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Improving Bayesian Learning Using Public 

Knowledge 



Farid Seifi 1 , Chris Drummond 2 , Nathalie Japkowicz 1 and Stan Matwin 1 ' 3 

School of Information Technology and Engineering 
University of Ottawa 
Ottawa Ontario Canada, KIN 6N5 
f seif 050@uottawa. ca,nat@site .uottawa. ca, stanOsite .uottawa. ca 
Institute for Information Technology, 
National Research Council Canada, 
Ottawa, Ontario, Canada, KlA 0R6 
Chris. Drummond@nrc-cnrc . gc . ca 
Institute for Computer Science, Polish Academy of Sciences, Warsaw, Poland 



Abstract. Both intensional and extensional background knowledge have 
previously been used in inductive problems to complement the training 
set used for a task. In this research, we propose to explore the useful- 
ness, for inductive learning, of a new kind of intensional background 
knowledge: the inter-relationships or conditional probability distribu- 
tions between subsets of attributes. Such information could be mined 
from publicly available knowledge sources but including only some of 
the attributes involved in the inductive task at hand. The purpose of our 
work is to show how this information can be useful in inductive tasks, 
and under what circumstances. We will consider injection of background 
knowledge into Bayesian Networks and explore its effectiveness on train- 
ing sets of different sizes. We show that this additional knowledge not 
only improves the estimate of classification accuracy it also reduces the 
variance in the accuracy of the model. 

Key 'words: Bayesian Networks, Public Knowledge, Classification. 



1 Introduction 

While standard machine learning acquires knowledge from instances of the learn- 
ing problem, there has always been interest in a more cognitively plausible sce- 
nario in which learning - besides the training instances - utilizes also background 
knowledge relevant for the problem. In many inductive problems, the training 
set, which is a set of labeled samples, could be complemented using intensional or 
extensional background knowledge in order to improve the learning performance 
[11,19]. In Inductive Logic Programming, intensional background knowledge is 
provided in the form of a theory expressed in logical form. In Semi-Supervised 
Learning, the extensional background knowledge is provided in the form of un- 
labeled data. 



2 Farid Seifi, Chris Dmmmond, Nathalie Japkowicz and Stan Matwin 

In this research, we propose to explore a different type of intensional back- 
ground knowledge. In many domains, there exist publicly available very large, 
and related, data sets, for example from demographics and statistical surveys. 
This sort of information is ubiquitous: it is published by many national govern- 
ments [2,3,5]; international organizations [1,6,4]; and private companies. Such 
data sets may not have exactly the same attributes as the data set we are study- 
ing. However, using an intensionalising process [13], we can derive intensional 
background knowledge, in the form of distributions, from this extensional back- 
ground knowledge, given as collections of instances. A question that we consider 
here is whether it is possible to use such information to improve the performance 
of learning methods in machine learning problems. 

Let us consider a simple medical example. Suppose we are learning from 
data a model for the prediction of heart attacks in patients. The data used in 
the inductive learning of this model may include attributes describing sleep dis- 
turbance, as a disease outcome, and stress, as a disease, but does not include 
enough instances to relate these attributes in a statistically significant way. There 
exists, independently of the data used in model building, a large medical survey 
that describes quantitatively sleep disturbance in patients who experience car- 
diac problems or stress. This set could be used in learning a better predictive 
model, capturing the important relationship between sleep disturbance, stress, 
and a heart attack, if we can integrate the data from the medical study with the 
data we are using in learning the predictive model. 

The big challenge in this research is how such background knowledge can be 
integrated with the existing data sets. Bayesian learning is a natural candidate 
as it draws on distributional data for its assessment of the probabilities of an 
instance belonging to different classes of the concept. In Bayesian Networks the 
attribute inter-relationships are encoded into a network structure. We propose 
here to replace parts of this structure, some of the conditional probability dis- 
tributions, with more accurate alternatives, which are available as background 
knowledge contained in large public data sets, e.g. statistical surveys. 

The paper is structured as follows: In Section 2, Bayesian learning is reviewed 
with a simple example. Section 3 discusses how background knowledge is added 
to the network. In Section 4 experimental results are provided. Section 5 contains 
discussion and future work. 



2 Learning and classification using Bayesian Networks 

In a Bayesian network [17, 16], there is a structure which encodes a set of con- 
ditional independence assumptions between attributes; a node is conditionally 
independent of its non-descendants given its parents. Also, there are conditional 
probability distributions capturing each attribute's dependency on others, typ- 
ically represented by multi-dimensional tables. Together, these define the joint 
probability distribution of the attributes and class. With such a distribution, 
we can use Bayes rule to do inference, i.e. determine the probability of some 
unobserved variable. There exist many different ways of building Bayesian net- 



Improving Bayesian Learning Using Public Knowledge 3 

works from training data [7]. We used the software package BN predictor [9, 
10] to build the network and used a maximum likelihood estimator (frequency 
counts) to construct the tables. To build these tables, we need the number of 
training samples for each permutation of attribute value that is involved in the 
conditional probabilities. These are normalized to give probabilities. 

As a simple medical example, consider the diabetes diagnosis problem [12], 
whose network is given in figure 1. In the following equations, the terms A, N, 
M, I, G, D represent Age, Number of pregnancy, Mass, Insulin, Glucose and 
Diabetes, respectively. We need the posterior probability of the class Diabetes 
P(D\A, N, M, I, GQgiven the other attributes. From Bayes rule we can rewrite this 
as in equation 1. 

P(A,N,M,I,G,D) 

P(D\A,N,M,I,G)= — -^ — — — - — - (1) 

v ' ' ' ' P(A,N,M,I,G) v ' 

To classify a new example s = (A 4 ,iV«, Mi,Ii,Gi), given by values for all at- 
tributes except the class diabetes, we chose the class with the highest posterior 
probability, as in equation 2 

Argmax P{D\Ai, Ni, M t , h,G t ) = Argmax P{At, N it Mi, It, G t , D) (2) 

D^(Y&s,No) D£(Yes,No) 

Using a Bayesian network, we can construct the joint probability by simply 
multiplying a few independent terms as in equation 3. From figure 1, the arrows 
indicate which conditional probabilities must represented by tables. For example, 
there are 3 arrows going from the mass, age and jj= pregnacies nodes to that of 
the class. This accounts for the P(D\M, A, 7V)term in the equation. There is a single 
arrow going from diabetes to insulin accounting for the term p(i\d). Continuing 
this process for every arrow will produce equation 3. 

P(A, N, M, I, G, D) = P(A)P(N)(M\A, N)P(D\M, A, N)P(I\D)P(G\I, D) (3) 




Glucose 



Fig. 1. A Bayesian network for diabetes diagnosis 



4 Farid Seifi, Chris Dmmmond, Nathalie Japkowicz and Stan Matwin 

The probabilities in equation 3 which do not include a term for class D , like 
P(M\A, N) , have no effect on the result of equation 2. For a single sample from 
the test set, all the attributes except the class are defined. Thus any terms in 
the joint probability that do not include a term for the class are identical. They 
can be safely ignored for classification. 

3 Injecting Public Knowledge into a Network 

Normally, we obtain the conditional probability distributions which we use in 
Bayesian Network inference from the training set. If we do not have enough 
training data samples, our estimates of the true distribution will be poor and 
the result will not be an accurate classifier. These distributions are independent 
from each other, so it could be possible to improve the performance even by 
replacement of a few of them with accurate alternatives, which we could find 
from statistical surveys. 

We propose improving Bayesian networks by replacing some of the condi- 
tional probability distributions - represented in the form of tables and corre- 
sponding to the edges of the network - with their accurate alternatives which 
are available as background knowledge. 

For example, in the Bayesian Network for diabetes diagnosis presented in 
section 2, suppose we have an accurate distribution of insulin given the diabetes, 
P(I\D), from a large demographic survey. If we use this accurate distribution, 
instead of the one which is extracted from the limited training set, together 
with other distributions, which are extracted for other nodes of the network 
from small training set, and we apply them in formula 1, the performance of the 
Bayesian Network should improve. 

4 Experiments 

The ideal process to test this approach is to use real data along with some 
statistical surveys which could provide us with accurate conditional probability 
distributions that occur in our network. But if we are to experimentally inves- 
tigate the usefulness of our approach, we need to be sure that the distributions 
that we use as background knowledge are accurately representing the real distri- 
bution of our data. Otherwise, they may negatively impact our results. In order 
to avoid such situations we simulate the problem as explained below. 

Due to the imperfections of Bayesian Network constructors, it is probable 
that the extracted network for a data set contains some incorrect attribute de- 
pendencies. If we replace a conditional probability distribution, which is ex- 
tracted based on such relations, the result may not be a significantly better 
classifier. Such situations would also negatively bias any conclusions about the 
reliability and usefulness of our method. In order to avoid this problem, related 
to a lack of sufficient real-world knowledge, in our second experiment we use an 
artificial data set for which we know the correct attribute independencies. 



Improving Bayesian Learning Using Public Knowledge 5 

4.1 Experimental setup 

For the purpose of our experiments, we have made some simplifying assumptions 
about the sizes of the datasets used. These assumptions are parameters of the 
experiments and can be easily changed. In particular, we assume that a large 
data set, which is a representative sample of the "huge" dataset (the whole 
universe of interest), exists. We model our approach by using a large real data 
set (or a large generated artificial data set) to supply us with highly accurate 
conditional probability distributions for the attributes involved in a Bayesian 
Network classifier, trained on a much smaller sample of a huge dataset. In this 
manner we simulate having the relevant information available from statistical 
surveys. For this purpose a real or artificial data set with 20,000 instances, 
which represents the universe of interest, is considered a huge data set. In each 
experiment we sample a large data set from this huge data set, containing 50%, 
10,000 samples. Some of the conditional probability distributions are extracted 
using this large data set. Since these distributions are extracted from a large 
sets of instances, they are similar to what is available from statistical surveys. 
A part of the huge data set, 10%, 2,000 samples, is held out as testing set in 
each experiment. A very small subset of the huge data set is sampled as the 
training set. In these experiments 0.5%, 100 instances, of the huge data set are 
sampled as a training set. In many real world learning problems we only have 
such small training data sets. Using this small training set we build all conditional 
probability distributions, which are not very accurate, for all the nodes in the 
Bayesian Network. 




Large data set 

(for extracting 

accurate distributions ) 



<2) 



intensionalising 
process 



(1)/sampling (1)1 



A 



0,5 % 



Conditional probability + Smal1 train data set 
| distributions j 

(3)l Learnin fl 



Bayesian Network Classifier 



(1)1 Sampling 



W 



-*• 10% 

Test data set 



Fig. 2. Experimental setup. 



What we want to show is the effect of replacing these inaccurate conditional 
probability distributions, extracted from the small training set, with accurate al- 
ternatives, which in real problems might be available, for example from statistical 



6 Farid Seifi, Chris Dmmmond, Nathalie Japkowicz and Stan Matwin 

surveys. For concluding that the replacement of a selected set of distributions 
makes a better classifier we run a set of experiments. In each experiment the 
large data set as well as the training and testing sets are sampled again from the 
huge data set. Then the classifier is trained using the small training set. More 
specifically, potentially inaccurate conditional probability distributions are built 
from the training set. Instead of using statistical surveys to extract accurate 
distributions, we use the distributions which were obtained from the large data 
set. Then we replace the selected set of distributions with accurate alternatives 
and compute the performance of the new modified classifier. We run several 
experiments with the same replacements and then we use paired t-test to see 
whether these sets of replacements make a significantly better classifier or not. 
Our experiments show that replacing more distributions results in a more accu- 
rate classifier unless a distribution is not extracted based on correct attribute 
dependencies. The Letter data set from the UCI machine learning repository [8] 
is used as the real data set. In addition, an artificial data set from the heart 
attack domain is used in a second experiment. 

4.2 Experiments with the Letter data set 

In these experiments we will see the effect of replacing the conditional probability 
distributions on a real data set. The objective of classifiers on the letter data 
set is to identify each of a large number of black-and-white rectangular pixel 
displays as one of the 26 capital letters in the English alphabet. The character 
images were based on 20 different fonts and each letter within these 20 fonts was 
randomly distorted to produce a file of 20,000 unique stimuli. Each stimulus was 
converted into 16 primitive numerical attributes. All these numerical attributes 
contain statistical moments and edge counts, in the box containing the letter, 
which were then scaled to fit into a range of integer values from through 15. 
For example y-bar is the mean of y of 'on' pixels in the box; xy2br is the mean 
of x x y x y; and xegvy is the correlation of x-edge with y. See [14], where the 
dataset was introduced, for details. 

In these experiments we converted 26 classes to two classes by dividing the 
letters into two groups of the first and the second 13 letters in the English al- 
phabet. This binarization of the letter recognition task makes it hard, as there 
are no obvious differences between the letters in the first and second half of the 
alphabet. Using the Bayesian Network constructor package discussed in [10], the 
network, which is shown in figure 3, is extracted. In this network all 16 attributes, 
which are nodes of the network, are shown as rectangles. Conditional dependen- 
cies are represented by arrows. Arrows represent the parent-child relationship, 
with a parent in the start and a child in the end of an arrow. Each node in 
the network is conditionally dependent on its parents. For Bayesian inference we 
only need to extract the conditional probability distribution of the nodes which 
have at least one incoming arrow from the class node. In this network we need 
to extract these distributions for nodes y-bar, xegvy and xy2br. 

Figure 4 shows an example of how the difference between the accuracy of the 
unmodified model and of the modified model - in which the conditional proba- 



Improving Bayesian Learning Using Public Knowledge 7 



| x-box | | y-box | widlh | 




|yegvx | 

Fig. 3. Bayesian Network extracted for Letter data set. 



bility distribution of attribute xy2br is replaced with the accurate alternative - 
changes with respect to the size of the training set. The greatest difference be- 
tween the accuracy of both the modified and unmodified models appears when 
the size of the training set is very small. In order to focus on the effectiveness of 
our approach, we use small training sets, 0.5% of huge data set. 



'■■i thatthe accuracy improved after replacement 
12 -i 



£ 



by retracing table 

: ; :- t ' : : :- - 1»: ■• 



*^ 



umber of training samples 



Fig. 4. Accuracy against size of training set for real data. 



Next we want to show that replacements of the conditional probability distri- 
butions with accurate alternatives make significantly better classifiers. We run 
several experiments, as explained in the experimental setup subsection, all with 
the same replacements. The accuracies of these experiments on the modified 
models are compared with unmodified ones, using the paired t-test, to show 
that those specific replacements made a significantly better classifier. Figure 5 
illustrates an example of the normal distributions for the accuracies of the un- 
modified and modified models, in which the conditional probability distribution 
of attribute xy2br is replaced with the accurate alternative. The bold curve rep- 
resents the normal distribution for the accuracies of the unmodified model in 
different experiments. In all cases, as in the example of figure 5, the variance 
of the accuracies of the modified model is smaller than that of the unmodified 



8 Farid Seifi, Chris Drummond, Nathalie Japkowicz and Stan Matwin 

model. This means that when we replace a conditional probability distribution 
in a Bayesian Network with an accurate alternative, the new model tends to be 
more robust when sampling new data sets for training and testing. 









'-■ 


variance without replacement: 17.37 
variance with reolacement : 3.19 




3 




i/ '^v**"-"*^. 





Accuracy 

Fig. 5. Distribution of accuracies for unmodified (bold curve) and modified model. 



We have tested the effect of replacement of different permutations of condi- 
tional probability distributions in the letter data set. In the extracted network 
for the letter data set we only have 3 conditional probability distributions, so 
the number of permutations is 3! = 6. Table 1 shows the results for different 
sets of distribution replacements. For each set of replacements it tells whether 
the modified model is significantly better than the unmodified one or not. These 
results are obtained using the paired t-test with 95% confidence interval. 

Table 1. Accuracy for different replacements in the Bayesian Network on the letter 
data set as well as the results of the t-test for 20 different experiments. 



experiment no y-bar 
change 


xy2br xegvy 


y-bar 
xy2br 


y-bar 
xegvy 


Xy2br 
xegvy 


y-bar 
xy2br xegvy 


Average of 61.7 66.1 
the accuracy 


72.3 61.4 


72.9 


64.3 


71.4 


72.7 


Varianceof accuracy 4.36 


10.62 -0.338 


11.163 


2.583 


9.663 


11.015 


T - Testresult : ESS 


ESS NSS 


ESS 


VSS 


ESS 


ESS 



* ESS- extremely statistically significant * VSS- Very statistically significant * NSS- 
Not statistically significant * SS- Statistically Significant 



Replacing the conditional probability distribution of y-bar or xy2br leads to 
a significantly better classifier. But, when we replace xegvy with the accurate 
alternative we obtain a less accurate classifier. One reason is that, according to 
attribute evaluators (such as information gain and chi square), this attribute 
has less effect on the results of classification than the other two. The attribute 
evaluators ranked attributes xy2br, y-bar and xegvy, which are nodes of our 
network, as 1, 2 and 3, respectively. The effectiveness of replacement of the 



Improving Bayesian Learning Using Public Knowledge 



9 



conditional probability distribution of an attribute is directly related to the 
correctness of all its conditional dependencies. Therefore, another reason for 
this negative result is that the conditional dependencies of attribute xegvy may 
not extracted correctly. This problem is investigated in subsequent experiments 
and also discussed in more detail in the discussion section. 

4.3 Experiments 'with the artificial data set 

In these experiments, we want to show the effect of the accuracy of the ex- 
tracted conditional dependencies on the accuracy of modified classifiers using 
our approach. The data set, used in these experiments, is generated using a 
heart attack data generator (which we designed ourselves) which generates data 
samples with 21 different attributes including the class. The objective of clas- 
sifiers on this data set is heart attack diagnosis. The attributes are partitioned 



Weight 



Lung Condition | 




Infection 



Fig. 6. Bayesian Network extracted for Heart attack data set. 



into 4 groups: conditions, concept, outcomes and contexts. The data generator 
uses conditional probability distributions between attributes which are extracted 
from statistical surveys and the medical science literature. The data generator is 
used to generate a data set of 20,000 samples. The class attribute, heart attack, 
could be positive or negative. 

The first part of this experiment consists of extracting the Bayesian Network 
or in other words the conditional independence between attributes. Since we 
know the exact conditional dependencies, used for data generation, we have 
manually defined the "true" network. But the relation between stress and sleep 
disturbance in this network, which is shown with the bold arrow in figure 6, 
is omitted on purpose, while in the data generation process sleep disturbance 
is conditionally dependant on stress. This is done in order to find out what the 
effect of replacement of a conditional probability distribution, which is extracted 
based on wrong conditional dependencies in the network, would be. Figure 6 
shows the Bayesian Network which is used in this experiment. 



10 



Farid Seifi, Chris Dmmmond, Nathalie Japkowicz and Stan Matwin 



Again, to focus the effect of replacement of conditional probability distri- 
butions, we use a very small training data set. Figure 7 shows the difference in 
the accuracy of the unmodified model with the modified one — in which the upper 
body discomfort distribution ( Upbd) is replaced by a more accurate distribution — 
as a function of different training set sizes. 



% tiiatthe accuracy improved after replacement 















. . 


bvreclacino table 








ofthe node Upbd 





























1 1 1* 
1000 


* 2000 


3000 



numper or training samples 



Fig. 7. Accuracy against size of training set for artificial data. 

Now we want to show that the replacement of conditional probability distri- 
butions, which are in the form of tables, makes significantly better classifiers. For 
this purpose we run several experiments as explained in the experiment setup 
subsection. For each individual replacement, for example changing table Chest 
Pain {Chestp), the accuracies of different experiments on the modified model are 
compared with the unmodified ones, using paired t-test, to find out whether the 
modified model is significantly better than the unmodified one or not. Table 2 
contains the results for different distribution replacements. For each replacement, 
we mentioned whether the result is significantly better or not. These results are 
obtained using the paired t-test with 95% confidence interval. This table contains 
the results of replacing just one conditional probability distribution in each test. 
Each column has a header which indicates the name of the attribute whose con- 
ditional distribution is replaced. The modified models in six different cases out of 
eight are extremely statistically significant. In one case, it is statistically signifi- 
cant. In another case, when the conditional dependence ofthe sleep disturbance 
attribute is removed, it is not statistically significant. Incomplete dependencies 
of this attribute on others were intentionally used here to show what the effect 
of using incomplete or wrong dependencies would be. 

The results of these experiments again show that the variance in the accu- 
racy of the modified model is smaller than the variance in the accuracy of the 
unmodified model. 



5 Discussion and Future Work 

Replacement of conditional probability distributions of attributes which are ex- 
tracted according to wrong or incomplete dependencies or have a weak relation 



Improving Bayesian Learning Using Public Knowledge 11 

Table 2. Accuracy for different replacements in the Bayesian Network on the heart 
attack data set as well as the results of the t-test for 20 different experiments. 



experiment no Chstp Upbd 
change 


Shrtb Swetg Dizns 


Nasa 


Slepd 


Wkns 


Average of 89.5 89.9 90.4 
the accuracy 


90.2 90.1 90.2 


89.9 


89.6 


90.4 


Varianceof accuracy 0.445 0.945 


0.6625 0.64 0.725 


0.45 


0.1025 


0.925 


T - Testresult : SS ESS 


ESS ESS ESS 


ESS 


NSS 


ESS 



with the class, may impact negatively on the classification result. Suppose that 
we replace such a distribution with an accurate alternative and that we use the 
replaced distribution along with other attribute distributions to classify a given 
instance. If, using accurate conditional probability distribution, the two condi- 
tional probabilities of belonging to each class are close to each other, the effect 
of replacing the distribution on the joint probabilities is weak. But when condi- 
tional probabilities obtained from replaced distributions of such faulty attributes 
are far apart, they have a larger impact on the Bayesian classification results, 
and since the conditional distributions involving these attributes are incorrect, 
there is a negative impact on the results. 

One solution for such conditional probability distributions, which we pro- 
pose as future work, could be to assign a weight for each attribute based on its 
real effect on classification. Then, during classification, the difference between 
the values which belong to each attribute's conditional probability distribution 
could be smoothened based on the weight of the attribute which it belongs to. A 
similar approach has been used to improve the accuracy of Naive Bayes by weak- 
ening its attribute independence assumptions in Lazy Bayesian Rules [20], Tree 
Augmented Naive Bayes [15] and Averaged One-Dependence Estimators [18]. If 
we consider a small weight for problematic attributes of this kind, their effect 
on classification results would be reduced and therefore better results would be 
obtained. This solution would require a good strategy to measure these weights. 

Another result that we experienced in these tests was that the variance of 
the accuracy of any modified classifier is smaller than the variance of unmodified 
model. This means that the modified classifiers tend to be more robust with 
respect to learning and testing with different data sets sampled from the same 
domain. Testing the result of the modified classifiers on different types of drifts 
in the data sets and finding which of the modified and unmodified models are 
more robust in case of different types of changes in the data, such as concept 
drifts or population drifts, is also proposed as future work. 

6 Conclusion 

In this study we propose a practical method for improving Bayesian classifiers 
by using background knowledge from large, publicly available datasets existing 



12 Farid Seifi, Chris Dmmmond, Nathalie Japkowicz and Stan Matwin 

independently of the training data set. We present a method which manipulates 
the Bayesian Network's conditional probability distributions, given in the form 
of tables, based on background knowledge. The idea is tested on a real and 
an artificial data set. The results show that such changes produce significantly 
better classifiers than normal Bayesian Network classifiers. 

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