Hierarchical Clustering

Apes and Us

http://orangutan.org/orangutan-genome-part-1-the-quest-for-leakeys-ancestral-great-ape/
 The Tree of Life

http://pixgood.com/evolution-of-life-poster.html
 P450 protein superfamily

1600 sequences
http://www.whoi.edu/page.do?pid=75497&tid=441&cid=166573&ct=61&article=109489 16 species
 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 5
6

0.2 4
3 4
2
0.15 5
2
0.1

1
0.05 3 1

0
1 3 2 5 4 6

Tan, Steinbach, Kumar Chapter 8

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, 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

– 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
 Agglomerative Clustering Algorithm
• More popular hierarchical clustering technique
• 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
 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
 Intermediate Situation
• After some merging steps, we have some clusters
C1 C2 C3 C4 C5
C1
C2
C3 C3
C4 C4
C5
C1 Proximity Matrix

C2 C5

...
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 C2 C3 C4 C5
C1
C2
C3 C3
C4 C4
C5
C1 Proximity Matrix

C2 C5

...
p1 p2 p3 p4 p9 p10 p11 p12
 After Merging
• The question is “How do we update the proximity matrix?”
C2
U
C1 C3 C4
C5
C1 ?

C2 U C5 ? ? ? ?
C3
C3 ?
C4
C4 ?

Proximity Matrix
C1

C2 U C5

...
p1 p2 p3 p4 p9 p10 p11 p12
 How to Define Inter-Cluster Similarity

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
 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
 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
 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
 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
 Cluster Similarity: MIN or Single Link
• Similarity of two clusters is based on the two
most similar (closest) points in the different
clusters
– Determined by one pair of points, i.e., by one link
in the proximity graph.
 Hierarchical Clustering: MIN

5
1
3
5 0.2

2 1 0.15

2 3 6 0.1

0.05
4
4 0
3 6 2 5 4 1

Dendrogram
Nested Clusters

d(3,6)=0.11; d(5,2) = 0.14

D({3,6}, {2,5}) = min(d(3,2). d(3,5), d(6,5), d(6,5)) =d(2,3)= 0.15
 Strength of MIN

Original Points Two Clusters

• Can handle non-elliptical shapes

 Limitations of MIN

Original Points Two Clusters

• Sensitive to noise and outliers

 Cluster Similarity: MAX or Complete Linkage

• Similarity of two clusters is based on the two

least similar (most distant) points in the
different clusters
– Determined by all pairs of points in the two clusters
 Hierarchical Clustering: MAX

4 1
2 5 0.4

0.35
5
2 0.3

0.25

3 6 0.2

3 0.15
1 0.1

0.05
4
0
3 6 4 1 2 5

Nested Clusters Dendrogram

 Strength of MAX

Original Points Two Clusters

• Less susceptible to noise and outliers

 Limitations of MAX

Original Points Two Clusters

•Tends to break large clusters

•Biased towards globular clusters
 Cluster Similarity: Group Average
• Proximity of two clusters is the average of pairwise proximity
between points in the two clusters.
 proximity(p , p )
piClusteri
i j

p jClusterj
proximity(Clusteri , Clusterj ) 
|Clusteri ||Clusterj |

• Need to use average connectivity for scalability since total proximity

favors large clusters
Hierarchical Clustering: Group Average

5 4 1
2 0.25

5 0.2
2
0.15

3 6 0.1

1 0.05

4 0
3 3 6 4 1 2 5

Nested Clusters Dendrogram

Hierarchical Clustering: Group Average
• Compromise between Single and Complete
Link

• Strengths
– Less susceptible to noise and outliers

• Limitations
– Biased towards globular clusters
 Cluster Similarity: Ward’s Method
• Similarity of two clusters is based on the increase
in squared error when two clusters are merged
– Similar to group average if distance between points is
distance squared

• Less susceptible to noise and outliers

• Biased towards globular clusters
• Hierarchical analogue of K-means
– Can be used to initialize K-means
 Hierarchical Clustering: Comparison
5
1 4 1
3
2 5
5 5
2 1 2
MIN MAX
2 3 6 3 6
3
1
4 4
4

5
1 5 4 1
2 2
5 Ward’s Method 5
2 2
3 6 Group Average 3 6
3
4 1 1
4 4
3
 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
• 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
 Divisive Clustering
• Bisecting K-means algorithm
– Variant of K-means that can produce a partitional or a hierarchical
clustering
Bisecting k-means
Bisecting K-means Example
 Agglomerative vs Divisive
• Divisive clustering is more efficient if we do not generate a
complete hierarchy all the way down to individual data leaves.
– Time complexity of a naive agglomerative clustering is O(n3)
because we exhaustively scan the N x N matrix dist_mat for the
lowest distance in each of N-1 iterations.
– Using priority queue data structure we can reduce this complexity
to O(n2logn). By using some more optimizations it can be brought
down to O(n2).
– Whereas for divisive clustering given a fixed number of top levels,
using an efficient flat algorithm like K-Means, divisive algorithms
are linear in the number of patterns and clusters.
 Agglomerative vs Divisive
• Divisive algorithm is also more accurate.
– Agglomerative clustering makes decisions by
considering the local patterns or neighbor points
without initially taking into account the global
distribution of data.
– These early decisions cannot be undone. whereas
divisive clustering takes into consideration the global
distribution of data when making top-level partitioning
decisions.
 Competitive Learning
- An Online clustering algorithm
N 2

E   (mi ( j )  x j )
j 1

- mi(j) is the centroid closest to xj

- E is SSE

Finding mi by gradient descent:

mi   mi E

mi   mi E

mi ( j )   ( x j  mi ( j ) )
 Scale-based Clustering
• Clustering is done at a “scale”
• An answer to the question of “how many
clusters”
• Best clusters tend to live over the longest
range of scales
 Algorithm
• Start with a large number of clusters
• Initialize by selecting from data set
• Initialize “sigma” to a small value
• Update all centroids
• Eliminate duplicate centroids whenever there is a
merger
• Increase sigma by a constant factor
• If there are more than 1 unique centroid continue
update of centroids
• Stop only when a single unique centroid remains
Data set
 Clustering result:
Evolution of the centroids
Thank you