Improving Naïve Bayes Performance in Single Image
Pap Smear Using Weighted Principal Component
Analysis (WPCA)
Yumi Novita Dewi
STMIK Nusa Mandiri Jakarta
Jakarta, Indonesia
umi.ymd@bsi.ac.id
Teddy Mantoro
Faculty of Science and Technology, Sampoerna University
Jakarta, Indonesia
teddy@ieee.org
Abstract— The accuracy value for single image classification of
Pap smear for seven classes still has an unsatisfactory accuracy
whereas the determination of cell classes in single image of Pap
smear is very important to determine whether the cells are normal
or not. Pap smear image classification that produces good
accuracy will greatly assist in the process of detecting cells
automatically. This study aims to determine whether the use of the
method of weighted - Principal Component Analysis (PCA) models
can improve the performance of the Naïve Bayes algorithm to
classify cell images in the Herlev dataset. Accuracy will be checked
for the classification of two classes and seven classes. The method
used in this research consists of several stages that are
preprocessing, knowledge rule, evaluation, and performance
report. The results of this study indicate that the weighted PCA
method can improve the accuracy on the classification of seven
classes while the classification of two classes does not provide
better accuracy results.
Keywords—Pap smear images; Classification; Naïve Bayes;
Weighted - Principal Component Analysis (PCA).
I. INTRODUCTION
Cervical cancer is the fourth most common disease affecting
women. There were about 530,000 new cases in 2012
representing about 7.5% causing death for most women in the
world [1]. It is estimated that more than 270,000 deaths occur
due to cervical cancer every year. Cervical cancer is attacked on
the neck of the cervix caused by Human Papilloma Virus (HPV)
which is not directly felt by the sufferer, so mostly the patients
with this cervical cancer will just know when it reaches an
advanced stage.
Surely this will cause death for the sufferer if the medical
treatment is delayed. The lack of awareness for early
examination and limited availability of experts who can perform
Pap smear diagnoses leads to an ever increasing number of
deaths.
The first research about early detection of cervical cancer
was performed by scientist Georgeus Papanicolau in 1930 where
Dwiza Riana
STMIK Nusa Mandiri Jakarta
Jakarta, Indonesia
dwiza@nusamandiri.ac.id
Georgeus Papanicolau invented the mechanism of pre-cervical
cancer diagnosis, so early detection of cervical cancer was
known as Pap smear [2].
The cell cytologist performed the test by taking samples of
cells from the cervical neck and putting on a glass slide where
the next stage will perform coloring techniques in order to
facilitate the diagnosis on the microscope, so from that method
it can produce class category information on cervical cancer
cells [3].
There is a data set which is the result of Pap test [4]. This
data set has been used in many studies. Herlev data sets were
introduced by researchers named Jantzen, Norup, Dounias, &
Bjerregaard [5]. In many studies these datasets are used to
perform algorithmic examination and various classification
techniques [6], [7], [8].
In the previous study [5], 20 features have been extracted
from the segmentation result of Pap smear cell image and then
used as inputs recognize a single Pap smear cell image. Herlev
data set has 917 images that become classification objects. A
single cell image of Pap smear consists of seven class categories.
The normal class consists of three classes which are normal cell
class categories including normal superficial, normal
intermediate, and normal columnar while the other four
categories are abnormal cell class including mild (light)
dysplasia, moderate dysplasia, severe dysplasia, and carcinoma
in situ [5].
In its development, research on the single cell image
classification of Pap smear has become an interesting focus for
discussion [3]. Direct classification is also intended to determine
the form of classification between normal and abnormal cells.
Until now, the scope of classification is still carried out by
researchers to find out more about the development of cervical
cancer with the concept of data mining. Data mining is a process
of extracting knowledge of large databases from other databases
or data base repositories.
 Previous researches about image classification of Pap smear.
Research using the same dataset but with the features, method
and algorithm that are different use algorithm of Artificial
Neural Network (ANN), Euclidian Distance (ED) and Support
Vector Machine (SVM) [9], ConvNet [10] but this research only
classified which are normal and abnormal. On the other hand, it
is still difficult to do classification of seven classes on Herlev
data. The classification algorithm Naïve Bayes without feature
selection and ensemble using in [11]. The next research [12]
used WEKA for using Naïve Bayes classification, Nearest
Neighbor filters and Naïve Bayes transfers. The results of the
research show that the use of Naïve Bayes method have the
significant results.
Research on the integration of bagging and greedy forward
selection on Pap smear classification using Naïve Bayes has
been experimented on Herlev datasets with different
classification categories, namely the classification on two
classes of single cell of Pap smear and the classification on seven
classes of single cell image of Pap smear [13]. The results
obtained the highest accuracy value of 92.15% for the
classification of two classes, namely normal classes and Fig. 1. Columnar Epithelium and Squamous Epithelium Region
abnormal classes. However, the classification on seven classes
of single cell of Pap smear only reached an accuracy of 63.25%. Based on the diagnosis, there are 2 (two) types of pre-
In other words, the Naïve Bayes model with Bagging and cancerous cells, namely dysplasia which means irregular
Greedy Forward Selection is still not able to get the best development, and carcinoma in situ [15]. The dysplasia cell
accuracy in classification handling in seven classes [13] itself can be divided into three types, namely mild, moderate,
although the accuracy is still possible to be improved. To and severe dysplasia. Thus, every cell contained in the cervix
improve the best accuracy, it needs an integration of some other can be grouped into seven cell classes. Table I shows the
algorithm models, so the classification with single image cell characteristics of each single cell of each class.
dataset of Pap smear can produce the best accuracy value [14].
By considering the feature of single-cell Pap smear dataset TABLE I. SINGLE CELL CHARACTERISTICS OF PAP SMEAR [7]
categorized in dataset with large-scale dimensions, it is
necessary to have techniques for processing training data and
No Class Name Characteristics
attribute selection so that it is expected to improve the accuracy.
This research will perform reduction of dataset features using 1. Normal • The cells are oval.
PCA with weighting to measure the value of classification Superficial • The nucleus is very small.
accuracy for two classes and seven classes. • The comparison between the nucleus area
and the cytoplasm area is very small.
This paper is presented in several sections. The second part 2. Normal • The cells are round.
describes Pap smears. Section 3 discusses about materials and Intermediate • The nucleus is large.
methods used in the study. Section 4 describes the results and • The comparison between nucleus and
cytoplasm area is small.
discussions about the accuracy of the classification of two
3. Normal • The cells are shaped like columns.
classes and seven classes using a weighted PCA process on the Columnar • The nucleus is large.
Naïve Bayes algorithm, and the last sections consist of • The comparison between nucleus and
conclusions and further research plans. cytoplasm area is medium.
4. Mild (Light) • The nucleus is large and light-colored.
Dysplasia • The comparison between the area of
II. PAP SMEAR
nucleus and cytoplasm is medium.
Generally, a single Pap smear cell consists of 3 parts of the 5. Moderate • The nucleus is large and dark.
region, namely nucleus, cytoplasm that surrounds the nucleus, Dysplasia • The cytoplasm is dark.
and background that is not a cell area. The specimen cells are • The comparison between the area of the
mostly taken from the columnar region of epithelium and nucleus and cytoplasm is great.
6. Severe • The nucleus is large, dark, and irregular
squamous epithelium as shown in Figure 1. Dysplasia in shape.
Normal conditions will change when there are pre-cancerous • The cytoplasm is dark.
cells in the cervix or so-called dysplastic cells, and the genetic • The comparison between the area of the
nucleus and cytoplasm is large.
information of these cells will change, so the cells are no longer
7. Carcinoma In • The nucleus is large, dark, and irregular
divided into the developmental layers as they should [15]. Situ in shape.
• The comparison between the area of the
nucleus and cytoplasm is large.
 After 2003, Erik Martin classified Pap smear cells consisting
of seven classes including three normal classes and four
abnormal classes [4]. In 2005, Jantzen et al., proposed twenty
features that can be extracted from the segmentation result of
Pap smear cell image where twenty of these features represent a
considerable number of features [5].
III. MATERIAL AND METHOD
The proposed method design can be seen in Figure 2. The
proposed model scheme design used the input of single Pap
smear cell image, namely Herlev Data [5]. This dataset is
numerical data where the single Pap smear dataset has 20 feature
attributes divided into 7 classes: normal and abnormal classes of
917 datasets.
In the design of proposed method, processing process was
performed by preparing the datasets to be grouped into two
groups. The first dataset with 2 classes consisted of normal and
abnormal classes while the next data set consisted of 7 classes
which were superficial squamous, intermediate squamous,
columnar, mild dysplasia, moderate dysplasia, severe dysplasia,
and carcinoma in situ. The next process got the rule from each
data group or knowledge rule.
Fig. 2. Proposed Algorithm Model Scheme Design
A. Weighted Principal Component Analysis
PCA is one of the most widely used variable extraction
feature (reduction) [16]. PCA method is very useful if the
existing data has a large number of variables and has a
correlation among variables. The calculations of the PCA are
based on the calculation of the weigen value and eigen vectors
which express the data distribution from a dataset [17].
The purpose of PCA analysis is to reduce existing variables
to be fewer without losing information contained in original or
initial data [18]. By using PCA, variables that are initially in n
variables will be reduced to new variable of k (principal
component) with fewer k than n, and by only using k principal
component, it will yield the same value using n variable [19].
The result variable of the reduction is called the principal
component or can be called a factor. The character of the new
variables formed by PCA analysis will in addition not only have
fewer number of variables but also eliminate the correlation
among variables that are formed [16].
The next step is to normalize the class attributes that reflect
the relevance of the attribute weights with the class attribute
values [20]. The Weighted PCA process is:
Fig. 3. Examination Step of Naïve Bayes with Weighted - PCA
In Weighting, the value of accuracy can be seen from the
confusion matrix table with the formula:
Accuracy = (Amount of True Data) / (Amount of Data) x 100%
B. Naïve Bayes Algorithm
The most popular and widely used classification method is
Naïve Bayes method [13, 21]. Naive Bayes method is one of
the classification methods that can predict the probability
of membership of a class. The value of a class in Naive
Bayes method is independent, and it doesn’t depend on other
attributes. This classification is performed by using the
following formula: (x-µ)2
1
g(x, µ, a) = e 2CT2 (1)
√2m:
Where:
n xi
∑
µ= i=l
n
(2)
∑n (xi-µ)2
i=l
a= (3)
n1
Calculations with numerical data types in the Naïve Bayes
algorithm should be performed with the calculation of mean μ
and standard deviation σ using equations (1), (2), and (3). All
parts are tested until all datasets can be divided into two data
which are data training and data testing.
Each method and algorithm has its own characteristics, as
well as Naïve Bayes algorithm. The Naïve Bayes classification
works on the theory of probability which views all features of
the data as evidence in probability [14]. This gives its own
characteristics for Naïve Bayes, as for these characteristics are:
1. The Naïve Bayes method works robustly on isolated data
which is usually data with different characteristics (outliner).
Naive Bayes can also handle incorrect attribute values by
overwhelming training data during the model development
and prediction process.
2. It is robust to face irrelevant attributes.
3. Attributes that have a correlation can degrade the
performance of Naïve Bayes classification because the
assumption of attribute independence is gone.
IV. RESULT AND DISCUSSION
This study proposed the use of PCA method on Naïve Bayes
algorithm to improve the accuracy optimally on the
classification of seven classes of single Pap smear image. The
following is a comparison table of Naïve Bayes algorithm with
Weighted-PCA model:
TABLE II. COMPARISON NAÏVE BAYES WITH WEIGHTED-PCA
Class Accuracy Model Result
2 Naïve Bayes 90,42%
CLASS Naïve Bayes + Weighted-PCA 67,45%
7 Naïve Bayes 55,73%
CLASS Naïve Bayes + Weighted-PCA 87,24%
Table II shows the comparison of accuracy values on the
Naïve Bayes algorithm and the Weighted-Principal Component
Analysis (PCA) model where the accuracy of the Naïve Bayes
algorithm with the feature of seven classes is smaller than other
algorithm models. However, on the combination of Naïve Bayes
algorithm with Weighted-Principal Component Analysis (PCA)
model in the feature of two classes, the accuracy decreased to
67.45%.
Figure 4 is a graph of the comparison chart of the Naïve
Bayes algorithm with the Weighted - Principal Component
Analysis (PCA) model, which shows that the highest chart is
indicated by the accuracy of Naïve Bayes algorithm with the
features of two classes.
Fig. 4. Comparison graph of NB algorithm and W-PCA
In Figure 4, Naïve Bayes algorithm can be featured in the
accuracy measurements for single Pap Smear cell datasets with
two classes because Naïve Bayes algorithm will be able to
quickly and accurately handle datasets of small dimensions
while the dataset test with Naïve Bayes in the classification of
seven classes with weighted PCA showed an increase in
accuracy compared to the classification which only used the
Naïve Bayes algorithm. The overall comparison of Naïve Bayes
algorithm with Weighted -PCA shows the best accuracy value.
Furthermore, t-test will be conducted to see if the
improvement obtained gives significant influence to the data.
TABLE III. T TEST FOR 7 CLASSES AND 2 CLASSES
0,939 0,959
0,939 0,040 -
0,959 - -
The t-test of the Naïve Bayes algorithm with the Weighted -
Principal Component Analysis (PCA) model on the datasets of
seven classes and two classes was 0.040. This number is smaller
than the value of α which is 0.05. That shows that both models
have a significant difference to both Pap smear single cell
classes (Table III).
The solution of this problem is to compare between the
Naïve Bayes algorithm and the Weighted - Principal Component
Analysis (PCA) model used in dealing with datasets with large-
scale dimensions so that the accuracy value can be increased to
86.59 %.
V. CONCLUSION
The Naïve Bayes algorithm can be featured in the accuracy
measurements for datasets of two classes because Naïve Bayes
algorithms will be able to quickly and accurately handle datasets
in small-scale dimensions while the dataset test of Naïve Bayes
with large-scale dimensions experienced a decrease in the value
of accuracy. The solution of this problem is to compare between
the Naïve Bayes algorithm and the weighted - Principal
Component Analysis (PCA) model used in dealing with datasets
with large-scale dimensions so that the value of accuracy can be
increased to 67.45% and 87.28%.
The results of the t test were performed by Rapidminer
implementation of Naïve Bayes algorithm with Weighted - PCA
model with the rate of 0.023. This number is smaller than the
value of α which is 0.05. It shows that both models of the Naïve
Bayes algorithm with the Weighted-PCA model have significant
differences to both Pap smear single cell classes. This research
is a preliminary study of research on datasets which have
classification features in Pap smear images. Further research will
apply integration method of sample Bootstrapping and
Weighted PCA to classify single image Pap smear into seven
classes so that the better accuracy can be obtained.
ACKNOWLEDGMENT
This study used the data from: Pap smear Benchmark Data
for Pattern Classification J. Jantzen, J. Norup, G. Dounias, and
B. Bjerregaard, University Dept. of Pathology Herlev Ringvej
75, DK-2730 Herlev, Denmark.
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