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Data Preprocessing

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Data preprocessing

Universitatea Politehnica din Bucureti

Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

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Data types

Categorical vs. Numerical

Scale types

Nominal

Ordinal

Interval

Ratio (RO: scala proportionala)

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some categories, meaning that they belong to a

definable category. Example: color (with categories

red, green, blue and white) or gender (male, female).

The values of this type are not ordered, the usual

operations that may be performed being equality and

set inclusion.

Numerical data, consisting in numbers from a

continuous or discrete set of values.

Values are ordered, so testing this order is possible (<,

>, etc).

Sometimes we must or may convert categorical data in

numerical data by assigning a numeric value (or code)

for each label.

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Scale types

Stanley Smith Stevens, director of the

Psycho-Acoustic Laboratory, Harvard

University, proposed in a 1946 Science

article that all measurement in science are

using four different types of scales:

Nominal

Ordinal

Interval

Ratio

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Nominal

characterized by labels.

Values are unordered and equally weighted.

We cannot compute the mean or the median

from a set of such values

Instead, we can determine the mode, meaning

the value that occurs most frequently.

Nominal data are categorical but may be

treated sometimes as numerical by assigning

numbers to labels.

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Ordinal

Values of this type are ordered but the difference or

distance between two values cannot be determined.

The values only determine the rank order /position in the

set.

Examples: the military rank set or the order of

marathoners at the Olympic Games (without the times)

For these values we can compute the mode or the

median (the value placed in the middle of the ordered

set) but not the mean.

These values are categorical in essence but can be

treated as numerical because of the assignment of

numbers (position in set) to the values

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Interval

These are numerical values.

For interval scaled attributes the difference between two

values is meaningful.

Example: the temperature using Celsius scale is an

interval scaled attribute because the difference between

10 and 20 degrees is the same as the difference

between 40 and 50 degrees.

Zero does not mean nothing but is somehow arbitrarily

fixed. For that reason negative values are also allowed.

We can compute the mean, the standard deviation or we

can use regression to predict new values.

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Ratio

Ratio scaled attributes are like interval scaled

attributes but zero means nothing.

Negative values are not allowed.

The ratio between two values is meaningful.

Example: age - a 10 years child is two times

older than a 5 years child.

Other examples: temperature in Kelvin, mass in

kilograms, length in meters, etc.

All mathematical operations can be performed,

for example logarithms, geometric and harmonic

means, coefficient of variation

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Binary data

Sometimes an attribute may have only two values, as the

gender in a previous example. In that case the attribute is

called binary.

Symmetric binary: when the two values are of the same weight

and have equal importance (as in the gender case)

Asymmetric binary: one of the values is more important than

the other. Example: a medical bulletin containing blood tests for

identifying the presence of some substances, evaluated by

Present or Absent for each substance. In that case Present is

more important that Absent.

in most of the cases these attributes must be treated as

nominal (binary symmetric) or ordinal (binary asymmetric)

There are a set of similarity and dissimilarity (distance)

functions specific to binary attributes.

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

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Measuring data

Measuring central tendency:

Mean

Median

Mode

Midrange

Measuring dispersion:

Range

Kth percentile

IQR

Five-number summary

Standard deviation and variance

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Consider a set of n values of an attribute: x1, x2, , xn.

Mean: The arithmetic mean or average value is:

= (x1 + x2 + + xn) / n

If the values x have different weights, w1, , wn , then

the weighted arithmetic mean or weighted average is:

= (w1x1 + w2x2 + + wnxn) / (w1 + w2 + + wn)

If the extreme values are eliminated from the set

(smallest 1% and biggest 1%) a trimmed mean is

obtained.

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Median: The median value of an ordered set is

the middle value in the set.

Example: Median for {1, 3, 5, 7, 1001, 2002,

9999} is 7.

If n is even the median is the mean of the middle

values:

the median of {1, 3, 5, 7, 1001, 2002} is 6

(arithmetic mean of 5 and 7).

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Mode (RO: valoarea modala): The mode of a

dataset is the most frequent value.

A dataset may have more than a single mode.

For 1, 2 and 3 modes the dataset is called

unimodal, bimodal and trimodal.

When each value is present only once there is

no mode in the dataset.

For a unimodal dataset the mode is a measure

of the central tendency of data. For these

datasets we have the empirical relation:

mean mode = 3 x (mean median)

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Midrange (RO: mijlocul intervalului). The

midrange of a set of values is the arithmetic

mean of the largest and the smallest value.

For example the midrange of {1, 3, 5, 7, 1001,

2002, 9999} is 5000 (the mean of 1 and 9999).

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Dispersion (1)

Range. The range is the difference between the largest

and smallest values.

Example: for {1, 3, 5, 7, 1001, 2002, 9999} range is 9999

1 = 9998.

kth percentile. The kth percentile is a value xj having the

property that k percent of the values are less or equal

than xj.

Example: the median is the 50th percentile.

The most used percents are the median and the 25th and

75th percentiles, called also quartiles (notation: Q1 for

25% and Q3 for 75%).

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Dispersion (2)

Computing method: There are more than one different

methods for computing Q1, Q2 and Q3. The most

obvious method is the following:

Put the values of the data set in ascending order

Compute the median using its definition. It divides the

ordered dataset into two halves (lower and upper),

neither one including the median.

The median value is Q2

The median of the lower half is Q1 (or the lower

quartile)

The median of the upper half is Q3 (or the upper

quartile)

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Dispersion (3)

Interquartile range (IQR) is the difference between Q3

and Q1:

IQR = Q3 Q1

Potential outliers are values more than 1.5 x IQR below

Q1 or above Q3.

Five-number summary. Sometimes the median and the

quartiles are not enough for representing the spread of

the values

The smallest and biggest values must be considered

also.

(Min, Q1, Median, Q3, Max) is called the five-number

summary.

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Dispersion (4)

Examples:

For {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11}

Range = 10; Midrange = 6;

Q1 = 3; Q2 = 6; Q3 = 9; IQR = 9 - 3 = 6

For {1, 3, 3, 4, 5, 6, 6, 7, 8, 8}

Range = 7; Midrange = 4.5;

Q1 = 3; Q2 = 5.5 [=(5+6)/2]; Q3 = 7; IQR = 7 - 3 = 4

For {1, 3, 5, 7, 8, 10, 11, 13}

Range = 12; Midrange = 7;

Q1 = 4; Q2 = 7.5; Q3 = 10.5; IQR = 10.5 - 4 = 6.5

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Dispersion (5)

Standard deviation. The standard deviation of n values

(observations) is:

The standard deviation measures the spread of the

values around the mean value.

A value of 0 is obtained only when all values are

identical.

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

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Objectives

The main objectives of data cleaning are:

Replace (or remove) missing values,

Smooth noisy data,

Remove or just identify outliers

contain a NULL value.

In these cases the value stored in the database

(or the attribute value in the dataset) must be

something like Not applicable and not a NULL

value.

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May appear from various reasons:

human/hardware/software problems,

data not collected (considered unimportant at

collection time),

deleted data due to inconsistencies, etc.

data:

1. Ignore the data point / example with missing

attribute values. If the number of errors is

limited and these errors are not for sensitive

data, removing them may be a solution.

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2.

ways:

due to the huge volume of the datasets that must be cleaned.

Fill in with a (distinct from others) value not available or

unknown.

Fill in with a value measuring the central tendency, for

example attribute mean, median or mode.

Fill in with a value measuring the central tendency but only on

a subset (for example, for labeled datasets, only for examples

belonging to the same class).

The most probable value, if that value may be determined, for

example by decision trees, expectation maximization (EM),

Bayes, etc.

DMDW-2

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or variance in a measured variable ([Han,

Kamber 06]).

Wikipedia define noise as a colloquialism for

recognized amounts of unexplained

variation in a sample.

For removing the noise, some smoothing

techniques may be used:

1. Regression (was presented in first course)

2. Binning

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Binning

Binning can be used for smoothing an ordered

set of values. Smoothing is made based on

neighbor values. There are two steps:

Partitioning ordered data in several bins. Each bin

contains the same number of examples (data

points).

Smoothing for each bin: values in a bin are modified

based on some bin characteristics: mean, median,

boundaries.

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Example

Consider the following ordered data for some attribute:

1, 2, 4, 6, 9, 12, 16, 17, 18, 23, 34, 56, 78, 79, 81

Initial bins

binning

binning

for binning

1, 2, 4, 6, 9

4, 4, 4, 4, 4

4, 4, 4, 4, 4

1, 1, 1, 9, 9

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Result

So the smoothing result is:

Initial: 1, 2, 4, 6, 9, 12, 16, 17, 18, 23, 34, 56, 78, 79, 81

Using the mean: 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 66, 66,

66, 66, 66

Using the median: 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 78,

78, 78, 78, 78

Using the bin boundaries: 1, 1, 1, 9, 9, 12, 12, 12, 23, 23,

34, 34, 81, 81, 81

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Outliers

An outlier is an attribute value numerically distant from

the rest of the data.

Outliers may be sometimes correct values: for example,

the salary of the CEO of a company may be much bigger

that all other salaries. But in most of the cases outliers

are and must be handled as noise.

Outliers must be identified and then removed (or

replaced, as any other noisy value) because many data

mining algorithms are sensitive to outliers.

For example any algorithm using the arithmetic mean

(one of them is k-means) may produce erroneous results

because the mean is very sensitive to outliers.

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Identifying outliers

Use of IQR: values more than 1.5 x IQR below

Q1 or above Q3 are potential outliers. Boxplots

may be used to identify these outliers (boxplots

are a method for graphical representation of

data dispersion).

Use of standard deviation: values that are

more than two standard deviations away from

the mean for a given attribute are also

potential outliers.

Clustering. After clustering a certain dataset

some points are outside any cluster (or far

away from any cluster center.

DMDW-2

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

32

Objectives

Data integration means merging data from

different data sources into a coherent dataset.

The main activities are:

Schema integration

Remove duplicates and redundancy

Handle inconsistencies

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Schema integration

Must identify the translation of every source

scheme to the final scheme (entity identification

problem)

Subproblems:

The same thing is called differently in every data

source. Example: the customer id may be called

Cust-ID, Cust#, CustID, CID in different sources.

Different things are called with the same name in

different sources. Example: for employees data, the

attribute City means city where resides in a source

and city of birth in another source.

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Duplicates

Duplicates: The same information may be stored

in many data sources. Merging them can cause

sometimes duplicates of that information:

as duplicate attribute (same attribute with different

names is found multiple times in the final result) or

as duplicate instance (same object/entity is found

multiple times in the final database).

removed.

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Redundancy

Redundancy: Some information may be

deduced / computed.

For example age may be deduced from

birthdate, annual salary may be computed from

monthly salary and other bonuses recorded for

each employee.

Redundancy must be removed from the dataset

before running the data mining algorithm

Note that in existing data warehouses some

redundancy is allowed.

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Inconsistencies

Inconsistencies are conflicting values for a set of

attributes.

Example Birthdate = January 1, 1980, Age = 12

represents an obvious inconsistency but we may

find other inconsistencies that are not so

obvious.

For detecting inconsistencies extra knowledge

about data is necessary: for example, the

functional dependencies attached to a table

scheme can be used.

Available metadata describing the content of the

dataset may help in removing inconsistencies.

DMDW-2

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

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Objectives

Data is transformed and summarized in a better

form for the data mining process:

Normalization

New attribute construction

Summarization using aggregate functions

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Normalization

All attributes are scaled to fit a specified range:

0 to 1,

-1 to 1 or generally

|v| <= r where r is a given positive value.

is bigger only because the range of the values of

that attributes is bigger.

Example: Euclidian distance between A(0.5,

101) and B(0.01, 2111) is 2010, determined

almost exclusively by the second dimension.

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Normalization

We can achieve normalization using:

Min-max normalization:

vnew = (v vmin) / (vmax vmin)

For positive values the formula is:

vnew = v / vmax

z-score normalization ( is the standard deviation):

vnew = (v vmean) /

Decimal scaling: vnew = v / 10n

where n is the smallest integer for that all numbers become

(as absolute value) less than the range r (for r = 1, all

new values of v are <= 1) then

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Feature construction

New attribute construction is called also feature

construction.

It means: building new attributes based on the values of

existing ones.

Example: if the dataset contains an attribute Color with

only three distinct values {Red, Green, Blue} then three

attributes may be constructed: Red, Green and Blue

where only one of them equals 1 (based on the value of

Color) and the other two 0.

Another example: use a set of rules, decision trees or

other tools to build new attribute values from existing

ones. New attributes will contain the class labels

attached by the rules / decision tree used / labeling tool.

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Summarization

At this step aggregate functions may be used to

add summaries to the data.

Examples: adding sums for daily, monthly and

annually sales, counts and averages for number

of customers or transactions, and so on.

All these summaries are used for the slice and

dice process when data is stored in a data

warehouse.

The result is a data cube and each summary

information is attached to a level of granularity.

DMDW-2

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

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Objectives

Not all information produced by the

previous steps is needed for a certain data

mining process.

Reducing the data volume by keeping only

the necessary attributes leads to a better

representation of data and reduces the

time for data analysis.

DMDW-2

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Methods that may be used for data reduction (see [Han,

Kamber 06]) :

Data cube aggregation, already discussed.

Attribute selection: keep only relevant attributes. This

can be made by:

stepwise forward selection (start with an empty set and add

attributes),

stepwise backward elimination (start with all attributes and

remove some of them one by one)

a combination of forward selection and backward elimination.

decision tree induction: after building the decision tree, only

attributes used for decision nodes are kept.

DMDW-2

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Dimensionality reduction: encoding mechanisms are

used to reduce the data set size or compress data.

A popular method is Principal Component Analysis

(PCA): given N data vectors having n dimensions, find K

<= N orthogonal vectors (called principal components)

that can be used for representing data.

A PCA example is presented on the following slide, for

a multivariate Gaussian distribution centered at 1, 3

(source: wikipedia)

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PCA example

PCA for a multivariate Gaussian distribution (source:

http://2011.igem.org/Team:USTC-Software/parameter )

DMDW-2

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Numerosity reduction: the data are replaced

by smaller data representations such as

parametric models (only the model parameters

are stored in this case) or nonparametric

methods: clustering, sampling, histograms.

Discretization and concept hierarchy

generation, discussed in the following

paragraph.

DMDW-2

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Road Map

Data types

Measuring data

Data cleaning

Data integration

Data transformation

Data reduction

Data discretization

Summary

DMDW-2

50

Objectives

There are many data mining algorithms that

cannot use continuous attributes. Replacing

these continuous values with discrete ones is

called discretization.

Even for discrete attributes, is better to have a

reduced number of values leading to a reduced

representation of data. This may be performed

by concept hierarchies.

DMDW-2

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Discretization (1)

Discretization means reducing the number of

values for a given continuous attribute by

dividing its values in intervals.

Each interval is labeled and each attribute value

will be replaced with the interval label.

Some of the most popular methods to perform

discretization are:

1. Binning: equi-width bins or equi-frequency bins may

be used. Values in the same bin receive the same

label.

DMDW-2

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Discretization (1)

Popular methods to perform discretization - cont:

2. Histograms: like binning, histograms partition values for an

attribute in buckets. Each bucket has a different label and labels

replace values.

3. Entropy based intervals: each attribute value is considered a

potential split point (between two intervals) and an information

gain is computed for it (reduction of entropy by splitting at that

point). Then the value with the greatest information gain is

picked. In this way intervals may be constructed in a top-down

manner.

4. Cluster analysis: after clustering, all values in the same cluster

are replaced with the same label (the cluster-id for example)

DMDW-2

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Concept hierarchies

Usage of a concept hierarchy to perform

discretization means replacing low-level

concepts (or values) with higher level concepts.

Example: replace the numerical value for age

with young, middle-aged or old.

For numerical values, discretization and concept

hierarchies are the same.

DMDW-2

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Concept hierarchies

For categorical data the goal is to replace a bigger set of

values with a smaller one (categorical data are discrete

by definition):

Manually define a partial order for a set of attributes. For

example the set {Street, City, Department, Country} is partially

ordered, Street City Department Country. In that case we

can construct an attribute Localization at any level of this

hierarchy, by using the n rightmost attributes (n = 1 .. 4).

Specify (manually) high level concepts for value sets of low level

attribute values associated with. For example {Muntenia, Oltenia,

Dobrogea} Tara_Romaneasca.

Automatically identify a partial order between attributes, based

on the fact that high level concepts are represented by attributes

containing a smaller number of values compared with low level

ones.

DMDW-2

55

Summary

This second course presented:

Data types: categorical vs. numerical, the four scales (nominal,

ordinal, interval and ratio) and binary data.

A short presentation of data preprocessing steps and some ways to

extract important characteristics of data: central tendency (mean,

mode, median, etc) and dispersion (range, IQR, five-number

summary, standard deviation and variance).

A description of every preprocessing step:

cleaning,

integration,

transformation,

reduction and

Discretization

DMDW-2

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References

[Han, Kamber 06] Jiawei Han, Micheline Kamber, Data Mining:

Concepts and Techniques, Second Edition, Morgan Kaufmann

Publishers, 2006, 47-101

[Stevens 46] Stevens, S.S, On the Theory of Scales of

Measurement. Science June 1946, 103 (2684): 677680.

[Wikipedia] Wikipedia, the free encyclopedia, en.wikipedia.org

[Liu 11] Bing Liu, 2011. CS 583 Data mining and text mining course

notes, http://www.cs.uic.edu/~liub/teach/cs583-fall-11/cs583.html

DMDW-2

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