Data Mining

Practical Machine Learning Tools and Techniques

Slides for Chapter 5, Evaluation

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

M. A. Hall and C. J. Pal
Credibility: Evaluating what’s been learned

• Issues: training, testing, tuning

• Predicting performance: confidence limits
• Holdout, cross-validation, bootstrap
• Hyperparameter selection
• Comparing machine learning schemes
• Predicting probabilities
• Cost-sensitive evaluation
• Evaluating numeric prediction
• The minimum description length principle
• Model selection using a validation set

2
 Evaluation: the key to success

• How predictive is the model we have learned?

• Error on the training data is not a good indicator of
performance on future data
• Otherwise 1-NN would be the optimum classifier!
• Simple solution that can be used if a large amount of
(labeled) data is available:
• Split data into training and test set
• However: (labeled) data is usually limited
• More sophisticated techniques need to be used

3
 Issues in evaluation

• Statistical reliability of estimated differences in performance

( significance tests)
• Choice of performance measure:
• Number of correct classifications
• Accuracy of probability estimates
• Error in numeric predictions
• Costs assigned to different types of errors
• Many practical applications involve costs

4
 Training and testing I

• Natural performance measure for classification

problems: error rate
• Success: instance’s class is predicted correctly
• Error: instance’s class is predicted incorrectly
• Error rate: proportion of errors made over the whole set of
instances
• Resubstitution error: error rate obtained by evaluating
model on training data
• Resubstitution error is (hopelessly) optimistic!

5
 Training and testing II

• Test set: independent instances that have played no part in

formation of classifier
• Assumption: both training data and test data are representative
samples of the underlying problem
• Test and training data may differ in nature
• Example: classifiers built using customer data from two different
towns A and B
• To estimate performance of classifier from town A in completely
new town, test it on data from B

6
 Note on parameter tuning

• It is important that the test data is not used in any way to

create the classifier
• Some learning schemes operate in two stages:
• Stage 1: build the basic structure
• Stage 2: optimize parameter settings
• The test data cannot be used for parameter tuning!
• Proper procedure uses three sets: training data, validation
data, and test data
• Validation data is used to optimize parameters

7
 Making the most of the data

• Once evaluation is complete, all the data can be used to

build the final classifier
• Generally, the larger the training data the better the
classifier (but returns diminish)
• The larger the test data the more accurate the error
estimate
• Holdout procedure: method of splitting original data into
training and test set
• Dilemma: ideally both training set and test set should be large!

8
 Predicting performance

• Assume the estimated error rate is 25%. How close is this to

the true error rate?
• Depends on the amount of test data
• Prediction is just like tossing a (biased!) coin
• “Head” is a “success”, “tail” is an “error”
• In statistics, a succession of independent events like this is
called a Bernoulli process
• Statistical theory provides us with confidence intervals for the true
underlying proportion

9
 Confidence intervals

• We can say: p lies within a certain specified interval with a

certain specified confidence
• Example: S=750 successes in N=1000 trials
• Estimated success rate: 75%
• How close is this to true success rate p?
• Answer: with 80% confidence p is located in [73.2,76.7]
• Another example: S=75 and N=100
• Estimated success rate: 75%
• With 80% confidence p in [69.1,80.1]

10
 Mean and variance
• Mean and variance for a Bernoulli trial:
p, p (1–p)
• Expected success rate f=S/N
• Mean and variance for f : p, p (1–p)/N
• For large enough N, f follows a Normal distribution
• c% confidence interval [–z  X  z] for a random variable X is
determined using:

• For a symmetric distribution such as the normal

distribution we have:
P(- z £X £ z) =1- 2 ´ P(x ³ 2)

11
 Confidence limits
• Confidence limits for the normal distribution with 0
mean and a variance of 1: Pr[X  z] z
0.1% 3.09
0.5% 2.58
1% 2.33
5% 1.65
10% 1.28
20% 0.84
40% 0.25
• Thus:

• To use this we have to transform our random variable f

to have 0 mean and unit variance
12
 Transforming f

• Transformed value for f :

(i.e., subtract the mean and divide by the standard deviation)

• Resulting equation:

• Solving for p yields an expression for the confidence limits:

13
 Examples

• f = 75%, N = 1000, c = 80% (so that z = 1.28):

 

• f = 75%, N = 100, c = 80% (so that z = 1.28):

 𝑝 ∈ [ 0.691,0 .801 ]

• Note that normal distribution assumption is only valid for

large N (i.e., N > 100)
• f = 75%, N = 10, c = 80% (so that z = 1.28):
 𝑝 ∈ [ 0.549,0 .881 ]

(should be taken with a grain of salt)

14
 Holdout estimation

• What should we do if we only have a single dataset?

• The holdout method reserves a certain amount for testing
and uses the remainder for training, after shuffling
• Usually: one third for testing, the rest for training
• Problem: the samples might not be representative
• Example: class might be missing in the test data
• Advanced version uses stratification
• Ensures that each class is represented with approximately equal
proportions in both subsets

15
 Repeated holdout method

• Holdout estimate can be made more reliable by

repeating the process with different subsamples
• In each iteration, a certain proportion is randomly selected
for training (possibly with stratificiation)
• The error rates on the different iterations are averaged to
yield an overall error rate
• This is called the repeated holdout method
• Still not optimum: the different test sets overlap
• Can we prevent overlapping?

16
 Cross-validation

• K-fold cross-validation avoids overlapping test sets

• First step: split data into k subsets of equal size
• Second step: use each subset in turn for testing, the remainder
for training
• This means the learning algorithm is applied to k different
training sets
• Often the subsets are stratified before the cross-validation
is performed to yield stratified k-fold cross-validation
• The error estimates are averaged to yield an overall error
estimate; also, standard deviation is often computed
• Alternatively, predictions and actual target values from the
k folds are pooled to compute one estimate
• Does not yield an estimate of standard deviation

17
 More on cross-validation

• Standard method for evaluation: stratified ten-fold cross-

validation
• Why ten?
• Extensive experiments have shown that this is the best choice to
get an accurate estimate
• There is also some theoretical evidence for this
• Stratification reduces the estimate’s variance
• Even better: repeated stratified cross-validation
• E.g., ten-fold cross-validation is repeated ten times and results
are averaged (reduces the variance)

18
 Leave-one-out cross-validation

• Leave-one-out:
a particular form of k-fold cross-validation:
• Set number of folds to number of training instances
• I.e., for n training instances, build classifier n times
• Makes best use of the data
• Involves no random subsampling
• Very computationally expensive (exception: using lazy
classifiers such as the nearest-neighbor classifier)

19
 Leave-one-out CV and stratification

• Disadvantage of Leave-one-out CV: stratification is not

possible
• It guarantees a non-stratified sample because there is only one
instance in the test set!
• Extreme example: random dataset split equally into
two classes
• Best inducer predicts majority class
• 50% accuracy on fresh data
• Leave-one-out CV estimate gives 100% error!

20
 The bootstrap

• CV uses sampling without replacement

• The same instance, once selected, can not be selected again for
a particular training/test set
• The bootstrap uses sampling with replacement to form
the training set
• Sample a dataset of n instances n times with replacement to
form a new dataset of n instances
• Use this data as the training set
• Use the instances from the original dataset that do not occur in
the new training set for testing

21
 The 0.632 bootstrap

• Also called the 0.632 bootstrap

• A particular instance has a probability of 1–1/n of not
being picked
• Thus its probability of ending up in the test data is:

• This means the training data will contain approximately

63.2% of the instances

22
 Estimating error with the 0.632 bootstrap

• The error estimate on the test data will be quite

pessimistic
• Trained on just ~63% of the instances
• Idea: combine it with the resubstitution error:

• The resubstitution error gets less weight than the error

on the test data
• Repeat process several times with different samples;
average the results

23
 More on the bootstrap

• Probably the best way of estimating performance for very

small datasets
• However, it has some problems
• Consider the random dataset from above
• A perfect memorizer will achieve
0% resubstitution error and ~50% error on test data
• Bootstrap estimate for this classifier:

• True expected error: 50%

24
 Hyperparameter selection
• Hyperparameter: parameter that can be tuned to optimize the
performance of a learning algorithm
• Different from basic parameter that is part of a model, such as a coefficient
in a linear regression model
• Example hyperparameter: k in the k-nearest neighbour classifier
• We are not allowed to peek at the final test data to choose the
value of this parameter
• Adjusting the hyperparameter to the test data will lead to optimistic
performance estimates on this test data!
• Parameter tuning needs to be viewed as part of the learning algorithm and
must be done using the training data only
• But how to get a useful estimate of performance for different
parameter values so that we can choose a value?
• Answer: split the data into a smaller “training” set and a validation set”
(normally, the data is shuffled first)
• Build models using different values of k on the new, smaller training set and
evaluate them on the validation set
• Pick the best value of k and rebuild the model on the full original training set

25
 Hyperparameters and cross-validation
• Note that k-fold cross-validation runs k different train-test
evaluations
• The above parameter tuning process using validation sets must be
applied separately to each of the k training sets!
• This means that, when hyperparameter tuning is applied, k
different hyperparameter values may be selected
• This is OK: hyperparameter tuning is part of the learning process
• Cross-validation evaluates the quality of the learning process, not the
quality of a particular model
• What to do when the training sets are very small, so that
performance estimates on a validation set are unreliable?
• We can use nested cross-validation (expensive!)
• For each training set of the “outer” k-fold cross-validation, run “inner”
p-fold cross-validations to choose the best hyperparameter value
• Outer cross-validation is used to estimate quality of learning process
• Inner cross-validations are used to choose hyperparameter values
• Inner cross-validations are part of the learning process! 26
 Comparing machine learning schemes

• Frequent question: which of two learning schemes

performs better?
• Note: this is domain dependent!
• Obvious way: compare 10-fold cross-validation estimates
• Generally sufficient in applications (we do not loose if the
chosen method is not truly better)
• However, what about machine learning research?
• Need to show convincingly that a particular method works
better in a particular domain from which data is taken

27
 Comparing learning schemes II
• Want to show that scheme A is better than scheme B in
a particular domain
• For a given amount of training data (i.e., data size)
• On average, across all possible training sets from that domain
• Let's assume we have an infinite amount of data from
the domain
• Then, we can simply
• sample infinitely many dataset of a specified size
• obtain a cross-validation estimate on each dataset for each
scheme
• check if the mean accuracy for scheme A is better than the
mean accuracy for scheme B

28
 Paired t-test
• In practice, we have limited data and a limited
number of estimates for computing the mean
• Student’s t-test tells us whether the means of two
samples are significantly different
• In our case the samples are cross-validation
estimates, one for each dataset we have sampled
• We can use a paired t-test because the individual
samples are paired
• The same cross-validation is applied twice, ensuring that
all the training and test sets are exactly the same

William Gosset
Born: 1876 in Canterbury; Died: 1937 in Beaconsfield, England
Obtained a post as a chemist in the Guinness brewery in Dublin in 1899.
Invented the t-test to handle small samples for quality control in
brewing. Wrote under the name "Student". 29
 Distribution of the means
• x1 ,x2 ,…, xk and y1 ,y2 ,… ,yk are the 2k samples for the k
different datasets
• mx and my are the means
• With enough samples, the mean of a set of independent
samples is normally distributed
(central limit theorem from statistics)
• Estimated variances of the means are
σx2/k and σy2/k

• If μx and μy are the true means then

are approximately normally distributed with

mean 0, variance 1

30
 Student’s distribution
• With small sample sizes (k < 100) the mean follows
Student’s distribution with k–1 degrees of freedom
• Confidence limits from Student’s distribution:

9 degrees of freedom normal distribution

Pr[X  z] z Pr[X  z] z
0.1% 4.30 0.1% 3.09
Assuming 0.5% 3.25 0.5% 2.58

we have 1% 2.82 1% 2.33

5% 1.83 5% 1.65
10 estimates
10% 1.38 10% 1.28
20% 0.88 20% 0.84

31
 Distribution of the differences

• Let md = mx – my
• The difference of the means (md) also has a Student’s
distribution with k–1 degrees of freedom
• Let σd2 be the variance of the differences
• The standardized version of md is called the t-statistic:

• We use t to perform the paired t-test

32
 Performing the test

• Fix a significance level

• If a difference is significant at the a% level,
there is a (100-a)% chance that the true means differ
• Divide the significance level by two because the test is two-
tailed
• I.e., the true difference can be +ve or – ve
• Look up the value for z that corresponds to a/2
• Compute the value of t based on the observed performance
estimates for the schemes being compared
• If t  –z or t z then the difference is significant
• I.e., the null hypothesis (that the difference is zero) can be rejected

33
 Unpaired observations

• If the CV estimates are from different datasets, they are no

longer paired
(or maybe we have k estimates for one scheme, and j
estimates for the other one)
• Then we have to use an unpaired t-test with min(k , j) – 1
degrees of freedom
• The statistic for the t-test becomes:

34
 Dependent estimates
• Unfortunately, we have assumed that we have enough data
to create several datasets of the desired size
• Need to re-use data if that is not the case
• E.g., running cross-validations with different randomizations on
the same data
• Samples become dependent  insignificant differences can
become significant
• A heuristic test that tries to combat this is the corrected
resampled t-test
• Assume we use the repeated hold-out method with k runs, with n1
instances for training and n2 for testing
• The new test statistic is:

35
 Predicting probabilities

• Performance measure so far: success rate

• Also called 0-1 loss function:

• Most classifiers produces class probabilities

• Depending on the application, we might want to check the
accuracy of the probability estimates
• 0-1 loss is not the right thing to use in those cases

36
 Quadratic loss function

• p1 … pk are probability estimates for an instance

• c is the index of the instance’s actual class
• a1 … ak = 0, except for ac which is 1
• Quadratic loss is:

• Want to minimize

• Can show that the expected value of this is minimized

when pj = pj*, where the latter are the true probabilities:

37
 Informational loss function
• The informational loss function is –log(pc),
where c is the index of the instance’s actual class
• Number of bits required to communicate the actual class
• Let p1* … pk* be the true class probabilities
• Then the expected value for the loss function is:

• Justification for informational loss is that this is minimized

when pj = pj*:

• Difficulty with informational loss : zero-frequency problem

38
 Discussion
• Which loss function to choose?
• Both encourage honesty
• Quadratic loss function takes into account all class probability
estimates for an instance
• Informational loss focuses only on the probability estimate for
the actual class
• Quadratic loss is bounded by
it can never exceed 2
• Informational loss can be infinite
• Informational loss is related to the MDL principle [later]

39
 Counting the cost

• In practice, different types of classification errors often

incur different costs
• Examples:
• Terrorist profiling: “Not a terrorist” correct 99.99…% of the time
• Loan decisions
• Oil-slick detection
• Fault diagnosis
• Promotional mailing

40
 Counting the cost

• The confusion matrix:

Predicted class
Yes No
Actual class Yes True positive False negative
No False positive True negative

• Different misclassification costs can be assigned to false

positives and false negatives
• There are many other types of cost!
• E.g., cost of collecting training data

41
 Aside: the kappa statistic
• Two confusion matrices for a 3-class problem:
actual predictor (left) vs. random predictor (right)

• Number of successes: sum of entries in diagonal (D)

• Kappa statistic: (success rate of actual predictor - success rate of
random predictor) / (1 - success rate of random predictor)
• Measures relative improvement on random predictor: 1 means
perfect accuracy, 0 means we are doing no better than random
42
 Classification with costs
• Two cost matrices:

• In cost-sensitive evaluation of classification methods,

success rate is replaced by average cost per prediction
• Cost is given by appropriate entry in the cost matrix

43
 Cost-sensitive classification
• Can take costs into account when making predictions
• Basic idea: only predict high-cost class when very confident
about prediction
• Given: predicted class probabilities
• Normally, we just predict the most likely class
• Here, we should make the prediction that minimizes the
expected cost
• Expected cost: dot product of vector of class probabilities and
appropriate column in cost matrix
• Choose column (class) that minimizes expected cost
• This is the minimum-expected cost approach to cost-sensitive
classification

44
 Cost-sensitive learning
• So far we haven't taken costs into account at training time
• Most learning schemes do not perform cost-sensitive
learning
• They generate the same classifier no matter what costs are
assigned to the different classes
• Example: standard decision tree learner
• Simple methods for cost-sensitive learning:
• Resampling of instances according to costs
• Weighting of instances according to costs
• Some schemes can take costs into account by varying a
parameter, e.g., naïve Bayes

45
 Lift charts

• In practice, costs are rarely known

• Decisions are usually made by comparing possible scenarios
• Example: promotional mailout to 1,000,000 households
• Mail to all; 0.1% respond (1000)
• Data mining tool identifies subset of 100,000 most promising, 0.4%
of these respond (400)
40% of responses for 10% of cost may pay off
• Identify subset of 400,000 most promising, 0.2% respond (800)
• A lift chart allows a visual comparison

46
 Generating a lift chart
• Sort instances based on predicted probability of being positive:

• x axis in lift chart is sample size for each probability threshold

• y axis is number of true positives above threshold

47
 A hypothetical lift chart

40% of responses 80% of responses

for 10% of cost for 40% of cost
48
Interactive cost-benefit analysis: Example I

49
Interactive cost-benefit analysis: Example II

50
 ROC curves

• ROC curves are similar to lift charts

• Stands for “receiver operating characteristic”
• Used in signal detection to show tradeoff between hit rate and
false alarm rate over noisy channel
• Differences to lift chart:
• y axis shows percentage of true positives in sample rather than
absolute number
• x axis shows percentage of false positives in samplerather than sample
size

51
 A sample ROC curve

• Jagged curve—one set of test data

• Smoother curve—use cross-validation
52
 Cross-validation and ROC curves

• Simple method of getting a ROC curve using cross-

validation:
• Collect probabilities for instances in test folds
• Sort instances according to probabilities
• This method is implemented in WEKA
• However, this is just one possibility
• Another possibility is to generate an ROC curve for each fold
and average them

53
 ROC curves for two schemes

• For a small, focused sample, use method A

• For a larger one, use method B
• Inbetween, choose between A and B with appropriate probabilities
54
 The convex hull

• Given two learning schemes we can achieve any point on the

convex hull!
• TP and FP rates for scheme 1: t1 and f1
• TP and FP rates for scheme 2: t2 and f2
• If scheme 1 is used to predict 100 × q % of the cases and
scheme 2 for the rest, then
• TP rate for combined scheme:
q × t1 + (1-q) × t2
• FP rate for combined scheme:
q × f1+(1-q) × f2

55
 More measures...
• Percentage of retrieved documents that are relevant:
precision=TP/(TP+FP)
• Percentage of relevant documents that are returned:
recall =TP/(TP+FN)
• Precision/recall curves have hyperbolic shape
• Summary measures: average precision at 20%, 50% and
80% recall (three-point average recall)
• F-measure=(2 × recall × precision)/(recall+precision)
• sensitivity × specificity = (TP / (TP + FN)) × (TN / (FP + TN))
• Area under the ROC curve (AUC):
probability that randomly chosen positive instance is
ranked above randomly chosen negative one

56
 Summary of some measures

Domain Plot Explanation

Lift chart Marketing TP TP

Subset (TP+FP)/
size (TP+FP+TN+FN)
ROC curve Communications TP rate TP/(TP+FN)
FP rate FP/(FP+TN)
Recall- Information Recall TP/(TP+FN)
precision retrieval Precision TP/(TP+FP)
curve

57
 Cost curves
• Cost curves plot expected costs directly
• Example for case with uniform costs (i.e., error):

58
Cost curves: example with costs

59
 Evaluating numeric prediction

• Same strategies: independent test set, cross-validation,

significance tests, etc.
• Difference: error measures
• Actual target values: a1 a2 …an
• Predicted target values: p1 p2 … pn
• Most popular measure: mean-squared error

• Easy to manipulate mathematically

60
 Other measures
• The root mean-squared error :

• The mean absolute error is less sensitive to outliers than the

mean-squared error:

• Sometimes relative error values are more appropriate (e.g.

10% for an error of 50 when predicting 500)

61
 Improvement on the mean

• How much does the scheme improve on simply

predicting the average?
• The relative squared error is:

• The root relative squared error and the relative absolute

error are:

62
 Correlation coefficient

• Measures the statistical correlation between the predicted

values and the actual values

• Scale independent, between –1 and +1

• Good performance leads to large values!

63
 Which measure?
• Best to look at all of them
• Often it doesn’t matter
• Example:

A B C D
Root mean-squared error 67.8 91.7 63.3 57.4
Mean absolute error 41.3 38.5 33.4 29.2
Root rel squared error 42.2% 57.2% 39.4% 35.8%
Relative absolute error 43.1% 40.1% 34.8% 30.4%
Correlation coefficient 0.88 0.88 0.89 0.91

• D best
• C second-best
• A, B arguable
64
 The MDL principle
• MDL stands for minimum description length
• The description length is defined as:
space required to describe a theory
+
space required to describe the theory’s mistakes
• In our case the theory is the classifier and the mistakes
are the errors on the training data
• Aim: we seek a classifier with minimal DL
• MDL principle is a model selection criterion
• Enables us to choose a classifier of an appropriate
complexity to combat overfitting

65
 Model selection criteria
• Model selection criteria attempt to find a good compromise
between:
• The complexity of a model
• Its prediction accuracy on the training data
• Reasoning: a good model is a simple model that achieves
high accuracy on the given data
• Also known as Occam’s Razor :
the best theory is the smallest one
that describes all the facts
William of Ockham, born in the village of Ockham in Surrey
(England) about 1285, was the most influential philosopher
of the 14th century and a controversial theologian.

66
 Elegance vs. errors

• Theory 1: very simple, elegant theory that explains the data

almost perfectly
• Theory 2: significantly more complex theory that reproduces
the data without mistakes
• Theory 1 is probably preferable
• Classical example: Kepler’s three laws on planetary motion
• Less accurate than Copernicus’s latest refinement of the Ptolemaic
theory of epicycles on the data available at the time

67
 MDL and compression
• MDL principle relates to data compression:
• The best theory is the one that compresses the data the most
• In supervised learning, to compress the labels of a dataset, we
generate a model and then store the model and its mistakes
• We need to compute
(a) the size of the model, and
(b) the space needed to encode the errors
• (b) easy: use the informational loss function
• (a) need a method to encode the model

68
 MDL and Bayes’s theorem

• L[T]=“length” of the theory

• L[E|T]=training set encoded wrt the theory
• Description length=
• Bayes’s theorem can be used to obtain the a posteriori
probability of a theory given the data:

• Equivalent to:

constant

69
 MDL and MAP

• MAP stands for maximum a posteriori probability

• Probabilistic approach to model selection
• Finding the MAP theory is the same as finding the MDL
theory, assuming coding scheme corresponds to prior
• Difficult bit in applying the MAP principle: determining the
prior probability P(T) of the theory
• Corresponds to difficult part in applying the MDL principle:
coding scheme for the theory
• Correspondence is clear: if we know a priori that a particular
theory is more likely, we need fewer bits to encode it

70
 Discussion of MDL principle

• Advantage: makes full use of the training data when

selecting a model
• Disadvantage 1: appropriate coding scheme/prior
probabilities for theories are crucial
• Disadvantage 2: no guarantee that the MDL theory is the
one which minimizes the expected error
• Note: Occam’s Razor is an axiom!
• Epicurus’s principle of multiple explanations: keep all
theories that are consistent with the data

71
 MDL and clustering

• Model selection in clustering: finding the most appropriate

number of clusters to model the data
• Description length of theory:
bits needed to encode the clusters
• e.g., cluster centers
• Description length of data given theory:
encode cluster membership and position relative to cluster
• e.g., distance to cluster center
• Works if coding scheme uses less code space for small
numbers than for large ones
• With nominal attributes, must communicate probability
distributions for each cluster

72
Using a validation set for model selection
• MDL principle is one example of a model selection criterion
• Model selection: finding the right model complexity
• Classic model selection problem in statistics:
• Finding the subset of attributes to use in a linear regression model
(yes, linear regression can overfit!)
• Other model selection problems: choosing the size of a
decision tree or artificial neural network
• Many model selection criteria exist, based on a variety of
theoretical assumptions
• Simple model selection approach: use a validation set
• Use the model complexity that yields best performance on the
validation set
• Alternative approach when data is scarce: internal cross-
validation
73