Data Mining: Exploring Data

Lecture Notes for Chapter 3

I t d ti to
Introduction t Data
D t Mining
Mi i
by
Tan Steinbach
Tan, Steinbach, Kumar

(modified by P. Radivojac)
What is data exploration?

A preliminary exploration of the data to better

understand its characteristics.

z Key motivations of data exploration include

– Helping to select the right tool for preprocessing or analysis
– Making
M ki use off humans’
h ’ abilities
biliti tto recognize
i patterns
tt
‹ People can recognize patterns not captured by data analysis
tools

z Related to the area of Exploratory Data Analysis (EDA)

– Created by statistician John Tukey
– Seminal
S i lb book k iis E
Exploratory
l t D
Data
t AAnalysis
l i b by Tukey
T k
– A nice online introduction can be found in Chapter 1 of the NIST
Engineering Statistics Handbook
htt //
http://www.itl.nist.gov/div898/handbook/index.htm
itl i t /di 898/h db k/i d ht
Techniques Used In Data Exploration

z In EDA, as originally defined by Tukey

– The focus was on visualization
– Clustering and anomaly detection were viewed as
exploratory techniques
– In data mining, clustering and anomaly detection are
major areas of interest, and not thought of as just
exploratory

z In our discussion of data exploration, we focus on

– Summary statistics
– Visualization
– Online Analytical
y Processing
g ((OLAP))
About Flowers

www.answers.com/topic/tetramery
Iris Data Set

z Many of the exploratory data techniques are illustrated

with the Iris Plant data set.
– Can be obtained from the UCI Machine Learning Repository
http://archive.ics.uci.edu/ml/machine-learning-databases/iris/
– From the statistician R.A. Fisher
– Three flower types (classes):
‹ Setosa
‹ Virginica

‹ Versicolour

– Four attributes
‹ Sepal width and length
‹ Petal width and length
Virginica. Robert H. Mohlenbrock. USDA
NRCS. 1995. Northeast wetland flora: Field
office guide to plant species. Northeast National
Technical Center, Chester, PA. Courtesy of
USDA NRCS Wetland Science Institute.
Summary Statistics

z Summary statistics are numbers that summarize

properties of the data

– Summarized properties include frequency, location and

spread
‹ Examples: location - mean
spread - standard deviation

– Most summary statistics can be calculated in a single

pass through the data
Frequency and Mode

z The frequency of an attribute value is the

percentage of time the value occurs in the
data set
– For example,
example given the attribute ‘gender’
gender and a
representative population of people, the gender
‘female’ occurs about 50% of the time.
z The mode of a an attribute is the most frequent
attribute value
z The notions of frequency and mode are typically
used with categorical data
Percentiles

z For continuous data, the notion of a percentile is

more useful.

z Given an ordinal or continuous attribute x and a

number p between 0 and 100, the pth percentile is
a value xp of x such that p
p% of the observed
values of x are less than xp.

z For instance, the 75th percentile is the value x75%

such that 75% of all values of x are less than x75% .
Measures of Location: Mean and Median

z The mean is the most common measure of the

location of a set of points.
z However, the mean is very sensitive to outliers.
z Thus,
Thus the median or a trimmed mean is also
commonly used.
Measures of Spread: Range and Variance

z Range is the difference between the max and min

z The variance or standard deviation is the most

common measure of the spread of a set of points.
Visualization

Visualization is the conversion of data into a visual

or tabular format so that the characteristics of the
data and the relationships among data items or
attributes can be analyzed or reported.

z Visualization of data is one of the most powerful

and appealing techniques for data exploration
exploration.
– Humans have a well developed ability to analyze large
amounts of information that is presented visually
– Can detect general patterns and trends
– Can detect outliers and unusual patterns
Example: Sea Surface Temperature

z The following shows the Sea Surface

Temperature (SST) for July 1982
– Tens of thousands of data points are summarized in a
single figure
Representation

z is the mapping of information to a visual format

z Data objects, their attributes, and the relationships
among data objects are translated into graphical
elements such as points, lines, shapes, and
colors.
colors
z Example:
– Objects are often represented as points
– Their attribute values can be represented as the
position of the points or the characteristics of the
points,
i t e.g., color,
l size,
i and
d shape
h
– If position is used, then the relationships of points, i.e.,
whether theyy form g groups
p or a p point is an outlier,, is
easily perceived.
Arrangement

z Is the placement of visual elements within a

display
z Can make a large difference in how easy it is to
understand the data
z Example:
Selection

z Is the elimination or the de-emphasis of certain

objects and attributes
z Selection may involve choosing a subset of
attributes
– Dimensionality reduction is often used to reduce the
number of dimensions to two or three

z Selection may also involve choosing a subset of

objects
– A region of the screen can only show so many points
– Can sample, but want to preserve points in sparse
areas
Visualization Techniques: Histograms

z Histogram
– Usually shows the distribution of values of a single variable
– Divide the values into bins and show a bar plot of the number of
objects in each bin.
– The height of each bar indicates the number of objects
– Shape of histogram depends on the number of bins
z Example: Petal Width (10 and 20 bins, respectively)
Two-Dimensional Histograms

z Show the joint distribution of the values of two

attributes
z Example: petal width and petal length
– What does this tell us?
Visualization Techniques: Box Plots

z Box Plots
– Invented byy J. Tukeyy
– Another way of displaying the distribution of data
– Following figure shows the basic part of a box plot
outlier

90th percentile

75th percentile

50th percentile
25th percentile

10th percentile
Example of Box Plots

z Box plots can be used to compare attributes

Box Plots for Quiz 1

Note: not for year 2009-2010

Visualization Techniques: Scatter Plots

z Scatter plots
– Attributes values determine the position
p
– Two-dimensional scatter plots most common, but can
have three-dimensional scatter plots
– Often additional attributes can be displayed by using
the size, shape, and color of the markers that
represent the objects
– It is useful to have arrays of scatter plots can
compactly summarize the relationships of several pairs
of attributes
‹ See example on the next slide
Scatter Plot Array of Iris Attributes
Visualization Techniques: Contour Plots

z Contour plots
– Useful when a continuous attribute is measured on a
spatial grid
– They partition the plane into regions of similar values
– The contour lines that form the boundaries of these
regions connect points with equal values
– The most common example is contour maps of
elevation
– Can also display temperature, rainfall, air pressure,
etc.
‹ An example for Sea Surface Temperature (SST) is provided
on the next slide
Contour Plot Example: SST Dec, 1998

Celsius
Visualization Techniques: Matrix Plots

z Matrix plots
– Can plot the data matrix
– This can be useful when objects are sorted according
to class
– Typically, the attributes are normalized to prevent one
attribute from dominating the plot
– Plots
Pl t off similarity
i il it or di
distance
t matrices
ti can also
l b be
useful for visualizing the relationships between objects
– Examples of matrix plots are presented on the next two
slides
Visualization of the Iris Data Matrix

standard
deviation
Visualization of the Iris Correlation Matrix
Visualization Techniques: Parallel Coordinates

z Parallel Coordinates
– Used to pplot the attribute values of high-dimensional
g
data
– Instead of using perpendicular axes, use a set of
parallel axes
– The attribute values of each object are plotted as a
point on each corresponding coordinate axis and the
points are connected by a line
– Thus, each object is represented as a line
– Often, the lines representing a distinct class of objects
group together, at least for some attributes
– Ordering of attributes is important in seeing such
groupings
Parallel Coordinates Plots for Iris Data
Other Visualization Techniques

z Star Plots
– Similar approach
pp to p
parallel coordinates,, but axes
radiate from a central point
– The line connecting the values of an object is a
polygon
z Chernoff Faces
– Approach
pp created by y Herman Chernoff
– This approach associates each attribute with a
characteristic of a face
– The values of each attribute determine the appearance
of the corresponding facial characteristic
– Each object becomes a separate face
– Relies on human’s ability to distinguish faces
Star Plots for Iris Data

S t
Setosa

Versicolour

Virginica
Chernoff Faces for Iris Data

Setosa

Versicolour

Virginica
Visualization via graphs

Community of political blogs (from 2004), 2004) where red nodes indicate conservative
blogs, and blue liberal. Orange links go from liberal to conservative, and purple
ones from conservative to liberal. The size of each blog reflects the number of other
blogs that link to it. (Lazer et al. Science, January 2009.)
Visualization via graphs

Each node represents a disease with the size corresponding to the number of genes
implicated in disease. An edge between diseases means that there is at least one
shared gene. Goh et al. PNAS, 104: 8685 (2007).