hierarchical clustering : Additive trees
  • In additive trees clustering, the objective is to partition a set of N objects into a set of clusters represented by additive rather than hierarchical trees.
  • For hierarchical trees, we assume: (1) all within-cluster distances are smaller than between cluster distances; (2) all within-cluster distances are the same. For additive trees, neither assumption need hold.

Bio 8102A Applied Multivariate Biostatistics

additive trees

1

2

3

4

5

Additive trees
  • In additive tree clustering, branch length can vary within clusters…
  • … and objects within clusters are compared by considering the sum of the branch lengths connecting them

Hierarchical tree

1

2

3

4

5

Additive tree

Bio 8102A Applied Multivariate Biostatistics

additive trees joining
Additive trees joining

5

Distance matrix

7

4

3

9

2

8

6

1

D1,3 = 1.5 + 4.0 + 0.5 = 6.0

Bio 8102A Applied Multivariate Biostatistics

deciding what to cluster and how to cluster them
Deciding what to cluster and how to cluster them

Bio 8102A Applied Multivariate Biostatistics