Data Mining: Data

Lecture Notes for Chapter 2

Introduction to Data Mining , 2nd Edition

by
Tan, Steinbach, Kumar

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Outline

● Attributes and Objects

● Types of Data

● Data Quality

● Similarity and Distance

● Data Preprocessing

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What is Data?

● Collection of data objects Attributes

and their attributes
● An attribute is a property or
characteristic of an object
– Examples: eye color of a
person, temperature, etc.
– Attribute is also known as

Objects
variable, field, characteristic,
dimension, or feature
● A collection of attributes
describe an object
– Object is also known as
record, point, case, sample,
entity, or instance
Attribute Values

● Attribute values are numbers or symbols

assigned to an attribute for a particular object

● Distinction between attributes and attribute values

– Same attribute can be mapped to different attribute
values
◆ Example: height can be measured in feet or meters

– Different attributes can be mapped to the same set of

values
◆ Example: Attribute values for ID and age are integers
– But properties of attribute can be different than the
properties of the values used to represent the
attribute Introduction to Data Mining, 2nd Edition
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 Measurement of Length
● The way you measure an attribute may not match the
attributes properties.

This scale This scale

preserves preserves
only the the ordering
ordering and additvity
property of properties of
length. length.
 Types of Attributes

● There are different types of attributes

– Nominal
◆ Examples: ID numbers, eye color, zip codes
– Ordinal
◆ Examples: rankings (e.g., taste of potato chips on a scale
from 1-10), grades, height {tall, medium, short}
– Interval
◆ Examples: calendar dates, temperatures in Celsius or
Fahrenheit.
– Ratio
◆ Examples: temperature in Kelvin, length, counts, elapsed
time (e.g., time to run a race)
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Properties of Attribute Values

● The type of an attribute depends on which of the

following properties/operations it possesses:
– Distinctness: = ≠
– Order: < >
– Differences are + -
meaningful :
– Ratios are * /
meaningful

– Nominal attribute: distinctness

– Ordinal attribute: distinctness & order
– Interval attribute: distinctness, order & meaningful differences
– Ratio attribute: all 4 properties/operations
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Difference Between Ratio and Interval

● Is it physically meaningful to say that a

temperature of 10 ° is twice that of 5° on
– the Celsius scale?
– the Fahrenheit scale?
– the Kelvin scale?

● Consider measuring the height above average

– If Bill’s height is three inches above average and
Bob’s height is six inches above average, then would
we say that Bob is twice as tall as Bill?
– Is this situation analogous to that of temperature?

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This categorization of attributes is due to S. S. Stevens
This categorization of attributes is due to S. S. Stevens
Discrete and Continuous Attributes

● Discrete Attribute
– Has only a finite or countably infinite set of values
– Examples: zip codes, counts, or the set of words in a
collection of documents
– Often represented as integer variables.
– Note: binary attributes are a special case of discrete
attributes
● Continuous Attribute
– Has real numbers as attribute values
– Examples: 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.
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Asymmetric Attributes

● Only presence (a non-zero attribute value) is regarded as

important
◆ Words present in documents
◆ Items present in customer transactions

● If we met a friend in the grocery store would we ever say

the following?
“I see our purchases are very similar since we didn’t buy most of
the same things.”

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Critiques of the attribute categorization

● Incomplete
– Asymmetric binary
– Cyclical
– Multivariate
– Partially ordered
– Partial membership
– Relationships between the data

● Real data is approximate and noisy

– This can complicate recognition of the proper attribute type
– Treating one attribute type as another may be approximately
correct

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Key Messages for Attribute Types

● The types of operations you choose should be

“meaningful” for the type of data you have
– Distinctness, order, meaningful intervals, and meaningful ratios
are only four (among many possible) properties of data

– The data type you see – often numbers or strings – may not
capture all the properties or may suggest properties that are
not present

– Analysis may depend on these other properties of the data

◆ Many statistical analyses depend only on the distribution

– In the end, what is meaningful can be specific to domain

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Important Characteristics of Data

– Dimensionality (number of attributes)

◆ High dimensional data brings a number of challenges

– Sparsity
◆ Only presence counts

– Resolution
◆ Patterns depend on the scale

– Size
◆ Type of analysis may depend on size of data

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Types of data sets
● Record
– Data Matrix
– Document Data
– Transaction Data
● Graph
– World Wide Web
– Molecular Structures
● Ordered
– Spatial Data
– Temporal Data
– Sequential Data
– Genetic Sequence Data

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Record Data

● Data that consists of a collection of records, each

of which consists of a fixed set of attributes

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Data Matrix

● If data objects have the same fixed set of numeric

attributes, then the data objects can be thought of as
points in a multi-dimensional space, where each
dimension represents a distinct attribute

● Such a data set can be represented by an m by n matrix,

where there are m rows, one for each object, and n
columns, one for each attribute

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Document Data

● Each document becomes a ‘term’ vector

– Each term is a component (attribute) of the vector
– The value of each component is the number of times
the corresponding term occurs in the document.

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Transaction Data

● A special type of data, where

– Each transaction involves a set of items.
– For example, consider a grocery store. The set of products
purchased by a customer during one shopping trip constitute a
transaction, while the individual products that were purchased are
the items.
– Can represent transaction data as record data

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 Graph Data

● Examples: Generic graph, a molecule, and webpages

Benzene Molecule:
C6H6
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Ordered Data

● Sequences of transactions
Items/Events

An element of
the sequence
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Ordered Data

● Genomic sequence data

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Ordered Data

● Spatio-Temporal Data

Average Monthly
Temperature of
land and ocean

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Data Quality

● Poor data quality negatively affects many data processing

efforts

● Data mining example: a classification model for detecting

people who are loan risks is built using poor data
– Some credit-worthy candidates are denied loans
– More loans are given to individuals that default

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Data Quality …

● What kinds of data quality problems?

● How can we detect problems with the data?
● What can we do about these problems?

● Examples of data quality problems:

– Noise and outliers
– Wrong data
– Fake data
– Missing values
– Duplicate data
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Noise

● For objects, noise is an extraneous object

● For attributes, noise refers to modification of original values
– Examples: distortion of a person’s voice when talking on a poor phone and
“snow” on television screen
– The figures below show two sine waves of the same magnitude and different
frequencies, the waves combined, and the two sine waves with random noise
◆ The magnitude and shape of the original signal is distorted

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Outliers

● Outliers are data objects with characteristics that

are considerably different than most of the other
data objects in the data set
– Case 1: Outliers are
noise that interferes
with data analysis

– Case 2: Outliers are

the goal of our analysis
◆ Credit card fraud
◆ Intrusion detection

● Causes?
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Missing Values

● Reasons for missing values

– Information is not collected
(e.g., people decline to give their age and weight)
– Attributes may not be applicable to all cases
(e.g., annual income is not applicable to children)

● Handling missing values

– Eliminate data objects or variables
– Estimate missing values
◆ Example: time series of temperature
◆ Example: census results
– Ignore the missing value during analysis

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Duplicate Data

● Data set may include data objects that are

duplicates, or almost duplicates of one another
– Major issue when merging data from heterogeneous
sources

● Examples:
– Same person with multiple email addresses

● Data cleaning
– Process of dealing with duplicate data issues

● When should duplicate data not be removed?

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Similarity and Dissimilarity Measures

● Similarity measure
– Numerical measure of how alike two data objects are.
– Is higher when objects are more alike.
– Often falls in the range [0,1]
● Dissimilarity measure
– 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
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 Similarity/Dissimilarity for Simple Attributes

The following table shows the similarity and dissimilarity

between two objects, x and y, with respect to a single, simple
attribute.

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Euclidean Distance

● Euclidean Distance

where n is the number of dimensions (attributes) and xk

and yk are, respectively, the kth attributes (components)
or data objects x and y.

● Standardization is necessary, if scales differ.

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Euclidean Distance

Distance Matrix
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Minkowski Distance

● Minkowski Distance is a generalization of Euclidean

Distance

Where r is a parameter, n is the number of dimensions

(attributes) and xk and yk are, respectively, the kth
attributes (components) or data objects x and y.

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Minkowski Distance: Examples

● r = 1. City block (Manhattan, taxicab, L1 norm) distance.

– A common example of this for binary vectors is the Hamming
distance, which is just the number of bits that are different
between two binary vectors

● r = 2. Euclidean distance

● r → ∞. “supremum” (Lmax norm, L∞ norm) distance.

– This is the maximum difference between any component of
the vectors

● Do not confuse r with n, i.e., all these distances are

defined for all numbers of dimensions.

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Minkowski Distance

Distance Matrix
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 Mahalanobis Distance

Σ is the covariance matrix

For red points, the Euclidean distance is 14.7, Mahalanobis distance is 6.

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Mahalanobis Distance

Covariance
Matrix:

B A: (0.5, 0.5)
B: (0, 1)
A
C: (1.5, 1.5)

Mahal(A,B) = 5
Mahal(A,C) = 4

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Common Properties of a Distance

● Distances, such as the Euclidean distance,

have some well known properties.
1. d(x, y) ≥ 0 for all x and y and d(x, y) = 0 if and only
if x = y.
2. d(x, y) = d(y, x) for all x and y. (Symmetry)
3. d(x, z) ≤ d(x, y) + d(y, z) for all points x, y, and z.
(Triangle Inequality)

where d(x, y) is the distance (dissimilarity) between

points (data objects), x and y.

● A distance that satisfies these properties is a

metric

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Common Properties of a Similarity

● Similarities, also have some well known

properties.

1. s(x, y) = 1 (or maximum similarity) only if x = y.

(does not always hold, e.g., cosine)
2. s(x, y) = s(y, x) for all x and y. (Symmetry)

where s(x, y) is the similarity between points (data

objects), x and y.

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Similarity Between Binary Vectors
● Common situation is that objects, x and y, have only
binary attributes
● Compute similarities using the following quantities
f01 = the number of attributes where x was 0 and y was 1
f10 = the number of attributes where x was 1 and y was 0
f00 = the number of attributes where x was 0 and y was 0
f11 = the number of attributes where x was 1 and y was 1

● Simple Matching and Jaccard Coefficients

SMC = number of matches / number of attributes
= (f11 + f00) / (f01 + f10 + f11 + f00)

J = number of 11 matches / number of non-zero attributes

= (f11) / (f01 + f10 + f11)
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SMC versus Jaccard: Example

x= 1000000000
y= 0000001001

f01 = 2 (the number of attributes where x was 0 and y was 1)

f10 = 1 (the number of attributes where x was 1 and y was 0)
f00 = 7 (the number of attributes where x was 0 and y was 0)
f11 = 0 (the number of attributes where x was 1 and y was 1)

SMC = (f11 + f00) / (f01 + f10 + f11 + f00)

= (0+7) / (2+1+0+7) = 0.7

J = (f11) / (f01 + f10 + f11) = 0 / (2 + 1 + 0) = 0

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Cosine Similarity

● If d1 and d2 are two document vectors, then

cos( d1, d2 ) = <d1,d2> / ||d1|| ||d2|| ,
where <d1,d2> indicates inner product or vector dot
product of vectors, d1 and d2, and || d || is the length of
vector d.
● Example:
d1 = 3 2 0 5 0 0 0 2 0 0
d2 = 1 0 0 0 0 0 0 1 0 2
<d1, d2> = 3*1 + 2*0 + 0*0 + 5*0 + 0*0 + 0*0 + 0*0 + 2*1 + 0*0 + 0*2 = 5
| d1 || = (3*3+2*2+0*0+5*5+0*0+0*0+0*0+2*2+0*0+0*0)0.5 = (42) 0.5 = 6.481
|| d2 || = (1*1+0*0+0*0+0*0+0*0+0*0+0*0+1*1+0*0+2*2) 0.5 = (6) 0.5 = 2.449
cos(d1, d2 ) = 0.3150
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Correlation measures the linear relationship between objects

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Visually Evaluating Correlation

Scatter plots
showing the
similarity from
–1 to 1.

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 Drawback of Correlation

● x = (-3, -2, -1, 0, 1, 2, 3)

● y = (9, 4, 1, 0, 1, 4, 9)

yi = xi2

● mean(x) = 0, mean(y) = 4
● std(x) = 2.16, std(y) = 3.74

● corr = (-3)(5)+(-2)(0)+(-1)(-3)+(0)(-4)+(1)(-3)+(2)(0)+3(5) / ( 6 * 2.16 * 3.74 )

=0

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Correlation vs Cosine vs Euclidean Distance
● Compare the three proximity measures according to their behavior under
variable transformation
– scaling: multiplication by a value
– translation: adding a constant
Property Cosine Correlation Euclidean Distance
Invariant to scaling Yes Yes No
(multiplication)
Invariant to translation No Yes No
(addition)

● Consider the example

– x = (1, 2, 4, 3, 0, 0, 0), y = (1, 2, 3, 4, 0, 0, 0)
– ys = y * 2 (scaled version of y), yt = y + 5 (translated version)

Measure (x , y) (x , ys) (x , yt)

Cosine 0.9667 0.9667 0.7940

Correlation 0.9429 0.9429 0.9429

Euclidean Distance 1.4142 5.8310 14.2127

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Correlation vs cosine vs Euclidean distance

● Choice of the right proximity measure depends on the domain

● What is the correct choice of proximity measure for the
following situations?
– Comparing documents using the frequencies of words
◆ Documents are considered similar if the word frequencies are similar

– Comparing the temperature in Celsius of two locations

◆ Two locations are considered similar if the temperatures are similar in
magnitude

– Comparing two time series of temperature measured in Celsius

◆ Two time series are considered similar if their “shape” is similar, i.e., they vary
in the same way over time, achieving minimums and maximums at similar
times, etc.

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Comparison of Proximity Measures

● Domain of application
– Similarity measures tend to be specific to the type of
attribute and data
– Record data, images, graphs, sequences, 3D-protein
structure, etc. tend to have different measures
● However, one can talk about various properties that
you would like a proximity measure to have
– Symmetry is a common one
– Tolerance to noise and outliers is another
– Ability to find more types of patterns?
– Many others possible
● The measure must be applicable to the data and
produce results that agree with domain knowledge
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Information Based Measures

● Information theory is a well-developed and

fundamental disciple with broad applications

● Some similarity measures are based on

information theory
– Mutual information in various versions
– Maximal Information Coefficient (MIC) and related
measures
– General and can handle non-linear relationships
– Can be complicated and time intensive to compute

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Information and Probability

● Information relates to possible outcomes of an event

– transmission of a message, flip of a coin, or
measurement of a piece of data

● The more certain an outcome, the less information

that it contains and vice-versa
– For example, if a coin has two heads, then an outcome
of heads provides no information
– More quantitatively, the information is related the
probability of an outcome
◆ The smaller the probability of an outcome, the more information
it provides and vice-versa
– Entropy is the commonly used measure
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Entropy

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Entropy Examples

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Entropy for Sample Data: Example

Hair Color Count p -plog2p

Black 75 0.75 0.3113
Brown 15 0.15 0.4105
Blond 5 0.05 0.2161
Red 0 0.00 0
Other 5 0.05 0.2161
Total 100 1.0 1.1540

Maximum entropy is log25 = 2.3219

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Entropy for Sample Data

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Mutual Information

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 Mutual Information Example

Student Count p -plog2p Student Grade Count p -plog2p

Status Status
Undergrad 45 0.45 0.5184
Undergrad A 5 0.05 0.2161
Grad 55 0.55 0.4744
Undergrad B 30 0.30 0.5211
Total 100 1.00 0.9928
Undergrad C 10 0.10 0.3322

Grade Count p -plog2p Grad A 30 0.30 0.5211

A 35 0.35 0.5301 Grad B 20 0.20 0.4644

B 50 0.50 0.5000 Grad C 5 0.05 0.2161
C 15 0.15 0.4105 Total 100 1.00 2.2710
Total 100 1.00 1.4406

Mutual information of Student Status and Grade = 0.9928 + 1.4406 - 2.2710 = 0.1624

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Maximal Information Coefficient
● Reshef, David N., Yakir A. Reshef, Hilary K. Finucane, Sharon R. Grossman, Gilean McVean, Peter J.
Turnbaugh, Eric S. Lander, Michael Mitzenmacher, and Pardis C. Sabeti. "Detecting novel associations
in large data sets." science 334, no. 6062 (2011): 1518-1524.

● Applies mutual information to two continuous variables

● Consider the possible binnings of the variables into
discrete categories
– nX × nY ≤ N0.6 where
◆ nX is the number of values of X
◆ nY is the number of values of Y
◆ N is the number of samples (observations, data objects)
● Compute the mutual information
– Normalized by log2(min( nX, nY )
● Take the highest value
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General Approach for Combining Similarities

● Sometimes attributes are of many different types, but an

overall similarity is needed.
1: For the kth attribute, compute a similarity, sk(x, y), in the
range [0, 1].
2: Define an indicator variable, δk, for the kth attribute as
follows:
δk = 0 if the kth attribute is an asymmetric attribute and
both objects have a value of 0, or if one of the objects
has a missing value for the kth attribute
δk = 1 otherwise
3. Compute

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Using Weights to Combine Similarities

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Data Preprocessing

● Aggregation
● Sampling
● Discretization and Binarization
● Attribute Transformation
● Dimensionality Reduction
● Feature subset selection
● Feature creation

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Aggregation

● Combining two or more attributes (or objects) into a single

attribute (or object)
● Purpose
– Data reduction - reduce the number of attributes or objects
– Change of scale
◆ Cities aggregated into regions, states, countries, etc.
◆ Days aggregated into weeks, months, or years
– More “stable” data - aggregated data tends to have less variability

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Example: Precipitation in Australia

● This example is based on precipitation in

Australia from the period 1982 to 1993.
The next slide shows
– A histogram for the standard deviation of average
monthly precipitation for 3,030 0.5◦ by 0.5◦ grid cells in
Australia, and
– A histogram for the standard deviation of the average
yearly precipitation for the same locations.
● The average yearly precipitation has less
variability than the average monthly precipitation.
● All precipitation measurements (and their
standard deviations) are in centimeters.
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Example: Precipitation in Australia …

Variation of Precipitation in Australia

Standard Deviation of Average Standard Deviation of

Monthly Precipitation Average Yearly Precipitation
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Sampling
● Sampling is the main technique employed for data
reduction.
– It is often used for both the preliminary investigation of
the data and the final data analysis.

● Statisticians often sample because obtaining the

entire set of data of interest is too expensive or
time consuming.

● Sampling is typically used in data mining because

processing the entire set of data of interest is too
expensive or time consuming.
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Sampling …

● The key principle for effective sampling is the

following:

– Using a sample will work almost as well as using the

entire data set, if the sample is representative

– A sample is representative if it has approximately the

same properties (of interest) as the original set of data

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Sample Size

8000 points 2000 Points 500 Points

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Types of Sampling
● Simple Random Sampling
– There is an equal probability of selecting any particular
item
– Sampling without replacement
◆ As each item is selected, it is removed from the
population
– Sampling with replacement
◆ Objects are not removed from the population as they
are selected for the sample.
◆ In sampling with replacement, the same object can be
picked up more than once
● Stratified sampling
– Split the data into several partitions; then draw random
samples from each partition
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Sample Size
● What sample size is necessary to get at least one
object from each of 10 equal-sized groups.

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Discretization

● Discretization is the process of converting a

continuous attribute into an ordinal attribute
– A potentially infinite number of values are mapped into
a small number of categories
– Discretization is used in both unsupervised and
supervised settings

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Unsupervised Discretization

Data consists of four groups of points and two outliers. Data is one-
dimensional, but a random y component is added to reduce overlap.

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Unsupervised Discretization

Equal interval width approach used to obtain 4 values.

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Unsupervised Discretization

Equal frequency approach used to obtain 4 values.

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Unsupervised Discretization

K-means approach to obtain 4 values.

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Discretization in Supervised Settings

– Many classification algorithms work best if both the independent

and dependent variables have only a few values
– We give an illustration of the usefulness of discretization using
the following example.

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Binarization

● Binarization maps a continuous or categorical

attribute into one or more binary variables

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Attribute Transformation

● An attribute transform is a function that maps the

entire set of values of a given attribute to a new set
of replacement values such that each old value can
be identified with one of the new values
– Simple functions: xk, log(x), ex, |x|
– Normalization
◆ Refers to various techniques to adjust to differences
among attributes in terms of frequency of
occurrence, mean, variance, range
◆ Take out unwanted, common signal, e.g., seasonality

– In statistics, standardization refers to subtracting off the

means and dividing by the standard deviation
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Example: Sample Time Series of Plant Growth
Minneapolis

Net Primary
Production (NPP)
is a measure of
plant growth used
by ecosystem
scientists.

Correlations between time series

Correlations between time series

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 Seasonality Accounts for Much Correlation
Minneapolis
Normalized using
monthly Z Score:
Subtract off monthly
mean and divide by
monthly standard
deviation

Correlations between time series

Correlations between time series

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 Curse of Dimensionality

● When dimensionality
increases, data becomes
increasingly sparse in the
space that it occupies

● Definitions of density and

distance between points,
which are critical for
clustering and outlier
detection, become less
meaningful • Randomly generate 500 points
• Compute difference between max and
min distance between any pair of points
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Dimensionality Reduction

● Purpose:
– Avoid curse of dimensionality
– Reduce amount of time and memory required by data
mining algorithms
– Allow data to be more easily visualized
– May help to eliminate irrelevant features or reduce
noise

● Techniques
– Principal Components Analysis (PCA)
– Singular Value Decomposition
– Others: supervised and non-linear techniques

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Dimensionality Reduction: PCA

● Goal is to find a projection that captures the

largest amount of variation in data
x2

x1
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Dimensionality Reduction: PCA

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Feature Subset Selection

● Another way to reduce dimensionality of data

● Redundant features
– Duplicate much or all of the information contained in
one or more other attributes
– Example: purchase price of a product and the amount
of sales tax paid
● Irrelevant features
– Contain no information that is useful for the data
mining task at hand
– Example: students' ID is often irrelevant to the task of
predicting students' GPA
● Many techniques developed, especially for
classification
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Feature Creation

● Create new attributes that can capture the

important information in a data set much more
efficiently than the original attributes

● Three general methodologies:

– Feature extraction
◆ Example: extracting edges from images
– Feature construction
◆ Example: dividing mass by volume to get density
– Mapping data to new space
◆ Example: Fourier and wavelet analysis

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Mapping Data to a New Space

● Fourier and wavelet transform

Frequency

Two Sine Waves + Noise Frequency

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