Data Mining

Practical Machine Learning Tools and Techniques

Slides for Chapter 8, Data transformations

of Data Mining by I. H. Witten, E. Frank,

M. A. Hall, and C. J. Pal
 Data transformations
• Attribute selection: Scheme-independent and scheme-specific
• Attribute discretization: Unsupervised, supervised, error- vs
entropy-based, converse of discretization
• Projections: principal component analysis (PCA), random
projections, partial least-squares, independent component
analysis (ICA), linear discriminant analysis (LDA), text, time series
• Sampling: Reservoir sampling
• Dirty data: Data cleansing, robust regression, anomaly detection
• Transforming multiple classes to binary ones
error-correcting codes, ensembles of nested dichotomies
• Calibrating class probabilities

2
 Just apply a learner? NO!

• Scheme/parameter selection
• Treat selection process as part of the learning process to avoid
optimistic performance estimates
• Modifying the input:
• Data engineering to make learning possible or easier
• Modifying the output
• Converting multi-class problems into two-class ones
• Re-calibrating probability estimates

3
 Attribute selection

• Attribute selection is often important in practice

• For example, adding a random (i.e., irrelevant) attribute can
significantly degrade C4.5’s performance
• Problem: C4.5’s built-in attribute selection is based on smaller and
smaller amounts of data
• Instance-based learning is particularly susceptible to
irrelevant attributes
• Number of training instances required increases exponentially with
number of irrelevant attributes
• Exception: naïve Bayes can cope well with irrelevant
attributes
• Note that relevant attributes can also be harmful if they
mislead the learning algorithm

4
 Scheme-independent attribute selection

• Filter approach to attribute selection: assess attributes

based on general characteristics of the data
• In this approach, the attributes are selected in a manner that
is independent of the target machine learning scheme
• One method: find smallest subset of attributes that
separates data
• Another method: use a fast learning scheme that is different
from the target learning scheme to find relevant attributes
• E.g., use attributes selected by C4.5 and 1R, or coefficients of linear
model, possibly applied recursively (recursive feature elimination)

5
 Scheme-independent attribute selection

• Attribute weighting techniques based on instance-based

learning can also be used for filtering
• Original approach for doing this cannot find redundant attributes (but
a fix has been suggested)
• Correlation-based Feature Selection (CFS):
• Correlation between attributes measured by symmetric uncertainty:
H(A) + H(B) - H(A, B)
U(A, B) = 2 Î [0,1]
H(A) + H(B)
• Goodness of subset of attributes measured by

å U(A ,C) å å U(A , A )

j j i j i j

breaking ties in favour of smaller subsets

6
Attribute subsets for weather data

7
 Searching the attribute space

• Number of attribute subsets is

exponential in the number of attributes
• Common greedy approaches:
• forward selection
• backward elimination
• More sophisticated strategies:
• Bidirectional search
• Best-first search: can find optimum solution
• Beam search: approximation to best-first search
• Genetic algorithms

8
 Scheme-specific selection
• Wrapper approach to attribute selection: attributes are
selected with target scheme in the loop
• Implement “wrapper” around learning scheme
Evaluation criterion: cross-validation performance
• Time consuming in general
• greedy approach, k attributes k2 time
• prior ranking of attributes linear in k
• Can use significance test to stop cross-validation for a
subset early if it is unlikely to “win” (race search)
Can be used with forward, backward selection, prior ranking, or special-
purpose schemata search
• Scheme-specific attribute selection is essential for learning
decision tables
• Efficient for decision tables and Naïve Bayes 9
 Attribute discretization

• Discretization can be useful even if a learning algorithm can

be run on numeric attributes directly
• Avoids normality assumption in Naïve Bayes and clustering
• Examples of discretization we have already encountered:
• 1R: uses simple discretization scheme
• C4.5 performs local discretization
• Global discretization can be advantageous because it is
based on more data
• Apply learner to
• k -valued discretized attribute or to
• k – 1 binary attributes that code the cut points
• The latter approach often works better when learning
decision trees or rule sets

10
 Discretization: unsupervised
• Unsupervised discretization: determine intervals without
knowing class labels
When clustering, the only possible way!
• Two well-known strategies:
• Equal-interval binning
• Equal-frequency binning
(also called histogram equalization)
• Unsupervised discretization is normally inferior to
supervised schemes when applied in classification tasks
But equal-frequency binning works well with naïve Bayes if the number
of intervals is set to the square root of the size of dataset
(proportional k-interval discretization)

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 Discretization: supervised

• Classic approach to supervised discretization is entropy-based

• This method builds a decision tree with pre-pruning on the
attribute being discretized
• Uses entropy as splitting criterion
• Uses the minimum description length principle as the stopping criterion
for pre-pruning
• Works well: still the state of the art
• To apply the minimum description length principle, the “theory”
is
• the splitting point (can be coded in log2[N – 1] bits)
• plus class distribution in each subset (a more involved expression)
• Description length is the number of bits needed for coding both
the splitting point and the class distributions
• Compare description lengths before/after adding split

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 Example: temperature attribute
Temperature 64 65 68 69 70 71 72 72 75 75 80 81 83 85
Play Yes No Yes Yes Yes No No Yes Yes Yes No Yes Yes No

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 Formula for MDL stopping criterion

• Can be formulated in terms of the information gain

• Assume we have N instances
• Original set: k classes, entropy E
• First subset: k1 classes, entropy E1
• Second subset: k2 classes, entropy E2

log 2 (N -1) log2 (3k - 2) - kE + k1E1 + k2 E2

gain > +
N N

• If the information gain is greater than the expression on

the right, we continue splitting
• Results in no discretization intervals for the
temperature attribute in the weather data 14
Supervised discretization: other methods

• Can replace top-down procedure by bottom-up method

• This bottom-up method has been applied in conjunction
with the chi-squared test
• Continue to merge intervals until they become significantly different
• Can use dynamic programming to find optimum k-way split
for given additive criterion
• Requires time quadratic in the number of instances
• But can be done in linear time if error rate is used instead of entropy
• However, using error rate is generally not a good idea when
discretizing an attribute as we will see

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 Error-based vs. entropy-based

• Question:
could the best discretization ever have two adjacent
intervals with the same class?
• Wrong answer: No. For if so,
• Collapse the two
• Free up an interval
• Use it somewhere else
• (This is what error-based discretization will do)
• Right answer: Surprisingly, yes.
• (and entropy-based discretization can do it)

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 Error-based vs. entropy-based
A 2-class,
2-attribute problem

Entropy-based discretization can detect change of class distribution

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 The converse of discretization

• Make nominal values into “numeric” ones

• Can use indicator attributes (as in IB1)
• Makes no use of potential ordering information if “nominal”
attribute is actually ordinal
• Alternative: code an ordered nominal attribute into binary
ones as in M5’
• Inequalities are explicitly represented as binary attributes, e.g.,
temperature < hot in the weather data
• Can be used for any ordered attribute
• Better than coding ordering into an integer (which implies a metric)
• In general: can code binary partition of a set of attribute
values as a binary attribute

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 Projections
• Simple transformations can often make a large
difference in performance
• Example transformations (not necessarily for
performance improvement):
• Difference of two date attributes
• Ratio of two numeric (ratio-scale) attributes
• Concatenating the values of nominal attributes
• Encoding cluster membership
• Adding noise to data
• Removing data randomly or selectively
• Obfuscating the data

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 Principal component analysis
• Unsupervised method for identifying the important
directions in a dataset
• We can then rotate the data into the (reduced) coordinate
system that is given by those directions
• PCA is a method for dimensionality reduction
• Algorithm:
1.Find direction (axis) of greatest variance
2.Find direction of greatest variance that is perpendicular to previous
direction and repeat
• Implementation: find eigenvectors of the covariance matrix
of the data
• Eigenvectors (sorted by eigenvalues) are the directions
• Mathematical details are covered in chapter on “Probabilistic methods”

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 Example: 10-dimensional data

• Data is normally standardized or mean-centered for PCA

• Can also apply this recursively in a tree learner
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 Random projections

• PCA is nice but expensive: cubic in number of attributes

• Alternative: use random directions instead of principal
components
• Surprising: random projections preserve distance
relationships quite well (on average)
• Can use them to apply kD-trees to high-dimensional data
• Can improve stability by using ensemble of models based on different
projections
• Different methods for generating random projection matrices
have been proposed

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 Partial least-squares regression
• PCA is often used as a pre-processing step before applying
a learning algorithm
• When linear regression is applied, the resulting model is known as
principal components regression
• Output can be re-expressed in terms of the original attributes because
PCA yields a linear transformation
• PCA is unsupervised and ignores the target attribute
• The partial least-squares transformation differs from PCA
in that it takes the class attribute into account
• Finds directions that have high variance and are strongly correlated
with the class
• Applying PLS as a pre-processing step for linear regression
yields partial least-squares regression

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 An algorithm for PLS
1. Start with standardized input attributes
2. Attribute coefficients of the first PLS direction:
● Compute the dot product between each attribute vector and the
class vector in turn, this yields the coefficients
3. Coefficients for next PLS direction:
● Replace attribute value by difference (residual) between the
attribute's value and the prediction of that attribute from a
simple regression based on the previous PLS direction
● Compute the dot product between each attribute's residual
vector and the class vector in turn, this yields the coefficients
4. Repeat from 3

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 Independent component analysis (ICA)

• PCA finds a coordinate system for a feature space that captures

the covariance of the data
• In contrast, ICA seeks a projection that decomposes the data into
sources that are statistically independent
• Consider the “cocktail party problem,” where people hear music
and the voices of other people: the goal is to un-mix these signals
• ICA finds a linear projection of the mixed signal that gives the
most statistically independent set of transformed variables

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 Correlation vs. statistical independence

• PCA is sometimes thought of as a method that seeks to

transform correlated variables into linearly uncorrelated ones
• Important: correlation and statistical independence are two
different criteria
• Uncorrelated variables have correlation coefficients equal to zero –
entries in a covariance matrix
• Two variables A and B are considered independent when their joint
probability is equal to the product of their marginal probabilities:

P(A, B) = P(A)P(B)

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 ICA and Mutual Information

• Mutual information (MI) measures the amount of info one

can obtain from one random variable given another one
• It can be used as an alternative criterion for finding a
projection of data
• We can aim to minimize the mutual information between the
dimensions of the data in a linearly transformed space
• Assume a model s = Ax, where A is an orthogonal matrix, x is
the input data and s is its decomposition into its sources
• Fact: minimizing the MI between the dimensions of s
corresponds to finding a transformation matrix A so that
a) the estimated probability distribution of the sources p(s) is as far
from Gaussian as possible and
b) the estimates s are constrained to be uncorrelated

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 ICA & FastICA

• A popular technique for performing independent component

analysis is known as fast ICA
• Uses a quantity known as the negentropy J(s) = H(z) – H(s),
where
• z is a Gaussian random variable with the same covariance matrix as s and
• H(.) is the “differential entropy,” defined as

H(x) = - ò p(x)logp(x)dx

• Negentropy measures the departure of s’s distribution from the

Gaussian distribution
• Fast ICA uses simple approximations to the negentropy allowing
learning to be performed more quickly.

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 Linear discriminant analysis

• Linear discriminant analysis is another way of finding a linear

transformation that reduces the number of dimensions
• Unlike PCA or ICA it uses labeled data: it is a supervised
technique like PLS, but designed for classification
• Often used for dimensionality reduction prior to classification,
but can be used as a classification technique itself
• When used for dimensionality reduction, it yields (k-1)
dimensions for a k-class classification problem
• We will first discuss LDA-based classification (and, for
completeness, QDA) before looking at data transformation

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 The LDA classifier

• Assumes data modeled by a multivariate Gaussian distribution

for each class c, with mean μc and a common covariance Σ
• Assumption of common covariance matrix implies
• the posterior distribution over the classes has a linear form and
• there is a linear discriminant function for each class
• The linear discriminant classifier is computed as

• where nc is the number of examples of class c and n is the total

number of examples
• Common variance matrix is obtained by pooling the covariance
matrices from the different classes using a weighted average
• The data is classified by choosing the largest yc

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 Quadratic discriminant analysis (QDA)

• The QDA classifier is obtained by giving each class its own

covariance matrix Σc
• In QDA, the decision boundaries defined by the posterior
over classes are described by quadratic equations
• The quadratic discriminant function for each class c is:

• These functions, as the ones for LDA, are produced by taking

the log of the corresponding Gaussian model for each class
• Constant terms can be ignored because such functions will be
compared with one another

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 Fisher’s linear discriminant analysis
• Let us now consider Fisher’s LDA projection for dimensionality
reduction, considering the two-class case first
• We seek a projection vector a that can be used to compute
scalar projections y = ax for input vectors x
• This vector is obtained by computing the means of each class,
μ1 and μ2, and then computing two special matrices
• The between-class scatter matrix is calculated as

(note the use of the outer product of two vectors here, which
gives a matrix)
• The within-class scatter matrix is

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 Fisher’s LDA: the solution vector

• The solution vector a for FLDA is found by maximizing the

“Rayleigh quotient”
a T SB a
J(a) = T
a SW a

• This leads to the solution

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 Multi-class FLDA

• FLDA can be generalized to multi-class problems

• Aim: projection A so that y = ATx yields points that are close when
they are in the same class relative to the overall spread
• To do this, first compute both the means for each class and the
global mean, and then compute the scatter matrices

A T SB A
• Then, find the projection matrix A that maximizes J(A) =
A T SW A
Determinants are analogs of variances computed in multiple dimensions,
along the principal directions of the scatter matrices, and multiplied together
• Solutions for finding A are based on solving a “generalized
eigenvalue problem” for each column of the matrix A.
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 Fisher’s LDA vs PCA

Class A
Class B

x2 FLDA

PCA

x1

Adapted from Belhumeur, Hespanha & Kriegman, 1997

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 Text to attribute vectors
• Many data mining applications involve textual data (e.g.,
string attributes in ARFF)
• Standard transformation: convert string into bag of
words by tokenization
• Attribute values are binary, word frequencies (fij),
log(1+fij), or TF  IDF: æ # documents ö
fij log ç ÷
è # documents that include word i ø
• Many configuration options:
• Only retain alphabetic sequences?
• What should be used as delimiters?
• Should words be converted to lowercase?
• Should stopwords be ignored?
• Should hapax legomena be included? Or even just the k most
frequent words?

36
 Time series
• In time series data, each instance represents a
different time step
• Some simple transformations:
• Shift values from the past/future
• Compute difference (delta) between instances (i.e., “derivative”)
• In some datasets, samples are not regular but time is
given by timestamp attribute
• Need to normalize by step size when transforming
• Transformations need to be adapted if attributes
represent different time steps

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 Sampling

• Sampling is typically a simple procedure

• What if training instances arrive one by one but we don't
know the total number in advance?
• Or perhaps there are so many that it is impractical to store them all
before sampling?
• Is it possible to produce a uniformly random sample of a
fixed size? Yes.
• Algorithm: Reservoir sampling
• Fill the reservoir, of size r, with the first r instances to arrive
• Subsequent, instances replace a randomly selected reservoir element
with probability r/i, where i is the number of instances seen so far

38
 Automatic data cleansing

• To (potentially) improve a decision tree:

• Remove misclassified instances, then re-learn!
• Better (of course!):
• Human expert checks misclassified instances
• Attribute noise vs. class noise
• Attribute noise should be left in the training set
(i.e., do not train on clean set and test on dirty one)
• Systematic class noise (e.g., one class substituted for another): leave
in training set
• Unsystematic class noise: eliminate from training set, if possible

39
 Robust regression

• “Robust” statistical method one that addresses

problem of outliers
• Possible ways to make regression more robust:
• Minimize absolute error, not squared error
• Remove outliers (e.g., 10% of points farthest from the
regression plane)
• Minimize median instead of mean of squares (copes with
outliers in x and y direction)
• Least median of squares regression finds the narrowest
strip covering half the observations
• Expensive to compute

40
 Example: least median of squares
Number of international phone calls from Belgium,
1950–1973

41
 Detecting anomalies

• Visualization can help to detect anomalies

• Automatic approach: apply committee of different learning
schemes, e.g.,
• decision tree
• nearest-neighbor learner
• linear discriminant function
• Conservative consensus approach: delete instances
incorrectly classified by all of them
• Problem: might sacrifice instances of small classes

42
 One-Class Learning

• Usually training data is available for all classes

• Some problems exhibit only a single class at training time
• Test instances may belong to this class or a new class not
present at training time
• This the problem of one-class classification
• Predict either target or unknown
• Note that, in practice, some one-class problems can be re-
formulated into two-class ones by collecting negative data
• Other applications truly do not have negative data, e.g.,
password hardening

43
 Outlier detection

• One-class classification is often used for

outlier/anomaly/novelty detection
• First, a one-class models is built from the dataset
• Then, outliers are defined as instances that are
classified as unknown
• Another method: identify outliers as instances that lie
beyond distance d from percentage p of training data
• Density estimation is a very useful approach for one-
class classification and outlier detection
• Estimate density of the target class and mark low probability
test instances as outliers
• Threshold can be adjusted to calibrate sensitivity

44
Using artificial data for one-class classification
• Can we apply standard multi-class techniques to obtain
one-class classifiers?
• Yes: generate artificial data to represent the unknown
non-target class
• Can then apply any off-the-shelf multi-class classifier
• Can tune rejection rate threshold if classifier produces probability
estimates
• Too much artificial data will overwhelm the target class!
• But: unproblematic if multi-class classifier produces accurate class
probabilities and is not focused on misclassification error
• Generate uniformly random data?
• Curse of dimensionality – as # attributes increases it becomes
infeasible to generate enough data to get good coverage of the space

45
 Generating artificial data
• Idea: generate data that is close to the target class
• T – target class, A – artificial class
• Generate artificial data using appropriate distribution P(X | A)
• Data no longer uniformly distributed ->
must take this distribution into account when computing
membership scores for the one-class model
• Want P(X | T), for any instance X; we know P(X | A)
• Train probability estimator P(T | X) on two classes T and A
• Then, rewrite Bayes' rule:
(1- Pr[T ])Pr[T | X]
Pr[X | T ] = Pr[X | A]
Pr[T ](1- Pr[T | X])
• For classification, choose a threshold to tune rejection rate
• How to choose P(X | A)? Apply a density estimator to the target
class and use resulting function to model the artificial class
46
Transforming multiple classes to binary ones

• Some learning algorithms only work with two class problems

• Sophisticated multi-class variants exist in many cases but can
be very slow or difficult to implement
• A common alternative is to transform multi-class problems
into multiple two-class ones
• Simple methods:
• Discriminate each class against the union of the others – one-vs.-rest
• Build a classifier for every pair of classes – pairwise classification
• We will discuss error-correcting output codes and ensembles
of nested dichotomies, which can often improve on these

47
 Error-correcting output codes

• Multiclass problem multiple binary problems

Simple one-vs.rest scheme:
class class vector
One-per-class coding
a 1000
• Idea: use error-correcting
b 0100
codes instead
c 0010
base classifiers predict d 0001
1011111, true class = ??
class class vector
• Use bit vectors (codes) sot that we
a 1111111
have large Hamming distance
b 0000111
between any pair of bit vectors:
c 0011001
Can correct up to (d – 1)/2 single-bit errors
d 0101010

48
 More on ECOCs
• Two optimization criteria for code matrix:
1. Row separation: minimum distance between rows
2. Column separation: minimum distance between columns (and
columns’ complements)
• Why is column separation important? Because if columns are
identical, column classifiers will likely make the same errors
• Even if columns are not identical, error-correction is
weakened if errors are correlated
• 3 classes only 23 possible columns
• (and 4 out of the 8 are complements)
• Cannot achieve row and column separation
• ECOCs only work for problems with > 3 classes

49
 Exhaustive ECOCs

• Exhaustive code for k classes: Exhaustive code, k = 4

• Columns comprise every class class vector
possible k-string … a 1111111
• … except for complements b 0000111
and all-zero/one strings c 0011001
d 0101010
• Each code word contains
2k–1 – 1 bits
• Class 1: code word is all ones
• Class 2: 2k–2 zeroes followed by 2k–2 –1 ones
• Class i : alternating runs of 2k–i 0s and 1s
• last run is one short
50
 More on ECOCs

• #classes >> 10 exhaustive codes infeasible

Number of columns increases exponentially
• But: it turns out that random code words have good error-
correcting properties on average!
• Alternatively, there are sophisticated methods for
generating ECOCs with just a few columns
• Note: ECOCs do not work with NN classifiers because
errors of column classifiers will be perfectly correlated
But: works if different attribute subsets are used in nearest neighbor
classifiers applied to predict each column/output bit

51
 Ensembles of nested dichotomies

• ECOCs produce classifications, but what if we want class

probability estimates as well?
E.g., for cost-sensitive classification via minimum expected cost
• Nested dichotomies provide an alternative
• Also decompose multi-class problems to binary ones
• Work with two-class classifiers that can produce class
probability estimates: yield multi-class probability estimates
• Recursively split the full set of classes into smaller and
smaller subsets
• Set of instances is split into subsets corresponding to these
subsets of classes
• Yields a binary tree of classes called a nested dichotomy

52
 Example with four classes
Full set of classes: [a, b, c, d] A two-class
classifier is learned
Two disjoint subsets: [a, b] [c, d] at each internal node
of this tree

[a] [b] [c] [d]

Nested dichotomy as a code matrix:

Class Class vector

a 00X
b 1X0
c 01X
d 1X1
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 Probability estimation
• Suppose we want to compute P(a | x)?
• Learn two class models for each of the three internal nodes
• From the two-class model at the root:
P({a, b} | x)
• From the left-hand child of the root:
P({a} | x, {a , b})
• Using the chain rule:
P({a} | x) = P({a} | x, {a , b}) × P({a, b} | x)
• Issues
• Estimation errors for deep hierarchies
• How to decide on hierarchical decomposition of classes?

54
 Ensembles of nested dichotomies
• If there is no reason a priori to prefer any particular
decomposition, then use them all
• Impractical for any non-trivial number of classes
• Consider a subset by taking a random sample of possible
tree structures
• Implement caching of models for efficiency (since a given two class
problem may occur in multiple trees)
• Average probability estimates over the trees
• Experiments show that this approach yields accurate multiclass
classifiers
• Can even improve the performance of methods that can already
handle multiclass problems!

55
 Calibrating class probabilities
• Class probability estimation is harder than
classification:
• Classification error is minimized as long as the correct class
is predicted with maximum probability
• Estimates that yield correct classification may be quite poor
with respect to quadratic or informational loss
• But: it is often important to have accurate class
probabilities
• E.g. cost-sensitive prediction using the minimum expected
cost method

56
Visualizing inaccurate probability estimates
• Consider a two class problem. Probabilities that are correct for
classification may be:
• Too optimistic – too close to either 0 or 1
• Too pessimistic – not close enough to 0 or 1

Reliability diagram
showing overoptimistic
probability estimation
for a two-class problem

57
 Calibrating class probabilities

• Reliability diagram is generated by collecting predicted probabilities

and relative class frequencies from a 10-fold cross-validation
• Predicted probabilities are discretized into 20 ranges via equal-
frequency discretization
• We can use this for calibration of the probability estimates: correct
bias by mapping observed curve to the diagonal
• Yields a discretization-based approach to the calibration of class
probability estimates
• Discretization-based calibration is fast but determining an
appropriate number of discretization intervals is not easy

58
 Calibrating class probabilities
• Can view calibration as a function estimation problem
• One input – estimated class probability – and one output – the calibrated
probability
• Reasonable assumption in many cases: the function is
piecewise constant and monotonically increasing
• Can use isotonic regression, which estimates a monotonically
increasing piece-wise constant function:
Minimizes squared error between observed class
“probabilities” (0/1) and resulting calibrated class probabilities
• Alternatively, can use logistic regression to estimate the
calibration function
• Note: must use the log-odds of the estimated class probabilities as input
• Advantage: multiclass logistic regression can be used for
calibration in the multiclass case
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 Weka implementations

• Attribute selection
• CfsSubsetEval (correlation-based attribute subset evaluator)
• ConsistencySubsetEval (measures class consistency for a given set of
attributes, in the consistencySubsetEval package)
• ClassifierSubsetEval (uses a classifier for evaluating subsets of attributes, in the
classifierBasedAttributeSelection package)
• SVMAttributeEval (ranks attributes according to the magnitude of the
coefficients learned by an SVM, in the SVMAttributeEval package)
• ReliefF (instance-based approach for ranking attributes)
• WrapperSubsetEval (uses a classifier plus cross-validation)
• GreedyStepwise (forward selection and backward elimination search)
• LinearForwardSelection (forward selection with a sliding window of attribute
choices at each step of the search, in the linearForwardSelection package)
• BestFirst (search method that uses greedy hill-climbing with backtracking)
• RaceSearch (uses the race search methodology, in the raceSearch package)
• Ranker (ranks individual attributes according to their evaluation)

60
 Weka implementations

• Learning decision tables: DecisionTable

• Discretization
• Discretize (unsupervised and supervised versions)
• PKIDiscretize (proportional k-interval discretization)
• Discriminant analysis for classification
• LDA, FLDA, and QDA (in the discriminantAnalysis package)
• Discriminant analysis for dimensionality reduction
• MultiClassFLDA (in the discriminantAnalysis package)
• PrincipalComponents and RandomProjection
• FastICA (independent component analysis, in the StudentFilters
package)
• StringToWordVector (text to attribute vectors)
• PLSFilter (partial least squares transformation)
• Resampling and reservoir sampling

61
 Weka implementations

• OneClassClassifier
• Implements one-class classification using artificial data (available in
the oneClassClassifier package)
• MultiClassClassifier
• Includes several ways of handling multiclass problems with two-class
classifiers, including error-correcting output codes
• END
• Ensembles of nested dichotomies, in the
ensemblesOfNestedDichotomies package
• Many other preprocessing tools are available:
• Arithmetic operations; time-series operations; obfuscation;
generating cluster membership values; adding noise; various
conversions between numeric, binary, and nominal attributes; and
various data cleansing operations

62
 Further Reading and Bibliographic Notes

• Backward elimination, e.g., was introduced in (Marill & Green, 1963)

• Kittler (1978) surveys feature selection algorithms in pattern recognition.
• Best-first search and genetic algorithms are standard artificial intelligence
techniques (Goldberg, 1989; Winston, 1992)
• John (1997) shows that the performance of decision tree learners can
deteriorate when new attributes are added
• Langley and Sage (1997): the number of training instances must grow
exponentially with the number of attributes in instance-based learning
• The idea of finding the smallest attribute set that carves up the instances
uniquely is from Almuallin and Dietterich (1991, 1992)
• It was further developed by Liu and Setiono (1996)
• Kibler and Aha (1987) and Cardie (1993) both investigated the use of decision
tree algorithms to identify features for nearest-neighbor learning
• Holmes and Nevill-Manning (1995) used 1R to order features for selection

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 Further Reading and Bibliographic Notes

• Kira and Rendell (1992) used instance-based methods to select features, leading to
a scheme called RELIEF for Recursive Elimination of Features
• Gilad-Bachrach, Navot, and Tishby (2004) show how this scheme can be modified
to work better with redundant attributes
• The correlation-based feature selection method is due to Hall (2000)
• The use of wrapper methods for feature selection is due to John, Kohavi, and
Pfleger (1994) and Kohavi and John (1997)
• Genetic algorithms have been applied within a wrapper framework by Vafaie and
DeJong (1992) and Cherkauer and Shavlik (1996)
• The selective naïve Bayes learning scheme is due to Langley and Sage (1994)
• Guyon, Weston, Barnhill, and Vapnik (2002) present and evaluate the recursive
feature elimination scheme in conjunction with support vector machines
• The method of raced search was developed by Moore and Lee (1994)
• Gütlein, Frank, Hall, and Karwath (2009) show how to speed up scheme-specific
selection for datasets with many attributes using simple ranking-based methods

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 Further Reading and Bibliographic Notes

• Dougherty, Kohavi, and Sahami (1995) show results comparing the entropy-
based discretization method with equal-width binning and the 1R method
• Frank and Witten (1999) describe the effect of using the ordering information
in discretized attributes
• Proportional k-interval discretization for Naive Bayes was proposed by Yang
and Webb (2001)
• The entropy-based method for discretization, including the use of the MDL
stopping criterion, was developed by Fayyad and Irani (1993)
• The bottom-up statistical method using the χ2 test is due to Kerber (1992)
• An extension to an automatically determined significance level is described by
Liu and Setiono (1997)
• Fulton, Kasif, and Salzberg (1995) use dynamic programming for discretization
and present a linear-time algorithm for error-based discretization
• The example used for showing the weakness of error-based discretization is
adapted from Kohavi and Sahami (1996)

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 Further Reading and Bibliographic Notes

• Fradkin and Madigan (2003) analyze the performance of random projections

• The algorithm for partial least squares regression is from Hastie et al. (2009)
• The TFxIDF metric is described by Witten et al. (1999b)
• Hyvärinen and Oja (2000) created the fast ICA method
• Duda et al. (2001) and Murphy (2012) explain the algebra underlying FLDA
• Sugiyama (2007) presents a variant called “local Fisher discriminant analysis”
• John (1995) showed experiments on using C4.5 to filter its own training data
• The more conservative consensus filter is due to Brodley and Fried (1996)
• Rousseeuw and Leroy (1987) describe the least median of squares method
and the telephone data
• Quinlan (1986) shows how removing attribute noise can be detrimental

66
 Further Reading and Bibliographic Notes

• Barnett and Lewis (1994) address the general topic of outliers in data from a
statistical point of view
• Pearson (2005) describes the statistical approach of fitting a distribution to
the target data
• Schölkopf, Williamson, Smola, Shawe-Taylor, and Platt (2000) describe the
use of support vector machines for novelty detection
• Abe, Zadrozny, and Langford (2006), amongst others, use artificial data as a
second class
• Combining density estimation and class probability estimation using artificial
data is suggested for unsupervised learning by Hastie et al. (2009)
• Hempstalk, Frank, and Witten (2008) describe it in the context of one-class
classification
• Hempstalk and Frank (2008) discuss how to fairly compare one-class and
multiclass classification when discriminating against new classes of data

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 Further Reading and Bibliographic Notes
• Vitter (1985) describes the algorithm for reservoir sampling we used, he
called it method R; its computational complexity is O(#instances)
• Rifkin and Klautau (2004) show that the one-vs-rest method for multiclass
classification can work well if appropriate parameter tuning is applied
• Friedman (1996) describes the technique of pairwise classification and
Fürnkranz (2002) further analyzes it
• Hastie and Tibshirani (1998) extend it to estimate probabilities using
pairwise coupling
• Fürnkranz (2003) evaluates pairwise classification as a technique for
ensemble learning
• ECOCs for multi-class classification were proposed by Dietterich and Bakiri
(1995); Ricci and Aha (1998) showed how to apply them to nearest
neighbor classifiers
• Frank and Kramer (2004) introduce ensembles of nested dichotomies
• Dong, Frank, and Kramer (2005) considered balanced nested dichotomies
to reduce training time

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 Further Reading and Bibliographic Notes

• Zadrozny and Elkan (2002) applied isotonic regression and logistic

regression to the calibration of class probability estimates
• They also investigated how to deal with multiclass problems
• Niculescu-Mizil and Caruana (2005) compared a variant of logistic
regression and isotonic regression
• They considered a large set of underlying class probability estimators
• Stout (2008) describes a linear-time algorithm for isotonic regression
based on minimizing squared error (called the PAV algorithm)

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