Concepts and

Techniques

— Chapter 2 —

Jiawei Han, Micheline Kamber, and Jian Pei

University of Illinois at Urbana-Champaign
Simon Fraser University
©2011 Han, Kamber, and Pei. All rights
reserved.
1
Chapter 2: Getting to Know Your
Data

 Data Objects and Attribute Types

 Basic Statistical Descriptions of Data

 Data Visualization

 Measuring Data Similarity and Dissimilarity

 Summary

2
 Types of Data Sets
 Record

Relational records

Data matrix, e.g., numerical matrix,

timeout

season
coach

game
score
team

ball

lost
pla

wi
crosstabs

n
y

Document data: text documents: term-
frequency vector
Document 1 3 0 5 0 2 6 0 2 0 2

Transaction data
 Graph and network Document 2 0 7 0 2 1 0 0 3 0 0

World Wide Web
Document 3 0 1 0 0 1 2 2 0 3 0

Social or information networks

Molecular Structures
 Ordered TID Items

Video data: sequence of images
1 Bread, Coke, Milk

Temporal data: time-series

Sequential Data: transaction 2 Beer, Bread
sequences 3 Beer, Coke, Diaper, Milk

Genetic sequence data 4 Beer, Bread, Diaper, Milk
 Spatial, image and multimedia:
5 Coke, Diaper, Milk

Spatial data: maps

Image data:

Video data:
3
 Important Characteristics of
Structured Data

 Dimensionality
 Curse of dimensionality
 Sparsity
 Only presence counts
 Resolution

Patterns depend on the scale
 Distribution
 Centrality and dispersion

4
 Data Objects

 Data sets are made up of data objects.

 A data object represents an entity.
 Examples:
 sales database: customers, store items, sales

medical database: patients, treatments

university database: students, professors, courses
 Also called samples , examples, instances, data
points, objects, tuples.
 Data objects are described by attributes.
 Database rows -> data objects; columns -
>attributes.
5
 Attributes
 Attribute (or dimensions, features,
variables): a data field, representing a
characteristic or feature of a data object.
 E.g., customer _ID, name, address

 Types:
 Nominal

 Binary

 Numeric: quantitative


Interval-scaled

Ratio-scaled
6
 Attribute Types
 Nominal: categories, states, or “names of things”
 Hair_color = {auburn, black, blond, brown, grey, red,
white}
 marital status, occupation, ID numbers, zip codes
 Binary
 Nominal attribute with only 2 states (0 and 1)
 Symmetric binary: both outcomes equally important

e.g., gender
 Asymmetric binary: outcomes not equally important.

e.g., medical test (positive vs. negative)

Convention: assign 1 to most important outcome
(e.g., HIV positive)
 Ordinal
 Values have a meaningful order (ranking) but magnitude
between successive values is not known.
 Size = {small, medium, large}, grades, army rankings
7
 Numeric Attribute Types
 Quantity (integer or real-valued)
 Interval

Measured on a scale of equal-sized units

Values have order
 E.g., temperature in C˚or F˚, calendar dates

No true zero-point
 Ratio

Inherent zero-point

We can speak of values as being an order of
magnitude larger than the unit of
measurement (10 K˚ is twice as high as 5 K˚).
 e.g., temperature in Kelvin, length, counts,
monetary quantities

8
 Discrete vs. Continuous
Attributes
 Discrete Attribute
 Has only a finite or countably infinite set of values


E.g., zip codes, profession, or the set of words in
a collection of documents
 Sometimes, represented as integer variables

 Note: Binary attributes are a special case of

discrete attributes
 Continuous Attribute
 Has real numbers as attribute values


E.g., temperature, height, or weight
 Practically, real values can only be measured and

represented using a finite number of digits

 Continuous attributes are typically represented as

floating-point variables
9
Chapter 2: Getting to Know Your
Data

 Data Objects and Attribute Types

 Basic Statistical Descriptions of Data

 Data Visualization

 Measuring Data Similarity and Dissimilarity

 Summary

10
Basic Statistical Descriptions of
Data
 Motivation
 To better understand the data: central tendency,
variation and spread
 Data dispersion characteristics
 median, max, min, quantiles, outliers, variance, etc.
 Numerical dimensions correspond to sorted intervals
 Data dispersion: analyzed with multiple granularities
of precision
 Boxplot or quantile analysis on sorted intervals
 Dispersion analysis on computed measures
 Folding measures into numerical dimensions
 Boxplot or quantile analysis on the transformed
cube
11
Measuring the Central Tendency
 Mean (algebraic measure) (sample vs. population): 1 n
x   xi   x
Note: n is sample size and N is population size. n i 1 N
n
 Weighted arithmetic mean:

w x i i
Trimmed mean: chopping extreme values x  i 1
n
 Median: w
i 1
i
 Middle value if odd number of values, or average
of the middle two values otherwise
 Estimated by interpolation (for grouped data):
n / 2  ( freq )l

median L1  ( ) width
Mode freq median
 Value that occurs most frequently in the data
 Unimodal, bimodal, trimodal
 Empirical formula:
mean  mode 3 (mean  median)
12
 Symmetric vs.
Skewed Data
 Median, mean and mode of symmetric
symmetric, positively and
negatively skewed data

positively negatively
skewed skewed

Data Mining: Concepts and

November 19, 2024 Techniques 13
 Measuring the Dispersion of
Data
 Quartiles, outliers and boxplots
 Quartiles: Q1 (25th percentile), Q3 (75th percentile)
 Inter-quartile range: IQR = Q3 – Q1
 Five number summary: min, Q1, median, Q3, max
 Boxplot: ends of the box are the quartiles; median is marked; add
whiskers, and plot outliers individually
 Outlier: usually, a value higher/lower than 1.5 x IQR
 Variance and standard deviation (sample: s, population: σ)
 Variance: (algebraic, scalable computation)
1 n 1 n 2 1 n 1 n 1 n
2
s  
n  1 i 1
2

( xi  x )   2
[ xi  ( xi ) ]
n  1 i 1 n i 1
   ( xi   ) 2 
2

N i 1 N
 xi   2
i 1
2

 Standard deviation s (or σ) is the square root of variance s2 (or σ2)

14
 Boxplot Analysis
 Five-number summary of a distribution
 Minimum, Q1, Median, Q3, Maximum
 Boxplot
 Data is represented with a box
 The ends of the box are at the first and
third quartiles, i.e., the height of the
box is IQR
 The median is marked by a line within
the box
 Whiskers: two lines outside the box
extended to Minimum and Maximum
 Outliers: points beyond a specified
outlier threshold, plotted individually
15
 Visualization of Data Dispersion: 3-D
Boxplots

Data Mining: Concepts and

November 19, 2024 Techniques 16
 Properties of Normal Distribution
Curve

 The normal (distribution) curve

 From μ–σ to μ+σ: contains about 68% of the

measurements (μ: mean, σ: standard deviation)

 From μ–2σ to μ+2σ: contains about 95% of it
 From μ–3σ to μ+3σ: contains about 99.7% of it

17
Graphic Displays of Basic Statistical
Descriptions

 Boxplot: graphic display of five-number summary

 Histogram: x-axis are values, y-axis repres.
frequencies
 Quantile plot: each value xi is paired with fi indicating
that approximately 100 fi % of data are  xi
 Quantile-quantile (q-q) plot: graphs the quantiles of
one univariant distribution against the corresponding
quantiles of another
 Scatter plot: each pair of values is a pair of
coordinates and plotted as points in the plane
18
 Histogram Analysis
 Histogram: Graph display of
tabulated frequencies, shown as 40
bars 35
 It shows what proportion of cases
30
fall into each of several categories
25
 Differs from a bar chart in that it
is the area of the bar that denotes 20
the value, not the height as in bar 15
charts, a crucial distinction when
the categories are not of uniform 10
width 5
 The categories are usually 0
specified as non-overlapping 10000 30000 50000 70000 90000

intervals of some variable. The

categories (bars) must be
adjacent
19
Histograms Often Tell More than
Boxplots

 The two histograms

shown in the left
may have the same
boxplot
representation
 The same values
for: min, Q1,
median, Q3, max
 But they have
rather different data
distributions

20
 Quantile Plot
 Displays all of the data (allowing the user to assess
both the overall behavior and unusual occurrences)
 Plots quantile information

For a data xi data sorted in increasing order, fi
indicates that approximately 100 fi% of the data
are below or equal to the value xi

Data Mining: Concepts and

Techniques 21
 Quantile-Quantile (Q-Q) Plot
 Graphs the quantiles of one univariate distribution against the
corresponding quantiles of another
 View: Is there is a shift in going from one distribution to another?
 Example shows unit price of items sold at Branch 1 vs. Branch 2
for each quantile. Unit prices of items sold at Branch 1 tend to
be lower than those at Branch 2.

22
 Scatter plot
 Provides a first look at bivariate data to see
clusters of points, outliers, etc
 Each pair of values is treated as a pair of
coordinates and plotted as points in the plane

23
Positively and Negatively Correlated
Data

 The left half fragment is positively

correlated
 The right half is negative correlated

24
Uncorrelated Data

25
Chapter 2: Getting to Know Your
Data

 Data Objects and Attribute Types

 Basic Statistical Descriptions of Data

 Data Visualization

 Measuring Data Similarity and Dissimilarity

 Summary

26
 Data Visualization
 Why data visualization?
 Gain insight into an information space by mapping data onto
graphical primitives
 Provide qualitative overview of large data sets
 Search for patterns, trends, structure, irregularities, relationships
among data
 Help find interesting regions and suitable parameters for further
quantitative analysis
 Provide a visual proof of computer representations derived
 Categorization of visualization methods:
 Pixel-oriented visualization techniques
 Geometric projection visualization techniques
 Icon-based visualization techniques
 Hierarchical visualization techniques
 Visualizing complex data and relations
27
 Pixel-Oriented Visualization
Techniques
 For a data set of m dimensions, create m windows on the
screen, one for each dimension
 The m dimension values of a record are mapped to m pixels
at the corresponding positions in the windows
 The colors of the pixels reflect the corresponding values

(a) Income (b) Credit (c) transaction (d) age

Limit volume 28
 Laying Out Pixels in Circle
Segments
 To save space and show the connections among multiple
dimensions, space filling is often done in a circle segment

(a) Representing a data

(b) Laying out pixels in circle
record in circle segment
segment
29
 Geometric Projection Visualization
Techniques

 Visualization of geometric transformations and

projections of the data
 Methods
 Direct visualization
 Scatterplot and scatterplot matrices
 Landscapes
 Projection pursuit technique: Help users find
meaningful projections of multidimensional data
 Prosection views
 Hyperslice
 Parallel coordinates
30
Ribbons with Twists Based on Vorticity
Direct Data Visualization

Data Mining: Concepts and

Techniques 31
 Scatterplot Matrices

Used by ermission of M. Ward, Worcester Polytechnic Institute

Matrix of scatterplots (x-y-diagrams) of the k-dim. data [total of (k2/2-k) scatterplots]

32
 Landscapes
Used by permission of B. Wright, Visible Decisions Inc.

news articles
visualized as
a landscape

 Visualization of the data as perspective landscape

 The data needs to be transformed into a (possibly artificial) 2D spatial
representation which preserves the characteristics of the data

33
 Parallel Coordinates
 n equidistant axes which are parallel to one of the screen
axes and correspond to the attributes
 The axes are scaled to the [minimum, maximum]: range of
the corresponding attribute
 Every data item corresponds to a polygonal line which
intersects each of the axes at the point which corresponds to
the value for the attribute

• • •

Attr. 1 Attr. 2 Attr. 3 Attr. k

34
Parallel Coordinates of a Data Set

35
 Icon-Based Visualization
Techniques

 Visualization of the data values as features of icons

 Typical visualization methods
 Chernoff Faces
 Stick Figures
 General techniques
 Shape coding: Use shape to represent certain
information encoding
 Color icons: Use color icons to encode more
information
 Tile bars: Use small icons to represent the
relevant feature vectors in document retrieval
36
 Chernoff Faces
 A way to display variables on a two-dimensional surface, e.g.,
let x be eyebrow slant, y be eye size, z be nose length, etc.
 The figure shows faces produced using 10 characteristics--
head eccentricity, eye size, eye spacing, eye eccentricity,
pupil size, eyebrow slant, nose size, mouth shape, mouth
size, and mouth opening): Each assigned one of 10 possible
values, generated using Mathematica (S. Dickson)
 REFERENCE: Gonick, L. and Smith, W.
The Cartoon Guide to Statistics. New York:
Harper Perennial, p. 212, 1993
 Weisstein, Eric W. "Chernoff Face." From
MathWorld--A Wolfram Web Resource.
mathworld.wolfram.com/ChernoffFace.htm
l
37
 Stick Figure
A census data
figure showing
age, income,
used by permission of G. Grinstein, University of Massachusettes at Lowell

gender,
education, etc.

A 5-piece
stick figure (1
body and 4
limbs w.
different
angle/length)
Two attributes mapped to axes, remaining attributes mapped to angle or length of limbs”. Look at 38
 Hierarchical Visualization
Techniques

 Visualization of the data using a

hierarchical partitioning into subspaces
 Methods
 Dimensional Stacking
 Worlds-within-Worlds
 Tree-Map
 Cone Trees
 InfoCube

39
 Dimensional Stacking

attribute 4
attribute 2

attribute 3

attribute 1

 Partitioning of the n-dimensional attribute space in 2-D

subspaces, which are ‘stacked’ into each other
 Partitioning of the attribute value ranges into classes. The
important attributes should be used on the outer levels.
 Adequate for data with ordinal attributes of low cardinality
 But, difficult to display more than nine dimensions
 Important to map dimensions appropriately

40
 Dimensional Stacking
Used by permission of M. Ward, Worcester Polytechnic Institute

Visualization of oil mining data with longitude and latitude mapped to

the outer x-, y-axes and ore grade and depth mapped to the inner x-, y-
axes
41
 Worlds-within-Worlds
 Assign the function and two most important parameters to
innermost world
 Fix all other parameters at constant values - draw other (1 or 2
or 3 dimensional worlds choosing these as the axes)
 Software that uses this paradigm
 N–vision: Dynamic
interaction through
data glove and stereo
displays, including
rotation, scaling
(inner) and translation
(inner/outer)
 Auto Visual: Static
interaction by means
of queries
42
 Tree-Map
 Screen-filling method which uses a hierarchical partitioning
of the screen into regions depending on the attribute values
 The x- and y-dimension of the screen are partitioned
alternately according to the attribute values (classes)

MSR Netscan Image

Ack.: 43
Tree-Map of a File System
(Schneiderman)

44
 InfoCube
 A 3-D visualization technique where
hierarchical information is displayed as
nested semi-transparent cubes
 The outermost cubes correspond to the top
level data, while the subnodes or the lower
level data are represented as smaller cubes
inside the outermost cubes, and so on

45
 Three-D Cone Trees
 3D cone tree visualization technique
works well for up to a thousand nodes or
so
 First build a 2D circle tree that arranges
its nodes in concentric circles centered
on the root node
 Cannot avoid overlaps when projected to
2D
 G. Robertson, J. Mackinlay, S. Card.
“Cone Trees: Animated 3D Visualizations
of Hierarchical Information”, ACM
SIGCHI'91
 Graph from Nadeau Software Consulting
website: Visualize a social network data
set that models the way an infection
spreads from one person to the next
Ack.: http://nadeausoftware.com/articles/visualization
46
 Visualizing Complex Data and
Relations
 Visualizing non-numerical data: text and social networks
 Tag cloud: visualizing user-generated tags

 The importance
of tag is
represented by
font size/color
 Besides text data,
there are also
methods to
visualize
relationships, such
as visualizing social
networks
Newsmap: Google News Stories in
Chapter 2: Getting to Know Your
Data

 Data Objects and Attribute Types

 Basic Statistical Descriptions of Data

 Data Visualization

 Measuring Data Similarity and Dissimilarity

 Summary

48
 Similarity and Dissimilarity
 Similarity
 Numerical measure of how alike two data objects

are
 Value is higher when objects are more alike

 Often falls in the range [0,1]

 Dissimilarity (e.g., distance)

 Numerical measure of how different two data

objects are
 Lower when objects are more alike

 Minimum dissimilarity is often 0

 Upper limit varies

 Proximity refers to a similarity or dissimilarity

49
 Data Matrix and Dissimilarity
Matrix
 Data matrix
 n data points with  x11 ... x1f ... x1p 
 
p dimensions  ... ... ... ... ... 
 Two modes x ... xif ... xip 
 i1 
 ... ... ... ... ... 
x ... xnf ... xnp 
 n1 
 Dissimilarity matrix
 n data points, but
 0 
 d(2,1) 0 
registers only the  
 d(3,1) d ( 3,2) 0 
distance  
 A triangular matrix  : : : 
 d ( n,1) d ( n,2) ... ... 0
 Single mode

50
 Proximity Measure for Nominal
Attributes
 Can take 2 or more states, e.g., red, yellow,
blue, green (generalization of a binary attribute)
 Method 1: Simple matching

m: # of matches, p: total # of variables

d (i, j)  p p m
 Method 2: Use a large number of binary
attributes

creating a new binary attribute for each of the
M nominal states

51
 Proximity Measure for Binary
Attributes
Object j
 A contingency table for binary data
Object i

 Distance measure for symmetric

binary variables:
 Distance measure for asymmetric
binary variables:
 Jaccard coefficient (similarity
measure for asymmetric binary
variables):

 Note: Jaccard coefficient is the same as “coherence”:

52
 Dissimilarity between Binary
Variables
 Example
Name Gender Fever Cough Test-1 Test-2 Test-3 Test-4
Jack M Y N P N N N
Mary F Y N P N P N
Jim M Y P N N N N
 Gender is a symmetric attribute
 The remaining attributes are asymmetric binary
 Let the values Y and P be 1, and the value N 0
0 1
d ( jack , mary )  0.33
2  0 1
11
d ( jack , jim )  0.67
111
1 2
d ( jim , mary )  0.75
11 2
53
 Standardizing Numeric Data
x  
 Z-score: z  
 X: raw score to be standardized, μ: mean of the
population, σ: standard deviation
 the distance between the raw score and the population
mean in units of the standard deviation
 negative when the raw score is below the mean, “+”
when above

s 1Calculate
An alternative way: (| x  m the
f n 1f |  | xmean
 mabsolute
f
| ... | x deviation
2f f
 m |) nf f
m f  1n (x1 f  x2 f  ...  xnf )
xif  m f
.

where
zif  s
f
 standardized measure (z-score):
 Using mean absolute deviation is more robust than using
standard deviation
54
 Example:
Data Matrix and Dissimilarity Matrix
Data Matrix
x2 x4
point attribute1 attribute2
4 x1 1 2
x2 3 5
x3 2 0
x4 4 5
2 x1
Dissimilarity Matrix
(with Euclidean Distance)
x3
0 4 x1 x2 x3 x4
2
x1 0
x2 3.61 0
x3 5.1 5.1 0
x4 4.24 1 5.39 0

55
Distance on Numeric Data: Minkowski
Distance
 Minkowski distance: A popular distance measure

where i = (xi1, xi2, …, xip) and j = (xj1, xj2, …, xjp) are two
p-dimensional data objects, and h is the order (the
distance so defined is also called L-h norm)
 Properties
 d(i, j) > 0 if i ≠ j, and d(i, i) = 0 (Positive definiteness)
 d(i, j) = d(j, i) (Symmetry)
 d(i, j)  d(i, k) + d(k, j) (Triangle Inequality)
 A distance that satisfies these properties is a metric

56
Special Cases of Minkowski Distance
 h = 1: Manhattan (city block, L1 norm) distance
 E.g., the Hamming distance: the number of bits that are
different between two binary vectors
d (i, j) | x  x |  | x  x | ... | x  x |
i1 j1 i2 j 2 ip jp

 h = 2: (L2 norm) Euclidean distance

d (i, j)  (| x  x |2  | x  x |2 ... | x  x |2 )
i1 j1 i2 j 2 ip jp

 h  . “supremum” (Lmax norm, L norm) distance.

 This is the maximum difference between any component
(attribute) of the vectors

57
 Example: Minkowski Distance
Dissimilarity Matrices
point attribute 1 attribute 2 Manhattan
x1 1 2 (L1)L x1 x2 x3 x4
x2 3 5 x1 0
x3 2 0 x2 5 0
x4 4 5 x3 3 6 0
x4 6 1 7 0
Euclidean (L2)
x2 x4
L2 x1 x2 x3 x4
4 x1 0
x2 3.61 0
x3 2.24 5.1 0
x4 4.24 1 5.39 0

2 x1
Supremum
L x1 x2 x3 x4
x1 0
x2 3 0
x3 x3 2 5 0
0 2 4 x4 3 1 5 0
58
 Ordinal Variables

 An ordinal variable can be discrete or continuous

 Order is important, e.g., rank
 Can be treated like interval-scaled
 replace x by their rank rif {1,..., M f }
if

 map the range of each variable onto [0, 1] by

replacing i-th object in the f-th variable by
rif  1
zif 
Mf 1

 compute the dissimilarity using methods for

interval-scaled variables

59
 Attributes of Mixed Type
 A database may contain all attribute types
 Nominal, symmetric binary, asymmetric binary,

numeric, ordinal
 One may use a weighted formula to combine their
effects
 pf 1 ij( f ) dij( f )
d (i, j)  p
 f 1 ij( f )
 f is binary or nominal:
dij(f) = 0 if xif = xjf , or dij(f) = 1 otherwise
 f is numeric: use the normalized distance
 f is ordinal

Compute ranks rif and zif  rif  1


Treat zif as interval-scaled Mf 1
60
 Cosine Similarity
 A document can be represented by thousands of attributes, each
recording the frequency of a particular word (such as keywords)
or phrase in the document.

 Other vector objects: gene features in micro-arrays, …

 Applications: information retrieval, biologic taxonomy, gene
feature mapping, ...
 Cosine measure: If d1 and d2 are two vectors (e.g., term-frequency
vectors), then
cos(d1, d2) = (d1  d2) /||d1|| ||d2|| ,
where  indicates vector dot product, ||d||: the length of vector
d
61
 Example: Cosine Similarity
 cos(d1, d2) = (d1  d2) /||d1|| ||d2|| ,
where  indicates vector dot product, ||d|: the length of vector d

 Ex: Find the similarity between documents 1 and 2.

d1 = (5, 0, 3, 0, 2, 0, 0, 2, 0, 0)
d2 = (3, 0, 2, 0, 1, 1, 0, 1, 0, 1)

d1d2 = 5*3+0*0+3*2+0*0+2*1+0*1+0*1+2*1+0*0+0*1 = 25
||d1||= (5*5+0*0+3*3+0*0+2*2+0*0+0*0+2*2+0*0+0*0)0.5=(42)0.5
= 6.481
||d2||= (3*3+0*0+2*2+0*0+1*1+1*1+0*0+1*1+0*0+1*1)0.5=(17)0.5
= 4.12
cos(d1, d2 ) = 0.94

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Chapter 2: Getting to Know Your
Data

 Data Objects and Attribute Types

 Basic Statistical Descriptions of Data

 Data Visualization

 Measuring Data Similarity and Dissimilarity

 Summary

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 Summary
 Data attribute types: nominal, binary, ordinal, interval-scaled,
ratio-scaled
 Many types of data sets, e.g., numerical, text, graph, Web,
image.
 Gain insight into the data by:
 Basic statistical data description: central tendency,
dispersion, graphical displays
 Data visualization: map data onto graphical primitives
 Measure data similarity
 Above steps are the beginning of data preprocessing.
 Many methods have been developed but still an active area of
research.

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 References
 W. Cleveland, Visualizing Data, Hobart Press, 1993
 T. Dasu and T. Johnson. Exploratory Data Mining and Data Cleaning. John Wiley, 2003
 U. Fayyad, G. Grinstein, and A. Wierse. Information Visualization in Data Mining and
Knowledge Discovery, Morgan Kaufmann, 2001
 L. Kaufman and P. J. Rousseeuw. Finding Groups in Data: an Introduction to Cluster
Analysis. John Wiley & Sons, 1990.
 H. V. Jagadish, et al., Special Issue on Data Reduction Techniques. Bulletin of the Tech.
Committee on Data Eng., 20(4), Dec. 1997
 D. A. Keim. Information visualization and visual data mining, IEEE trans. on Visualization
and Computer Graphics, 8(1), 2002
 D. Pyle. Data Preparation for Data Mining. Morgan Kaufmann, 1999
 S. Santini and R. Jain,” Similarity measures”, IEEE Trans. on Pattern Analysis and
Machine Intelligence, 21(9), 1999
 E. R. Tufte. The Visual Display of Quantitative Information, 2nd ed., Graphics Press,
2001
 C. Yu , et al., Visual data mining of multimedia data for social and behavioral studies,
Information Visualization, 8(1), 2009
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