Data Mining: Concepts and techniques: Chapter 11,Review: Basic Cluster Analysis Methods 11 clusadvanced

1
Data Mining:
Concepts and Techniques
(3rd ed.)
— Chapter 11 —
Jiawei Han, Micheline Kamber, and Jian Pei
University of Illinois at Urbana-Champaign &
Simon Fraser University
©2012 Han, Kamber & Pei. All rights reserved.

September 14, 2014 Data Mining: Concepts and Techniques 2

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Review: Basic Cluster Analysis Methods (Chap.
10)
 Cluster Analysis: Basic Concepts
 Group data so that object similarity is high within clusters but low
across clusters
 Partitioning Methods
 K-means and k-medoids algorithms and their refinements
 Hierarchical Methods
 Agglomerative and divisive method, Birch, Cameleon
 Density-Based Methods
 DBScan, Optics and DenCLu
 Grid-Based Methods
 STING and CLIQUE (subspace clustering)
 Evaluation of Clustering
 Assess clustering tendency, determine # of clusters, and measure
clustering quality

K-Means Clustering
K=2
Arbitrarily
partition
objects into
k groups
Update the
cluster
centroids
Loop if Reassign objects
needed
Update the
cluster
centroids
4
The initial data set
 Partition objects into k nonempty
subsets
 Repeat
 Compute centroid (i.e., mean
point) for each partition
 Assign each object to the
cluster of its nearest centroid
 Until no change

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
a
b
c
d
e
a b
d e
a b c d e
c d e
Step 4 Step 3 Step 2 Step 1 Step 0
agglomerative
(AGNES)
divisive
(DIANA)
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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
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BIRCH and the Clustering Feature
(CF) Tree Structure
CF1
child1
CF3
child3
CF2
child2
CF6
child6
Root
CF1
child1
CF3
child3
CF2
child2
CF5
child5
10
9
8
7
6
5
4
3
2
1
prev CFCFCFnext CFCFCF1 2 6
1 2 4
prev next
B = 7
L = 6
Non-leaf node
Leaf node Leaf node
7
0
0 1 2 3 4 5 6 7 8 9 10
CF = (5,
(16,30),(54,190))
(3,4)
(2,6)
(4,5)
(4,7)
(3,8)

Overall Framework of CHAMELEON
Construct (K-NN)
Sparse Graph Partition the Graph
Merge Partition
Final Clusters
Data Set
K-NN Graph
P and q are connected if
q is among the top k
closest neighbors of p
Relative interconnectivity:
connectivity of c1 and c2
over internal connectivity
Relative closeness:
closeness of c1 and c2 over
internal closeness
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Density-Based Clustering: DBSCAN
 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:
|NEps (q)| ≥ MinPts
MinPts = 5
Eps = 1 cm
p
q
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10
Density-Based Clustering: OPTICS & Its Applications

DENCLU: Center-Defined and Arbitrary
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STING: A Statistical Information Grid Approach
 Wang, Yang and Muntz (VLDB’97)
 The spatial area is divided into rectangular cells
 There are several levels of cells corresponding to different
levels of resolution
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Evaluation of Clustering Quality
 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
 Determine the Number of Clusters
 Empirical method: # of clusters ≈√n/2
 Elbow method: Use the turning point in the curve of sum of within
cluster variance w.r.t # of clusters
 Cross validation method
 Measuring Clustering Quality
 Extrinsic: supervised
 Compare a clustering against the ground truth using certain
clustering quality measure
 Intrinsic: unsupervised
 Evaluate the goodness of a clustering by considering how well
the clusters are separated, and how compact the clusters are
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Outline of Advanced Clustering Analysis
 Probability Model-Based Clustering
 Each object may take a probability to belong to a cluster
 Clustering High-Dimensional Data
 Curse of dimensionality: Difficulty of distance measure in high-D
space
 Clustering Graphs and Network Data
 Similarity measurement and clustering methods for graph and
networks
 Clustering with Constraints
 Cluster analysis under different kinds of constraints, e.g., that raised
from background knowledge or spatial distribution of the objects

Chapter 11. Cluster Analysis: Advanced Methods
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 Summary

Fuzzy Set and Fuzzy Cluster
 Clustering methods discussed so far
 Every data object is assigned to exactly one cluster
 Some applications may need for fuzzy or soft cluster assignment
 Ex. An e-game could belong to both entertainment and software
 Methods: fuzzy clusters and probabilistic model-based clusters
 Fuzzy cluster: A fuzzy set S: FS : X → [0, 1] (value between 0 and 1)
 Example: Popularity of cameras is defined as a fuzzy mapping
 Then, A(0.05), B(1), C(0.86), D(0.27)
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Fuzzy (Soft) Clustering
 Example: Let cluster features be
 C1 :“digital camera” and “lens”
 C2: “computer“
 Fuzzy clustering
 k fuzzy clusters C1, …,Ck ,represented as a partition matrix M = [wij]
 P1: for each object oi and cluster Cj, 0 ≤ wij ≤ 1 (fuzzy set)
 P2: for each object oi, , equal participation in the clustering
 P3: for each cluster Cj , ensures there is no empty cluster
 Let c1, …, ck as the center of the k clusters
 For an object oi, sum of the squared error (SSE), p is a parameter:
 For a cluster Ci, SSE:
 Measure how well a clustering fits the data:
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Probabilistic Model-Based Clustering
 Cluster analysis is to find hidden categories.
 A hidden category (i.e., probabilistic cluster) is a distribution over the
data space, which can be mathematically represented using a
probability density function (or distribution function).
 Ex. 2 categories for digital cameras sold
 consumer line vs. professional line
 density functions f1, f2 for C1, C2
 obtained by probabilistic clustering
 A mixture model assumes that a set of observed objects is a mixture
of instances from multiple probabilistic clusters, and conceptually
each observed object is generated independently
 Out task: infer a set of k probabilistic clusters that is mostly likely to
generate D using the above data generation process
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Model-Based Clustering
 A set C of k probabilistic clusters C1, …,Ck with probability density
functions f1, …, fk, respectively, and their probabilities ω1, …, ωk.
 Probability of an object o generated by cluster Cj is
 Probability of o generated by the set of cluster C is
 Since objects are assumed to be generated
independently, for a data set D = {o1, …, on}, we have,
 Task: Find a set C of k probabilistic clusters s.t. P(D|C) is maximized
 However, maximizing P(D|C) is often intractable since the probability
density function of a cluster can take an arbitrarily complicated form
 To make it computationally feasible (as a compromise), assume the
probability density functions being some parameterized distributions

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Univariate Gaussian Mixture Model
 O = {o1, …, on} (n observed objects), Θ = {θ1, …, θk} (parameters of the
k distributions), and Pj(oi| θj) is the probability that oi is generated from
the j-th distribution using parameter θj, we have
 Univariate Gaussian mixture model
 Assume the probability density function of each cluster follows a 1-
d Gaussian distribution. Suppose that there are k clusters.
 The probability density function of each cluster are centered at μj
with standard deviation σj, θj, = (μj, σj), we have

The EM (Expectation Maximization) Algorithm
 The k-means algorithm has two steps at each iteration:
 Expectation Step (E-step): Given the current cluster centers, each
object is assigned to the cluster whose center is closest to the
object: An object is expected to belong to the closest cluster
 Maximization Step (M-step): Given the cluster assignment, for
each cluster, the algorithm adjusts the center so that the sum of
distance from the objects assigned to this cluster and the new
center is minimized
 The (EM) algorithm: A framework to approach maximum likelihood or
maximum a posteriori estimates of parameters in statistical models.
 E-step assigns objects to clusters according to the current fuzzy
clustering or parameters of probabilistic clusters
 M-step finds the new clustering or parameters that maximize the
sum of squared error (SSE) or the expected likelihood
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Fuzzy Clustering Using the EM Algorithm
 Initially, let c1 = a and c2 = b
 1st E-step: assign o to c1,w. wt =

 1st M-step: recalculate the centroids according to the partition matrix,
minimizing the sum of squared error (SSE)
 Iteratively calculate this until the cluster centers converge or the change
is small enough

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Univariate Gaussian Mixture Model
 O = {o1, …, on} (n observed objects), Θ = {θ1, …, θk} (parameters of the
k distributions), and Pj(oi| θj) is the probability that oi is generated from
the j-th distribution using parameter θj, we have
 Univariate Gaussian mixture model
 Assume the probability density function of each cluster follows a 1-
d Gaussian distribution. Suppose that there are k clusters.
 The probability density function of each cluster are centered at μj
with standard deviation σj, θj, = (μj, σj), we have

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Computing Mixture Models with EM
 Given n objects O = {o1, …, on}, we want to mine a set of parameters Θ
= {θ1, …, θk} s.t.,P(O|Θ) is maximized, where θj = (μj, σj) are the mean and
standard deviation of the j-th univariate Gaussian distribution
 We initially assign random values to parameters θj, then iteratively
conduct the E- and M- steps until converge or sufficiently small change
 At the E-step, for each object oi, calculate the probability that oi belongs
to each distribution,
 At the M-step, adjust the parameters θj = (μj, σj) so that the expected
likelihood P(O|Θ) is maximized

Advantages and Disadvantages of Mixture Models
 Strength
 Mixture models are more general than partitioning and fuzzy
clustering
 Clusters can be characterized by a small number of parameters
 The results may satisfy the statistical assumptions of the
generative models
 Weakness
 Converge to local optimal (overcome: run multi-times w. random
initialization)
 Computationally expensive if the number of distributions is large,
or the data set contains very few observed data points
 Need large data sets
 Hard to estimate the number of clusters
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26
 Summary

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Clustering High-Dimensional Data
 Clustering high-dimensional data (How high is high-D in clustering?)
 Many applications: text documents, DNA micro-array data
 Major challenges:
 Many irrelevant dimensions may mask clusters
 Distance measure becomes meaningless—due to equi-distance
 Clusters may exist only in some subspaces
 Methods
 Subspace-clustering: Search for clusters existing in subspaces of
the given high dimensional data space
 CLIQUE, ProClus, and bi-clustering approaches
 Dimensionality reduction approaches: Construct a much lower
dimensional space and search for clusters there (may construct new
dimensions by combining some dimensions in the original data)
 Dimensionality reduction methods and spectral clustering

Traditional Distance Measures May Not
Be Effective on High-D Data
 Traditional distance measure could be dominated by noises in many
dimensions
 Ex. Which pairs of customers are more similar?
 By Euclidean distance, we get,
 despite Ada and Cathy look more similar
 Clustering should not only consider dimensions but also attributes
(features)
 Feature transformation: effective if most dimensions are relevant
(PCA & SVD useful when features are highly correlated/redundant)
 Feature selection: useful to find a subspace where the data have
nice clusters
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The Curse of Dimensionality
(graphs adapted from Parsons et al. KDD Explorations 2004)
 Data in only one dimension is relatively
packed
 Adding a dimension “stretch” the
points across that dimension, making
them further apart
 Adding more dimensions will make the
points further apart—high dimensional
data is extremely sparse
 Distance measure becomes
meaningless—due to equi-distance

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Why Subspace Clustering?
(adapted from Parsons et al. SIGKDD Explorations 2004)
 Clusters may exist only in some subspaces
 Subspace-clustering: find clusters in all the subspaces

Subspace Clustering Methods
 Subspace search methods: Search various subspaces to
find clusters
 Bottom-up approaches
 Top-down approaches
 Correlation-based clustering methods
 E.g., PCA based approaches
 Bi-clustering methods
 Optimization-based methods
 Enumeration methods

Subspace Clustering Method (I):
Subspace Search Methods
 Search various subspaces to find clusters
 Bottom-up approaches
 Start from low-D subspaces and search higher-D subspaces only
when there may be clusters in such subspaces
 Various pruning techniques to reduce the number of higher-D
subspaces to be searched
 Ex. CLIQUE (Agrawal et al. 1998)
 Top-down approaches
 Start from full space and search smaller subspaces recursively
 Effective only if the locality assumption holds: restricts that the
subspace of a cluster can be determined by the local neighborhood
 Ex. PROCLUS (Aggarwal et al. 1999): a k-medoid-like method
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CLIQUE: SubSpace Clustering with
Salary
(10,000)
age
0 1 2 3 4 5 6 7
20 30 40 50 60
age
0 1 2 3 4 5 6 7
20 30 40 50 60
Vacation
(week)
age
Vacatio
n
30 50
 = 3
Aprori Pruning

Subspace Clustering Method (II):
Correlation-Based Methods
 Subspace search method: similarity based on distance or
density
 Correlation-based method: based on advanced correlation
models
 Ex. PCA-based approach:
 Apply PCA (for Principal Component Analysis) to derive a
set of new, uncorrelated dimensions,
 then mine clusters in the new space or its subspaces
 Other space transformations:
 Hough transform
 Fractal dimensions
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Subspace Clustering Method (III):
Bi-Clustering Methods
 Bi-clustering: Cluster both objects and attributes
simultaneously (treat objs and attrs in symmetric way)
 Four requirements:
 Only a small set of objects participate in a cluster
 A cluster only involves a small number of attributes
 An object may participate in multiple clusters, or
does not participate in any cluster at all
 An attribute may be involved in multiple clusters, or
is not involved in any cluster at all
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 Ex 1. Gene expression or microarray data: a gene
sample/condition matrix.
 Each element in the matrix, a real number,
records the expression level of a gene under a
specific condition
 Ex. 2. Clustering customers and products
 Another bi-clustering problem

Types of Bi-clusters
 Let A = {a1, ..., an} be a set of genes, B = {b1, …, bn} a set of conditions
 A bi-cluster: A submatrix where genes and conditions follow some
consistent patterns
 4 types of bi-clusters (ideal cases)
 Bi-clusters with constant values:
 for any i in I and j in J, eij = c
 Bi-clusters with constant values on rows:
 eij = c + αi
 Also, it can be constant values on columns
 Bi-clusters with coherent values (aka. pattern-based clusters)
 eij = c + αi + βj
 Bi-clusters with coherent evolutions on rows
 eij (ei1j1− ei1j2)(ei2j1− ei2j2) ≥ 0
 i.e., only interested in the up- or down- regulated changes across
genes or conditions without constraining on the exact values
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Bi-Clustering Methods
 Real-world data is noisy: Try to find approximate bi-clusters
 Methods: Optimization-based methods vs. enumeration methods
 Optimization-based methods
 Try to find a submatrix at a time that achieves the best significance
as a bi-cluster
 Due to the cost in computation, greedy search is employed to find
local optimal bi-clusters
 Ex. δ-Cluster Algorithm (Cheng and Church, ISMB’2000)
 Enumeration methods
 Use a tolerance threshold to specify the degree of noise allowed in
the bi-clusters to be mined
 Then try to enumerate all submatrices as bi-clusters that satisfy the
requirements
 Ex. δ-pCluster Algorithm (H. Wang et al.’ SIGMOD’2002, MaPle:
Pei et al., ICDM’2003)
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Bi-Clustering for Micro-Array Data Analysis
 Left figure: Micro-array “raw” data shows 3 genes and their
values in a multi-D space: Difficult to find their patterns
 Right two: Some subsets of dimensions form nice shift and
scaling patterns
 No globally defined similarity/distance measure
 Clusters may not be exclusive
 An object can appear in multiple clusters

Bi-Clustering (I): δ-Bi-Cluster
 For a submatrix I x J, the mean of the i-th row:
 The mean of the j-th column:
 The mean of all elements in the submatrix is
 The quality of the submatrix as a bi-cluster can be measured by the mean
squared residue value
 A submatrix I x J is δ-bi-cluster if H(I x J) ≤ δ where δ ≥ 0 is a threshold.
When δ = 0, I x J is a perfect bi-cluster with coherent values. By setting δ > 0,
a user can specify the tolerance of average noise per element against a
perfect bi-cluster
 residue(eij) = eij − eiJ − eIj + eIJ
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Bi-Clustering (I): The δ-Cluster Algorithm
 Maximal δ-bi-cluster is a δ-bi-cluster I x J such that there does not exist
another δ-bi-cluster I′ x J′ which contains I x J
 Computing is costly: Use heuristic greedy search to obtain local optimal clusters
 Two phase computation: deletion phase and additional phase
 Deletion phase: Start from the whole matrix, iteratively remove rows and
columns while the mean squared residue of the matrix is over δ
 At each iteration, for each row/column, compute the mean squared residue:
 Remove the row or column of the largest mean squared residue
 Addition phase:
 Expand iteratively the δ-bi-cluster I x J obtained in the deletion phase as
long as the δ-bi-cluster requirement is maintained
 Consider all the rows/columns not involved in the current bi-cluster I x J by
calculating their mean squared residues
 A row/column of the smallest mean squared residue is added into the
current δ-bi-cluster
 It finds only one δ-bi-cluster, thus needs to run multiple times: replacing the
elements in the output bi-cluster by random numbers
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Bi-Clustering (II): δ-pCluster
 Enumerating all bi-clusters (δ-pClusters) [H. Wang, et al., Clustering by pattern
similarity in large data sets. SIGMOD’02]
 Since a submatrix I x J is a bi-cluster with (perfect) coherent values iff ei1j1 − ei2j1
= ei1j2 − ei2j2. For any 2 x 2 submatrix of I x J, define p-score
 A submatrix I x J is a δ-pCluster (pattern-based cluster) if the p-score of every 2
x 2 submatrix of I x J is at most δ, where δ ≥ 0 is a threshold specifying a user's
tolerance of noise against a perfect bi-cluster
 The p-score controls the noise on every element in a bi-cluster, while the mean
squared residue captures the average noise
 Monotonicity: If I x J is a δ-pClusters, every x x y (x,y ≥ 2) submatrix of I x J is
also a δ-pClusters.
 A δ-pCluster is maximal if no more row or column can be added into the cluster
and retain δ-pCluster: We only need to compute all maximal δ-pClusters.
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MaPle: Efficient Enumeration of δ-
pClusters
 Pei et al., MaPle: Efficient enumerating all maximal δ-
pClusters. ICDM'03
 Framework: Same as pattern-growth in frequent pattern
mining (based on the downward closure property)
 For each condition combination J, find the maximal subsets
of genes I such that I x J is a δ-pClusters
 If I x J is not a submatrix of another δ-pClusters
 then I x J is a maximal δ-pCluster.
 Algorithm is very similar to mining frequent closed itemsets
 Additional advantages of δ-pClusters:
 Due to averaging of δ-cluster, it may contain outliers
but still within δ-threshold
 Computing bi-clusters for scaling patterns, take
logarithmic on
d /
d
xa ya
d /
d
will lead to the p-score form
42

xb yb

Dimensionality-Reduction Methods
 Dimensionality reduction: In some situations, it is
more effective to construct a new space instead
of using some subspaces of the original data
43
 Ex. To cluster the points in the right figure, any subspace of the original
one, X and Y, cannot help, since all the three clusters will be projected
into the overlapping areas in X and Y axes.
 Construct a new dimension as the dashed one, the three clusters
become apparent when the points projected into the new dimension
 Dimensionality reduction methods
 Feature selection and extraction: But may not focus on clustering
structure finding
 Spectral clustering: Combining feature extraction and clustering (i.e.,
use the spectrum of the similarity matrix of the data to perform
dimensionality reduction for clustering in fewer dimensions)
 Normalized Cuts (Shi and Malik, CVPR’97 or PAMI’2000)
 The Ng-Jordan-Weiss algorithm (NIPS’01)

Spectral Clustering:
The Ng-Jordan-Weiss (NJW) Algorithm
 Given a set of objects o1, …, on, and the distance between each pair
of objects, dist(oi, oj), find the desired number k of clusters
 Calculate an affinity matrix W, where σ is a scaling parameter that
controls how fast the affinity Wij decreases as dist(oi, oj) increases.
In NJW, set Wij = 0
 Derive a matrix A = f(W). NJW defines a matrix D to be a diagonal
matrix s.t. Dii is the sum of the i-th row of W, i.e.,
Then, A is set to
 A spectral clustering method finds the k leading eigenvectors of A
 A vector v is an eigenvector of matrix A if Av = λv, where λ is the
corresponding eigen-value
 Using the k leading eigenvectors, project the original data into the
new space defined by the k leading eigenvectors, and run a
clustering algorithm, such as k-means, to find k clusters
 Assign the original data points to clusters according to how the
transformed points are assigned in the clusters obtained
44

Spectral Clustering: Illustration and
Comments
 Spectral clustering: Effective in tasks like image processing
 Scalability challenge: Computing eigenvectors on a large matrix is costly
 Can be combined with other clustering methods, such as bi-clustering
45

46
 Summary

Clustering Graphs and Network Data
 Applications
 Bi-partite graphs, e.g., customers and products,
authors and conferences
 Web search engines, e.g., click through graphs and
Web graphs
 Social networks, friendship/coauthor graphs
 Similarity measures
 Geodesic distances
 Distance based on random walk (SimRank)
 Graph clustering methods
 Minimum cuts: FastModularity (Clauset, Newman &
Moore, 2004)
 Density-based clustering: SCAN (Xu et al., KDD’2007)
47

Similarity Measure (I): Geodesic
Distance
 Geodesic distance (A, B): length (i.e., # of edges) of the shortest path
between A and B (if not connected, defined as infinite)
 Eccentricity of v, eccen(v): The largest geodesic distance between v
and any other vertex u ∈ V − {v}.
 E.g., eccen(a) = eccen(b) = 2; eccen(c) = eccen(d) = eccen(e) = 3
 Radius of graph G: The minimum eccentricity of all vertices, i.e., the
distance between the “most central point” and the “farthest border”
 r = min v∈V eccen(v)
 E.g., radius (g) = 2
 Diameter of graph G: The maximum eccentricity of all vertices, i.e., the
largest distance between any pair of vertices in G
 d = max v∈V eccen(v)
 E.g., diameter (g) = 3
 A peripheral vertex is a vertex that achieves the diameter.
 E.g., Vertices c, d, and e are peripheral vertices
48

SimRank: Similarity Based on Random
Walk and Structural Context
 SimRank: structural-context similarity, i.e., based on the similarity of its
neighbors
 In a directed graph G = (V,E),
 individual in-neighborhood of v: I(v) = {u | (u, v) ∈ E}
 individual out-neighborhood of v: O(v) = {w | (v, w) ∈ E}
 Similarity in SimRank:
 Initialization:
 Then we can compute si+1 from si based on the definition
 Similarity based on random walk: in a strongly connected component
 Expected distance:
 Expected meeting distance:
 Expected meeting probability:
P[t] is the probability of the tour
49

Graph Clustering: Sparsest Cut
 G = (V,E). The cut set of a cut is the set
of edges {(u, v) ∈ E | u ∈ S, v ∈ T } and
S and T are in two partitions
 Size of the cut: # of edges in the cut set
 Min-cut (e.g., C1) is not a good partition
 A better measure: Sparsity:
 A cut is sparsest if its sparsity is not greater than that of any other cut
 Ex. Cut C2 = ({a, b, c, d, e, f, l}, {g, h, i, j, k}) is the sparsest cut
 For k clusters, the modularity of a clustering assesses the quality of the
clustering:
li: # edges between vertices in the i-th cluster
di: the sum of the degrees of the vertices in the i-th cluster
 The modularity of a clustering of a graph is the difference between the
fraction of all edges that fall into individual clusters and the fraction that
would do so if the graph vertices were randomly connected
 The optimal clustering of graphs maximizes the modularity
50

Graph Clustering: Challenges of Finding Good Cuts
 High computational cost
 Many graph cut problems are computationally expensive
 The sparsest cut problem is NP-hard
 Need to tradeoff between efficiency/scalability and quality
 Sophisticated graphs
 May involve weights and/or cycles.
 High dimensionality
 A graph can have many vertices. In a similarity matrix, a vertex is
represented as a vector (a row in the matrix) whose
dimensionality is the number of vertices in the graph
 Sparsity
 A large graph is often sparse, meaning each vertex on average
connects to only a small number of other vertices
 A similarity matrix from a large sparse graph can also be sparse
51

Two Approaches for Graph Clustering
 Two approaches for clustering graph data
 Use generic clustering methods for high-dimensional data
 Designed specifically for clustering graphs
 Using clustering methods for high-dimensional data
 Extract a similarity matrix from a graph using a similarity measure
 A generic clustering method can then be applied on the similarity
matrix to discover clusters
 Ex. Spectral clustering: approximate optimal graph cut solutions
 Methods specific to graphs
 Search the graph to find well-connected components as clusters
 Ex. SCAN (Structural Clustering Algorithm for Networks)
 X. Xu, N. Yuruk, Z. Feng, and T. A. J. Schweiger, “SCAN: A
Structural Clustering Algorithm for Networks”, KDD'07
52

SCAN: Density-Based Clustering of
Networks
 How many clusters?
 What size should they be?
 What is the best partitioning?
 Should some points be
segregated?
53
An Example Network
 Application: Given simply information of who associates with whom,
could one identify clusters of individuals with common interests or
special relationships (families, cliques, terrorist cells)?

A Social Network Model
 Cliques, hubs and outliers
 Individuals in a tight social group, or clique, know many of the
same people, regardless of the size of the group
 Individuals who are hubs know many people in different groups
but belong to no single group. Politicians, for example bridge
multiple groups
 Individuals who are outliers reside at the margins of society.
Hermits, for example, know few people and belong to no group
 The Neighborhood of a Vertex
54
v
 Define () as the immediate
neighborhood of a vertex (i.e. the set
of people that an individual knows )

Structure Similarity
 The desired features tend to be captured by a measure
we call Structural Similarity

v w
|  ( ) 
( ) |
v w
| ( ) || ( ) |
v w

( , )
 

 Structural similarity is large for members of a clique
and small for hubs and outliers
55
v

Structural Connectivity [1]
 -Neighborhood:
 Core:
 Direct structure reachable:
 Structure reachable: transitive closure of direct structure
reachability
 Structure connected:
( ) { ( ) | ( , )  }  N v  w v v w 
    ( )| ( ) | , CORE v N v
( , ) ( ) ( ) , , DirRECH v w CORE v w N v        
( , ) : ( , ) ( , ) , , , CONNECT v w u V RECH u v RECH u w         
[1] M. Ester, H. P. Kriegel, J. Sander, & X. Xu (KDD'96) “A Density-Based
Algorithm for Discovering Clusters in Large Spatial Databases
56

Structure-Connected Clusters
 Structure-connected cluster C
 Connectivity:
 Maximality:
 Hubs:
, : ( , ) , v w C CONNECT v w    
v,wV : vC  REACH (v,w) wC  ,
 Not belong to any cluster
 Bridge to many clusters
 Outliers:
 Not belong to any cluster
 Connect to less clusters
hub
outlier
57

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
58

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.63
59

0.67
13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.75
0.82
60

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
61

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.67
62

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.73
0.73
0.73
63

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
64

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.51
65

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.68
66

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
0.51
67

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
68

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7 0.51
0.68
0.51
69

13
9
Algorithm
11
10
7
8
12
6
4
0
1
5
2
3
 = 2
 = 0.7
70

Running Time
 Running time = O(|E|)
 For sparse networks = O(|V|)
[2] A. Clauset, M. E. J. Newman, & C. Moore, Phys. Rev. E 70, 066111 (2004).
71

 Summary
72

73
Why Constraint-Based Cluster Analysis?
 Need user feedback: Users know their applications the best
 Less parameters but more user-desired constraints, e.g., an
ATM allocation problem: obstacle & desired clusters

74
Categorization of Constraints
 Constraints on instances: specifies how a pair or a set of instances
should be grouped in the cluster analysis
 Must-link vs. cannot link constraints
 must-link(x, y): x and y should be grouped into one cluster
 Constraints can be defined using variables, e.g.,
 cannot-link(x, y) if dist(x, y) > d
 Constraints on clusters: specifies a requirement on the clusters
 E.g., specify the min # of objects in a cluster, the max diameter of a
cluster, the shape of a cluster (e.g., a convex), # of clusters (e.g., k)
 Constraints on similarity measurements: specifies a requirement that
the similarity calculation must respect
 E.g., driving on roads, obstacles (e.g., rivers, lakes)
 Issues: Hard vs. soft constraints; conflicting or redundant constraints

75
Constraint-Based Clustering Methods (I):
Handling Hard Constraints
 Handling hard constraints: Strictly respect the constraints in cluster
assignments
 Example: The COP-k-means algorithm
 Generate super-instances for must-link constraints
 Compute the transitive closure of the must-link constraints
 To represent such a subset, replace all those objects in the
subset by the mean.
 The super-instance also carries a weight, which is the number
of objects it represents
 Conduct modified k-means clustering to respect cannot-link
constraints
 Modify the center-assignment process in k-means to a nearest
feasible center assignment
 An object is assigned to the nearest center so that the
assignment respects all cannot-link constraints

Constraint-Based Clustering Methods (II):
Handling Soft Constraints
 Treated as an optimization problem: When a clustering violates a soft
constraint, a penalty is imposed on the clustering
 Overall objective: Optimizing the clustering quality, and minimizing the
constraint violation penalty
 Ex. CVQE (Constrained Vector Quantization Error) algorithm: Conduct
k-means clustering while enforcing constraint violation penalties
 Objective function: Sum of distance used in k-means, adjusted by the
constraint violation penalties
 Penalty of a must-link violation
 If objects x and y must-be-linked but they are assigned to two
different centers, c1 and c2, dist(c1, c2) is added to the objective
function as the penalty
 Penalty of a cannot-link violation
 If objects x and y cannot-be-linked but they are assigned to a
common center c, dist(c, c′), between c and c′ is added to the
objective function as the penalty, where c′ is the closest cluster
to c that can accommodate x or y
76

77
Speeding Up Constrained Clustering
 It is costly to compute some constrained
clustering
 Ex. Clustering with obstacle objects: Tung,
Hou, and Han. Spatial clustering in the
presence of obstacles, ICDE'01
 K-medoids is more preferable since k-means
may locate the ATM center in the middle of a
lake
 Visibility graph and shortest path
 Triangulation and micro-clustering
 Two kinds of join indices (shortest-paths)
worth pre-computation
 VV index: indices for any pair of obstacle
vertices
 MV index: indices for any pair of micro-cluster
and obstacle indices

78
An Example: Clustering With Obstacle Objects
Not Taking obstacles into account Taking obstacles into account

79
User-Guided Clustering: A Special Kind of
Constraints
Professor
name
office
position
course-id
name
area
course
semester
instructor
Advise
Student
name
office
position
Publish
author
Register
student
course
semester
unit
grade
professor
student
degree
Work-In
person
group
Group
name
area
Publication
title
year
conf
title
User hint
Target of
clustering
Open-course Course
 X. Yin, J. Han, P. S. Yu, “Cross-Relational Clustering with User's Guidance”,
KDD'05
 User usually has a goal of clustering, e.g., clustering students by research area
 User specifies his clustering goal to CrossClus

80
Comparing with Classification
 User-specified feature (in the form
of attribute) is used as a hint, not
class labels
 The attribute may contain too
many or too few distinct values,
e.g., a user may want to
cluster students into 20
clusters instead of 3
 Additional features need to be
User hint
All tuples for clustering included in cluster analysis

81
Comparing with Semi-Supervised Clustering
 Semi-supervised clustering: User provides a training set
consisting of “similar” (“must-link) and “dissimilar”
(“cannot link”) pairs of objects
 User-guided clustering: User specifies an attribute as a
hint, and more relevant features are found for clustering
All tuples for clustering
Semi-supervised clustering
User-guided clustering
All tuples for clustering
x

82
Why Not Semi-Supervised Clustering?
 Much information (in multiple relations) is needed to judge
whether two tuples are similar
 A user may not be able to provide a good training set
 It is much easier for a user to specify an attribute as a hint,
such as a student’s research area
Tom Smith SC1211 TA
Jane Chang BI205 RA
Tuples to be compared
User hint

83
CrossClus: An Overview
 Measure similarity between features by how they group
objects into clusters
 Use a heuristic method to search for pertinent features
 Start from user-specified feature and gradually
expand search range
 Use tuple ID propagation to create feature values
 Features can be easily created during the expansion
of search range, by propagating IDs
 Explore three clustering algorithms: k-means, k-medoids,
and hierarchical clustering

84
Multi-Relational Features
 A multi-relational feature is defined by:
 A join path, e.g., Student → Register → OpenCourse → Course
 An attribute, e.g., Course.area
 (For numerical feature) an aggregation operator, e.g., sum or average
 Categorical feature f = [Student → Register → OpenCourse → Course,
Course.area, null]
areas of courses of each student
Tuple Areas of courses
DB AI TH
t1 5 5 0
t2 0 3 7
t3 1 5 4
t4 5 0 5
t5 3 3 4
Values of feature f f(t1)
Tuple Feature f
DB AI TH
t1 0.5 0.5 0
t2 0 0.3 0.7
t3 0.1 0.5 0.4
t4 0.5 0 0.5
t5 0.3 0.3 0.4
f(t2)
f(t3)
f(t4)
f(t5)
DB
AI
TH

85
Representing Features
 Similarity between tuples t1 and t2 w.r.t. categorical feature f
 Cosine similarity between vectors f(t1) and f(t2)


f t . p f t .
p


 Most important information of a
feature f is how f groups tuples into
clusters
 f is represented by similarities
between every pair of tuples
indicated by f
 The horizontal axes are the tuple
indices, and the vertical axis is the
similarity
 This can be considered as a vector
of N x N dimensions
Similarity vector Vf
 
   
     
 

L
k
k
L
k
k
L
k
k k
f
f t p f t p
t t
1
2
2
1
2
1
1
1 2
1 2
. .
sim ,

86
Similarity Between Features
Values of Feature f and g
Feature f (course) Feature g (group)
DB AI TH Info sys Cog sci Theory
t1 0.5 0.5 0 1 0 0
t2 0 0.3 0.7 0 0 1
t3 0.1 0.5 0.4 0 0.5 0.5
t4 0.5 0 0.5 0.5 0 0.5
t5 0.3 0.3 0.4 0.5 0.5 0
Similarity between two features –
cosine similarity of two vectors
Vf
Vg
f g
V V
  f g
V V
sim f g

, 

87
Computing Feature Similarity
Tuples
Feature f Feature g
DB
AI
TH
Info sys
Cog sci
Theory
Similarity between feature
values w.r.t. the tuples
sim(fk,gq)=Σi=1 to N f(ti).pk∙g(ti).pq
DB Info sys
2
l
m
     
f g V V sim t t sim t t sim f g Tuple similarities,
 , ,  ,
   
   
k
q
1 1 1 1
k q
N
i
N
j
f i j g i j
hard to compute
Feature value similarities,
easy to compute
DB
AI
TH
Info sys
Cog sci
Theory
Compute similarity
between each pair of
feature values by one
scan on data

88
Searching for Pertinent Features
 Different features convey different aspects of information
Research area
Research group area
Conferences of papers
Advisor
Academic Performances
GPA
GRE score
Number of papers
Demographic info
Permanent address
Nationality
 Features conveying same aspect of information usually
cluster tuples in more similar ways
 Research group areas vs. conferences of publications
 Given user specified feature
 Find pertinent features by computing feature similarity

Course
Publication
title
89
Heuristic Search for Pertinent Features
Overall procedure
1. Start from the user-specified
feature
2. Search in neighborhood
of existing pertinent
features
3. Expand search range
gradually
Professor
name
office
position
Advise
Student
name
office
position
Open-course
Publish
author
Register
student
course
semester
unit
grade
professor
student
degree
Work-In
person
group
Group
name
area
year
conf
title
User hint
Target of
clustering
course-id
name
area
course
semester
instructor
1
2
 Tuple ID propagation is used to create multi-relational features
 IDs of target tuples can be propagated along any join path, from
which we can find tuples joinable with each target tuple

90
Clustering with Multi-Relational Features
 Given a set of L pertinent features f1, …, fL, similarity
between two tuples
L
      
f i t t t t f weight
1 2 1 2 sim , sim , .
i
i
1
 Weight of a feature is determined in feature search by
its similarity with other pertinent features
 Clustering methods
 CLARANS [Ng & Han 94], a scalable clustering
algorithm for non-Euclidean space
 K-means
 Agglomerative hierarchical clustering

91
Experiments: Compare CrossClus with
 Baseline: Only use the user specified feature
 PROCLUS [Aggarwal, et al. 99]: a state-of-the-art
subspace clustering algorithm
 Use a subset of features for each cluster
 We convert relational database to a table by
propositionalization
 User-specified feature is forced to be used in every
cluster
 RDBC [Kirsten and Wrobel’00]
 A representative ILP clustering algorithm
 Use neighbor information of objects for clustering
 User-specified feature is forced to be used

92
Measure of Clustering Accuracy
 Accuracy
 Measured by manually labeled data
 We manually assign tuples into clusters according
to their properties (e.g., professors in different
research areas)
 Accuracy of clustering: Percentage of pairs of tuples in
the same cluster that share common label
 This measure favors many small clusters
 We let each approach generate the same number of
clusters

93
DBLP Dataset
Clustering Accurarcy - DBLP
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0
Conf
Word
Coauthor
Conf+Word
Word+Coauthor
Conf+Coauthor
All three
CrossClus K-Medoids
CrossClus K-Means
CrossClus Agglm
Baseline
PROCLUS
RDBC

94
 Summary

95
Summary
 Fuzzy clustering
 Probability-model-based clustering
 The EM algorithm
 Subspace clustering: bi-clustering methods
 Dimensionality reduction: Spectral clustering
 Graph clustering: min-cut vs. sparsest cut
 High-dimensional clustering methods
 Graph-specific clustering methods, e.g., SCAN
 Constraints on instance objects, e.g., Must link vs. Cannot Link
 Constraint-based clustering algorithms

96
References (I)
 R. Agrawal, J. Gehrke, D. Gunopulos, and P. Raghavan. Automatic subspace clustering of high
dimensional data for data mining applications. SIGMOD’98
 C. C. Aggarwal, C. Procopiuc, J. Wolf, P. S. Yu, and J.-S. Park. Fast algorithms for projected
clustering. SIGMOD’99
 S. Arora, S. Rao, and U. Vazirani. Expander flows, geometric embeddings and graph partitioning.
J. ACM, 56:5:1–5:37, 2009.
 J. C. Bezdek. Pattern Recognition with Fuzzy Objective Function Algorithms. Plenum Press, 1981.
 K. S. Beyer, J. Goldstein, R. Ramakrishnan, and U. Shaft. When is ”nearest neighbor” meaningful?
ICDT’99
 Y. Cheng and G. Church. Biclustering of expression data. ISMB’00
 I. Davidson and S. S. Ravi. Clustering with constraints: Feasibility issues and the k-means
algorithm. SDM’05
 I. Davidson, K. L. Wagstaff, and S. Basu. Measuring constraint-set utility for partitional clustering
algorithms. PKDD’06
 C. Fraley and A. E. Raftery. Model-based clustering, discriminant analysis, and density estimation.
J. American Stat. Assoc., 97:611–631, 2002.
 F. H¨oppner, F. Klawonn, R. Kruse, and T. Runkler. Fuzzy Cluster Analysis: Methods for
Classification, Data Analysis and Image Recognition. Wiley, 1999.
 G. Jeh and J. Widom. SimRank: a measure of structural-context similarity. KDD’02
 H.-P. Kriegel, P. Kroeger, and A. Zimek. Clustering high dimensional data: A survey on subspace
clustering, pattern-based clustering, and correlation clustering. ACM Trans. Knowledge Discovery
from Data (TKDD), 3, 2009.
 U. Luxburg. A tutorial on spectral clustering. Statistics and Computing, 17:395–416, 2007

References (II)
 G. J. McLachlan and K. E. Bkasford. Mixture Models: Inference and Applications to Clustering. John
Wiley & Sons, 1988.
 B. Mirkin. Mathematical classification and clustering. J. of Global Optimization, 12:105–108, 1998.
 S. C. Madeira and A. L. Oliveira. Biclustering algorithms for biological data analysis: A survey.
IEEE/ACM Trans. Comput. Biol. Bioinformatics, 1, 2004.
 A. Y. Ng, M. I. Jordan, and Y. Weiss. On spectral clustering: Analysis and an algorithm. NIPS’01
 J. Pei, X. Zhang, M. Cho, H. Wang, and P. S. Yu. Maple: A fast algorithm for maximal pattern-based
clustering. ICDM’03
 M. Radovanović, A. Nanopoulos, and M. Ivanović. Nearest neighbors in high-dimensional data: the
emergence and influence of hubs. ICML’09
 S. E. Schaeffer. Graph clustering. Computer Science Review, 1:27–64, 2007.
 A. K. H. Tung, J. Hou, and J. Han. Spatial clustering in the presence of obstacles. ICDE’01
 A. K. H. Tung, J. Han, L. V. S. Lakshmanan, and R. T. Ng. Constraint-based clustering in large
databases. ICDT’01
 A. Tanay, R. Sharan, and R. Shamir. Biclustering algorithms: A survey. In Handbook of Computational
Molecular Biology, Chapman & Hall, 2004.
 K. Wagstaff, C. Cardie, S. Rogers, and S. Schrödl. Constrained k-means clustering with background
knowledge. ICML’01
 H. Wang, W. Wang, J. Yang, and P. S. Yu. Clustering by pattern similarity in large data sets.
SIGMOD’02
 X. Xu, N. Yuruk, Z. Feng, and T. A. J. Schweiger. SCAN: A structural clustering algorithm for networks.
KDD’07
 X. Yin, J. Han, and P.S. Yu, “Cross-Relational Clustering with User's Guidance”, KDD'05

Slides Not to Be Used in Class
99

100
Conceptual Clustering
 Conceptual clustering
 A form of clustering in machine learning
 Produces a classification scheme for a set of unlabeled
objects
 Finds characteristic description for each concept (class)
 COBWEB (Fisher’87)
 A popular a simple method of incremental conceptual
learning
 Creates a hierarchical clustering in the form of a
classification tree
 Each node refers to a concept and contains a
probabilistic description of that concept

101
COBWEB Clustering Method
A classification tree

102
More on Conceptual Clustering
 Limitations of COBWEB
 The assumption that the attributes are independent of each other is
often too strong because correlation may exist
 Not suitable for clustering large database data – skewed tree and
expensive probability distributions
 CLASSIT
 an extension of COBWEB for incremental clustering of continuous
data
 suffers similar problems as COBWEB
 AutoClass (Cheeseman and Stutz, 1996)
 Uses Bayesian statistical analysis to estimate the number of
clusters
 Popular in industry

103
Neural Network Approaches
 Neural network approaches
 Represent each cluster as an exemplar, acting as a
“prototype” of the cluster
 New objects are distributed to the cluster whose
exemplar is the most similar according to some
distance measure
 Typical methods
 SOM (Soft-Organizing feature Map)
 Competitive learning
 Involves a hierarchical architecture of several units
(neurons)
 Neurons compete in a “winner-takes-all” fashion for
the object currently being presented

104
Self-Organizing Feature Map (SOM)
 SOMs, also called topological ordered maps, or Kohonen Self-
Organizing Feature Map (KSOMs)
 It maps all the points in a high-dimensional source space into a 2 to 3-d
target space, s.t., the distance and proximity relationship (i.e., topology)
are preserved as much as possible
 Similar to k-means: cluster centers tend to lie in a low-dimensional
manifold in the feature space
 Clustering is performed by having several units competing for the
current object
 The unit whose weight vector is closest to the current object wins
 The winner and its neighbors learn by having their weights adjusted
 SOMs are believed to resemble processing that can occur in the brain
 Useful for visualizing high-dimensional data in 2- or 3-D space

105
Web Document Clustering Using
SOM
 The result of
SOM clustering
of 12088 Web
articles
 The picture on
the right: drilling
down on the
keyword
“mining”
 Based on
websom.hut.fi
Web page

Data Mining: Concepts and techniques: Chapter 11,Review: Basic Cluster Analysis Methods 11 clusadvanced

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Data Mining: Concepts and techniques: Chapter 11,Review: Basic Cluster Analysis Methods 11 clusadvanced