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Classification of Wisconsin Breast Cancer Diagnostic

and Prognostic Dataset using Polynomial Neural


Network

A Dissertation Work
Submitted in Partial fulfillment for the award of

Post Graduate Degree of Master of Technology
In Computer Science & Engineering

Submitted to

Rajiv Gandhi Proudyogiki Vishwavidhyalaya,
Bhopal (M.P.)

Submitted By:
Shweta Saxena
0126CS10MT17

Under the Guidance of
Dr. Kavita Burse
Director, OCT, Bhopal.

Department of Computer Science & Engineering

ORIENTAL COLLGEGE OF TECHNOLOGY,
BHOPAL
(Formerly known as Thakral College of Technology, Bhopal)
Approved by AICTE New Delhi & Govt. of M.P.
Affiliated to Rajiv Gandhi Proudyogiki Vishwavidhyalaya, Bhopal (M.P.)
Session 2012-13
II


ORIENTAL COLLGEGE OF TECHNOLOGY, BHOPAL
(Formerly known as Thakral College of Technology, Bhopal)
Approved by AICTE New Delhi & Govt. of M.P. and Affiliated to Rajiv
Gandhi Proudyogiki Vishwavidhyalaya Bhopal (M.P.)
DEPARTMENT OF COMPUTER SCIENCE & ENGINEERING


CERTIFICATE


THIS IS TO CERTIFY THAT THE DISSERTATION ENTITLED
Classification of Wisconsin Breast Cancer
Diagnostic and Prognostic Dataset using Polynomial
Neural Network BEING SUBMITTED BY Shweta Saxena
IN PARTIAL FULFILLMENT OF THE REQUIREMENT FOR
THE AWARD OF M.TECH DEGREE IN COMPUTER
SCIENCE & ENGINEERING TO ORIENTAL COLLEGE OF
TECHNOLOGY, BHOPAL (M.P) IS A RECORD OF BONAFIDE
WORK DONE BY HIM UNDER MY GUIDANCE.








Dr. Kavita Burse Prof. Roopali
Soni
Director Head of
Department, CSE
OCT, Bhopal OCT, Bhopal
(Guide)





III




ORIENTAL COLLGEGE OF TECHNOLOGY, BHOPAL
(Formerly known as Thakral College of Technology, Bhopal)
Approved by AICTE New Delhi & Govt. of M.P. and Affiliated to Rajiv
Gandhi Proudyogiki Vishwavidhyalaya Bhopal (M.P.)
DEPARTMENT OF COMPUTER SCIENCE & ENGINEERING




APPROVAL CERTIFICATE


This dissertation work entitled Classification of
Wisconsin Breast Cancer Diagnostic and Prognostic
Dataset using Polynomial Neural Network submitted
by Shweta Saxena is approved for the award of degree of
Master of Technology in Computer Science & Engineering.







INTERNAL EXAMINER EXTERNAL EXAMINER


Date: Date:
IV

CANDIDATE DECLARATION

I hereby declare that the dissertation work presented in the report
entitled as Classification of Wisconsin Breast Cancer Diagnostic
and Prognostic Dataset using Polynomial Neural Network
submitted in the partial fulfillment of the requirements for the award
of the degree of Master of Technology in Computer Science &
Engineering of Oriental College of Technology is an authentic record
of my own work.


I have not submitted the part and partial of this report for the award
of any other degree or diploma.



Date: Shweta
Saxena

(0126CS10MT17)

This is to certify that the above statement made by the candidate is
correct to the best the best of my knowledge.



Dr. Kavita Burse
Director
OCT, Bhopal
(Guide)
V

ACKNOWLEDGEMENT

I would like to express my deep sense of respect and gratitude towards my advisor
and guide Dr. Kavita Burse, Director Oriental College of Technology who has
given me an opportunity to work under her. She has been a constant source of
inspiration throughout my work. She displayed unique tolerance and understanding at
every step of progress of this work and encouraged me incessantly. Her invaluable
knowledge and innovative ideas helped me to take the work to the final stage. I
consider it my good fortune work under such a wonderful person.

I express my respect to Prof. Roopali Soni, Head, Computer Science
Engineering Department, Oriental College of Technology for her constant
encouragement and invaluable advice in every aspect of my academic life. I am also
thankful to all faculty members of Computer Science and Engineering Department for
their support and guidance.
I am especially thankful to my father Mr. Damodar Saxena, my mother Mrs.
Nirmala Saxena, and my loving sisters Shikha and Shraddha for their love,
sacrifice and support on every path of my life. I extend a special word of thanks to my
husband Mr. Ashish Saxena for his moral support and help in achieving my aim.

Last but not the least I am extremely thankful to all who have directly or indirectly
helped me for the completion of my work.

Shweta Saxena
(0126CS10MT17)
VI

ORGANIZATION OF DISSERTATION

The report Classification of Wisconsin Diagnostic and Prognostic Dataset using
Polynomial Neural Network has been divided into 7 chapters as follows:

Chapter 2 Introduction
Chapter 1 first describes the motivation of this research work. It then describes breast
cancer disease, its symptoms and types in detail. The chapter also describes diagnosis
and prognosis process of the disease.

Chapter 2 Literature Review
Different Neural network techniques for diagnosis and prognosis of breast cancer
diagnosis and prognosis are described in this chapter along with the related work
concerned with these techniques. The chapter also compares the accuracies of
different techniques at the end.

Chapter 3 Artificial Neural Network and Principal Component
Analysis
In this chapter Artificial Neural network is described in detail along with its
advantages and medical applications. The chapter describes in detail the higher order
or polynomial neural network along with back propagation algorithm which are used
in this research for classification. The chapter next provides the detailed information
about data preprocessing technique named Principal Component Analysis and its
advantages.

Chapter 4 MATLAB
The technology used for implementation of proposed work is MATLAB. The chapter
gives a brief introduction of MATLAB along with its advantages and detailed
description of Neural Network Toolbox available in MATLAB for design of neural
network. The chapter also explains the neural network design process using neural
network toolbox.
VII

Chapter 5
Chapter 5 presents the description of dataset used for implementation of this research
and the results of implementation.

Chapter 6
Chapter 6 concludes the dissertation and provides possible directions for relevant
future work.
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ABSTRACT

Breast cancer is the most common form of cancer and major cause of death in
women. Normally, the cells of the breast divide in a regulated manner. If cells keep
on dividing when new cells are not needed, a mass of tissue forms. This mass is
called a tumor. This tumor can be cancerous or non-cancerous. The goal of diagnosis
is to distinguish between cancerous and non-cancerous cells. Once a patient is
diagnosed with breast cancer, the prognosis gives the anticipated long-term behavior
of the ailment. Breast cancer detection, classification, scoring and grading of
histopathological images is the standard clinical practice for the diagnosis and
prognosis of breast cancer. In a large hospital, a pathologist typically handles a
number of cancer detection cases per day. It is, therefore, a very difficult and time-
consuming task. Owing to their wide range of applicability and their ability to learn
complex and non linear relationships including noisy or less precise informat ion
Artificial Neural Networks (ANNs) are very well suited to solve problems in
biomedical engineering. ANNs can be applied to medicine in four basic fields:
modeling, bioelectric signal processing, diagnosing and prognostics. There are
several systems available for the diagnosis and selection of therapeutic strategies in
breast cancer.
In this research we propose neural network based clinical support system to provide
medical data analysis for diagnosis and prognosis of breast cancer. The system
classifies the breast cancer diagnostic data which are provided as input to neural
network into two sets- benign (non- cancerous) and malignant (cancerous) to get the
diagnostic results. For getting prognosis results the system classify the prognostic
data which are given as input to neural network into two classes- recurrent and non-
recurrent. Results belong to recurrent set shows that cancer is reoccurred after some
time. Polynomial neural network (PNN) structure is used along with back
propagation algorithm for classification of breast cancer data. Wisconsin Breast
Cancer (WBC) datasets from the UCI Machine Learning repository is used as input
datasets to PNN. Data pre-processing technique named Principal Component
Analysis (PCA) is used as a features reduction transformation method to improve the
accuracy of PNN. In our results the Mean Square error (MSE) is substantially
reduced for PCA preprocessed data as compared to normalized data. Hence we get
more accurate diagnosis and prognosis results.
Keywords- breast cancer, polynomial neural network, principal component
analysis, wisconsin breast cancer dataset.
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CONTENTS
DESCRIPTION PAGE NO.
List of Fig.s XII
List of Tables XIII

Chapter I
Introduction 1-7
1.1 Research Motivation 2
1.2 Introduction 3
1.3 Symptoms of breast cancer 4
1.4 Types of breast cancer 4
1.5 Breast cancer diagnosis 5
1.6 Breast cancer prognosis 6

Chapter - 2
Literature Review 8-26
2.1 Introduction 9
2.2 Neural network techniques for diagnosis and prognosis of breast cancer 11
2.3 Comparison of neural network techniques for breast cancer diagnosis and
prognosis 26

Chapter 3 27-40
Artificial Neural Network and Principal Component Analysis
3.1 Overview of ANN 28
3.2 Basics of ANN 28
3.3 Feed Forward Neural Network with Back propagation 29
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3.4 Higher order or polynomial neural network 33
3.5 Advantages of ANN 35
3.6 Medical Applications 35
3.7 Overview of data Preprocessing 36
3.7.1 Feature selection 37
3.7.2 Feature extraction 37
3.8 Principal Component Analysis 38
3.8.1 Dimension reduction 38
3.8.2 Lower dimensionality basis 39
3.8.3 Selection of principal components 39
3.8.4 Selecting best lower dimensional space 39
3.8.5 Linear transformation implied 40
3.9 Advantages of PCA 40

Chapter 4
41-48
MATLAB
4.1 Introduction 42
4.2 Advantages of MATLAB 42
4.3 Limitations of MATLAB 43
4.4 Neural Network Toolbox 44
4.5 Neural Network Design using Neural Network Toolbox 45
4.5.1 Collecting the data 46
4.5.1.1 Pre-processing and post-processing the data 46
4.5.1.2 Representing Unknown or Dont Care Targets 47
4.5.1.3 Dividing the Data 47
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4.5.2 Creating and configuring the network 47
4.5.3 Initializing weights and biases 47
4.5.4 Training the network 47
4.5.5 Validation of network 48
4.5.6 Use the network 48

Chapter 5
Simulation and Results 49-60
5.1 Introduction 50
5.2 Description of dataset 52
5.3 Results and discussions 57
5.3.1 Diagnosis Results 57
5.3.2 Prognosis Results 58
Chapter 6
Conclusion and Future Scope 61-62
6.1 Conclusion 62
6.2 Future work 62
List of Publications 63-64
References 65-74






LIST OF FIGURES
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FIGURE NO. TITLE PAGE NO.
Fig. 1.1 Breast Cancer 3
Fig. 1.2 FNA Images of benign and malignant breast mass 6
Fig. 2.1 An MLP structure 11
Fig. 2.2 Probabilistic neural network for cancer diagnosis 16
Fig. 3.1 A single neuron 26
Fig. 3.2 Feed Forward NN model for Breast Cancer diagnosis 27
Fig. 3.3 Node structure of PNN 30
Fig. 3.4 Polynomial Neural Network 30
Fig. 3.5 Data Pre-processing using PCA 34
Fig. 4.1 Pre-processing and post-processing 42
Fig. 5.1 Flow chart of ANN process 47
Fig. 5.2 Comparison of the convergence performance for WPBC dataset (50
iterations) 55
Fig. 5.3 (a) Testing error for normalization and PCA data for WPBC dataset over
100 data 55
Fig. 5.3 (b) Testing error for normalization PCA for WPBC dataset over 198 data
56


LIST OF TABLES
TABLE NO. TITLE PAGE NO.
Table 2.1 Accuracy comparison for test data classification 23
Table 4.1 Pre-processing and post-processing functions 42
Table 5.1 A brief description of breast cancer datasets 46
Table 5.2 Attribute information for WBC dataset 48
Table 5.3 Attribute information for WDBC dataset 49
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Table 5.4 Attribute information for WPBC dataset 50-51
Table 5.5 Training performance for WBC dataset 52
Table 5.6 Testing performance for WBC dataset 53
Table 5.7 Training performance for WDBC dataset 53
Table 5.8 Testing performance for WDBC dataset 53-54
Table 5.9 Training performance for WPBC dataset 54
Table 5.10 Testing performance for WPBC dataset 54
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Chapter 1
Introduction


1.1 Research Motivation
According to the World Health Organization (WHO), breast cancer is currently the
top cancer in women worldwide and the second highest cause of death for all female.
Diagnosis and prognosis of breast cancer at very early stage is recondite due to
various factors, which are cryptically interconnected to each other. We are oblivious
to many of them. Until an effective preventive measure becomes widely available,
early detection followed by effective treatment is the only recourse for reducing
breast cancer mortality. Most breast cancers are detected by the patient as the lump in
the breast. The majority of breast lumps are benign (non- cancerous) so it is the
physicians responsibility to diagnose breast cancer. The goal of diagnosis is to
distinguish between malignant (Cancerous) and benign breast lumps. Once a patient
is diagnosed with breast cancer, the malignant lump must be excised. During this
procedure, or during a different post-operative procedure, physicians must determine
the prognosis of the disease. Prognosis gives the anticipated long-term behavior of
the ailment. A major class of problems in medical science involves the diagnosis and
prognosis of breast cancer, based upon various tests performed upon the patient.
When several tests are involved, the ultimate diagnosis and prognosis may be
difficult to obtain, even for a medical expert. In human operator base analysis of test
results errors may also be created in calculation and this will result in faulty
treatment for the patients. This has given rise, over the past few decades, to
computerized diagnostic and prognostic tools, intended to aid the physician in
making sense out of the welter of data. A prime target for such computerized tools is
in the domain of cancer diagnosis and prognosis. Neural networks are computer-
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based tools inspired by the vertebrate nervous system that have been increasingly
used in the past decade to model biomedical domains. The motivation for this
research is to create neural network based tool for doctors to use for classifying the
results obtained from various tests performed upon the patient. The neural networks
based clinical support system proposed in this research provide medical data analysis
for diagnosis and prognosis in shorter time and remain unaffected by human errors
caused by inexperience or fatigue. Use of ANN increases the accuracy of most of the
methods and reduces the need of the human expert. The back propagation algorithm
has been used to train neural network keeping in view of the significant
characteristics of NN and its advantages for the implementation of the classification
problem. PCA is used as a features reduction transformation method to improve the
accuracy of ANN. Advantages of feature reduction includes the identification of a
reduced set of features among a large set of features that are used for outcome
prediction. Though the proposed neural network model is implemented on standard
Wisconsin dataset obtained from UCI machine learning repository, it can also be
implemented using similar dataset.
1.2 Introduction
Breast cancer is the major cause of death by cancer in the female population [1].
Most breast cancer cases occur in women aged 40 and above but certain women with
high-risk characteristics may develop breast cancer at a younger age [2]. Breast
cancer occurs in humans and other mammals. While theoverwhelming majority of
human cases occur in women, male breast cancer can also occur [3]. Cancer is a
disease in which cells become abnormal and form more cells in an uncontrolled way.
With breast cancer, the cancer begins in the tissues that make up the breasts. The
breast consists of lobes, lobules, and bulbs that are connected by ducts. The breast
also contains blood and lymph vessels. These lymph vessels lead to structures that
are called lymph nodes. Clusters of lymph nodes are found under the arm, above the
collarbone, in the chest, and in other parts of the body. Together, the lymph vessels
and lymph nodes make up the lymphatic system, which circulates fluid called lymph
throughout the body. Lymph contains cells that help fight infection and disease.
Normally, the cells of the breast divide in a regulated manner. If cells keep dividing
when new cells are not needed, a mass of tissue forms. This mass is called a tumor as
shown in fig. 1.1[4]. A tumor can be benign or malignant. A benign tumor is not
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cancer and will not spread to other parts of the body. A malignant tumor is cancer.
Cancer cells divide and damage tissue around them. When breast cancer spreads
outside the breast, cancer cells are most often found under the arm in the lymph
nodes. In many cases, if the cancer has reached the lymph nodes, cancer cells may
have also spread to other parts of the body via the lymphatic system or through the
bloodstream. This can be life-threatening [5].






Fig 1.1 Breast Cancer
In addition to being the most frequently diagnosed cancer among women in the
United States, breast cancer accounts for up to 20 percent of the total costs of cancer
overall. Women covered by Medicaid have unique challenges when it comes to this
disease. For example, Medicaid recipients are more likely to be diagnosed at an
advanced stage. They also have much lower screening rates compared to the general
population. A new study found a high prevalence of breast cancer in Medicaid
patients as well as significantly higher health care use and costs [6].
1.3 Symptoms of Breast Cancer
The first noticeable symptom of breast cancer is typically a lump that feels different
from the rest of the breast tissue. More than 80% of breast cancer cases are
discovered when the woman feels a lump. Lumps found in lymph nodes located in
the armpits can also indicate breast cancer [7]. Indications other than a lump may
include thickening different from the other breast tissue, one breast becoming larger
or lower, a nipple changing position or shape or becoming inverted, skin puckering
or dimpling, a rash on or around a nipple, discharge from nipple/s, constant pain in
part of the breast or armpit, and swelling beneath the armpit or around the collarbone
[8]. Inflammatory breast cancer is a particular type of breast cancer which can pose a
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substantial diagnostic challenge. Symptoms may resemble a breast inflammation and
may include itching, pain, swelling, nipple inversion, warmth and redness throughout
the breast, as well as an orange-peel texture to the skin [7]. Another reported
symptom complex of breast cancer is Paget's disease of the breast. This syndrome
presents as eczematoid skin changes such as redness and mild flaking of the nipple
skin. As Paget's advances, symptoms may include tingling, itching, increased
sensitivity, burning, and pain. There may also be discharge from the nipple.
Approximately half of women diagnosed with Paget's also have a lump in the breast
[9].

1.4 Types of Breast Cancer
Breast cancer can develop in different ways and may affect different parts of the
breast. The location of cancer will affect the progression of cancer and the treatment.
Breast cancer is divided mainly into the pre-invasive or in-situ form, or the
invasive or infiltrating form. The pre-invasive form is restricted to the breast itself
and has not yet invaded any of the lymphatics or blood vessels that surround the
breast tissue. Therefore, it does not spread to lymph nodes or other organs in the
body [5]. Pre-invasive Forms of breast cancer are-
a) Ductal carcinoma in situ (DCIS):
This is the most common pre-invasive breast cancer. More commonly seen now
because this form is generally seen on a mammogram and is identified by unusual
calcium deposits or puckering of the breast tissue (called stellate appearance). If left
untreated, DCIS will progress to invasive breast cancer.
b) Lobular carcinoma in situ (LCIS):
Unlike DCIS, LCIS is not really cancer at all. Most physicians consider the finding
of LCIS to be accidental, and it is thought to be a marker for breast cancer risk. That
is, women with LCIS seem to have a 7-10 times increased risk of developing some
form of breast cancer (usually invasive lobular carcinoma) over the next 20 years.
LCIS does not warrant treatment by surgery or radiation therapy. Close follow-up is
most commonly indicated, and LCIS is not easily seen on mammogram. Recent data
suggest that this condition may be a precursor to invasive lobular cancer. There may
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be some forms of LCIS (ie, the pleomorphic subtype) that require more aggressive
local therapy and closer follow-up.
Invasive Forms of cancer are-
a) Ductal carcinoma:
This is the most common form of breast cancer and accounts for 70% of breast
cancer cases. This cancer begins in the milk ducts and grows into surrounding
tissues.
b) Lobular carcinoma:
This originates in the milk-producing lobules of the breast. It can spread to the fatty
tissue and other parts of the body. About 1 in 10 breast cancers are of this type [10].
c) Medullary, mucinous, and tubular carcinomas:
These are three relatively slower-growing types of breast cancer.
d) Inflammatory carcinoma:
This is the fastest growing and most difficult type of breast cancer to treat. This
cancer invades the lymphatic vessels of the skin and can be very extensive. It is very
likely to spread to the local lymph nodes.
e) Pagets disease:
Paget's disease is cancer of the areola and nipple. It is very rare (about 1% of all
breast cancers). In general, women who develop this type of cancer have a history of
nipple crusting, scaling, itching, or inflammation.
1.5 Breast Cancer Diagnosis
Most breast cancers are detected by the patient as the lump in the breast. The
majority of breast lumps are benign (non- cancerous) so it is the physicians
responsibility to diagnose breast cancer. The goal of diagnosis is to distinguish
between malignant (Cancerous) and benign breast lumps. The three methods
currently used for breast cancer diagnosis are mammography, fine needle aspirate
(FNA) and surgical biopsy [11]. Mammography has a reported sensitivity
(probability of correctly identifying a malignant lump) which varies between 68%
and79% [12].Taking a fine needle aspirate (i.e. extracting fluid from a breast lump
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using a small-gauge needle) and visually inspecting the fluid under a microscope has
a reported sensitivity varying from 65% to 98% [13]. Fig 1.2 shows an FNA image
of benign and malignant breast mass.

Fig 1.2 FNA Images of benign and malignant breast mass
The more evasive and costly surgical biopsy has close to 100% sensitivity and
remains the only test that can confirm malignancy. Therefore mammography lacks
sensitivity, FNA sensitivity varies widely, and surgical biopsy, although accurate, is
invasive, time consuming and costly [11]. The goal of the diagnostic aspect of our
research is to develop a neural network system that diagnoses breast cancer with help
of Wisconsin Breast cancer database which is obtained from FNAs.

1.6 Breast Cancer Prognosis
Once a patient is diagnosed with breast cancer, the malignant lump must be excised.
During this procedure, or during a different post-operative procedure, physicians
must determine the prognosis of the disease[14]. This is simply the long-term
outlook for the disease for patients whose cancer has been surgically removed[11].
Prognosis is important because the type and intensity of the medications are based on
it. Currently, the most reliable method of determining the prognosis is by axillary
clearance (the dissection of axillary lymph nodes) [Choong]. Unfortunately, for
patients with unaffected lymph nodes, the result is unnecessary numbness, pain,
weakness, swelling, and stiffness[15]. Prognosis poses a more difficult problem than
that of diagnosis since the data is censored. That is, there are only a few cases where
we have an observed recurrence of the disease [14]. A patient can be classified as a
recur if the disease is observed at some subsequent time to tumor excision, a patient
for whom cancer has not been recurred and may never recur, has an unknown or
censored[16] time to recur (TTR). On the other hand, we do not observe recurrence
in most patients. For these, there is no real point at which we can consider the patient
a non recurrent case. So, the data is considered censored since we do not know the
time of recurrence. For such patients, all we know is the time of their last check-up.
We call this the disease-free survival time (DFS) [14]. Prognostic aspect of the
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proposed research is to develop a neural network system that classify Wisconsin
Breast cancer Prognostic database into two classes- Recur and non-recur patients.
XXI





Chapter 2
Literature Review




2.1 Introduction
Neural network techniques have been successfully applied to the diagnosis and
prognosis of breast cancer. This chapter reviews the existing/popular neural network
techniques for the diagnosis and prognosis of breast cancer. Various neural network
techniques are compared at the end. The Wisconsin breast cancer data set is used to
study the classification accuracy of the neural networks. Two research papers which
were helpful for getting the idea of survey are-
An Analysis of the methods employed for breast cancer diagnosis by M. M.
Beg and M. Jain.
Breast cancer diagnosis using statistical neural networks by T. Kiyan, T
Yildirim
A brief description of above two papers is as follows-
An Analysis of the methods employed for breast cancer diagnosis, Author:
M. M. Beg and M. Jain [17]
Abstract:
Breast cancer research over the last decade has been tremendous. The ground
breaking innovations and novel methods help in the early detection, in setting the
stages of the therapy and in assessing the response of the patient to the treatment. The
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prediction of the recurrent cancer is also crucial for the survival of the patient. This
paper studies various techniques used for the diagnosis of breast cancer. Different
methods are explored for their merits and de-merits for the diagnosis of breast lesion.
Some of the methods are yet unproven but the studies look very encouraging. It was
found that the recent use of the combination of Artificial Neural Networks in most of
the instances gives accurate results for the diagnosis of breast cancer and their use
can also be extended to other diseases.
Comments:
This paper reviews the existing/popular methods which employ the soft computing
techniques to the diagnosis of breast cancer. The paper demonstrated the better
performance of the multiple neural networks over the monolithic neural networks for
the diagnosis of breast cancer. It can be concluded from this study that the neural
networks based clinical support systems provide the medical experts with a second
opinion thus removing the need for biopsy, excision and reduce the unnecessary
expenditure. Use of ANN increases the accuracy of most of the methods and reduces
the need of the human expert. The ANN, Support Vector Machine, Genetic algorithm
(GA), and K-nearest neighbor may be used for the classification problems. The GA is
better used for the feature selection. The fuzzy co-occurrence matrix and fuzzy
entropy method can also be used for feature extraction. Almost all intelligent
computational learning algorithms use supervised learning. Supervised ANN
outperforms the unsupervised network but in the case of a patient with no previous
medical records the unsupervised ANN is the only solution.

Breast cancer diagnosis using statistical neural networks, Author: M. M.
Beg and M. Jain[18]
Abstract:
Breast cancer is the second largest cause of cancer deaths among women. The
performance of the statistical neural network structures, radial basis network (RBF),
general regression neural network (GRNN) and probabilistic neural network (PNN)
are examined on the Wisconsin breast cancer data (WBCD) in this paper. This is a
well-used database in machine learning, neural network and signal processing.
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Statistical neural networks are used to increase the accuracy and objectivity of breast
cancer diagnosis.
Comments:
This paper shows that how statistical neural networks are used in actual clinical
diagnosis of breast cancer. The simulations were realized by using MATLAB 6.0
Neural Network Toolbox. Four different neural network structures, multi layer
perceptron (MLP), RBF, PNN and GRNN were applied to WBCD database to show
the performance of statistical neural networks on breast cancer data. According to the
results RBF and PNN are the best classifiers in training set whereas GRNN gives the
best classification accuracy when the test set is considered. According to overall
results, it is seen that the most suitable neural network model for classifying WBCD
data is GRNN.
2.2 Neural network techniques for diagnosis and prognosis of breast cancer
Various techniques for diagnosis and prognosis of breast cancer are-
Multilayer Perceptron (MLP):
MLP has been widely used for the aim of cancer prediction and prognosis [19]. MLP
is a class of feed forward neural networks which is trained in a supervised manner to
become capable of outcome prediction for new data [20]. The structure of MLP is
shown in fig 2.1. An MLP consists of a set of interconnected artificial neurons
connected only in a forward manner to form layers. One input, one or more hidden
and one output layer are the layers forming an MLP [21]. Artificial neuron is basic
processing element of a neural network. It receives signal from other neurons,
multiplies each signal by the corresponding connection strength that is weight, sums
up the weighted signals and passes them through an activation function and feeds the
output to other neurons [22].


Fig. 2.1 MLP structure

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The simplest form of trainable neural network, first developed (Rosenblatt, 1958),
composed of two layers of nodes namely input and output layer. A mapping between
the input and output data could be established by assigning weights to the input
numerical data during training. More complicated MLPs which are commonly used
consist of some hidden layers in addition to the input and output layers. These hidden
layers enable the MLP to extract higher order statistics from a set of given data and
hence, capture the complex relationship between input-output data. Therefore, MLPs
commonly consist of an input layer for which the number of nodes are defined by
size of input vector, one or more hidden layers which can have variable number of
nodes depending on the application and an output layer which has one or more nodes
depending on the number of output classes. Connections between these layers are
defined by weights which are assigned in a supervised learning process so that the
neural network would respond correctly to new data. This can be done via a training
algorithm, in which a cost function is computed by comparing the networks output
and the desired output and is then minimized with respect to the network parameters
[21]. Neural network classification process consists of two steps- training and testing.
The classification accuracy depends on training [23]. A mapping between the input
and output data could be established by assigning weights to the input numerical data
during training [21]. The training requires a series of input and associated output
vectors. During the training, the network is repeatedly presented with the training
data and the weights and thresholds in the network are adjusted from time to time till
the desired input output mapping occurs [22]. Training is done on known examples
and testing is done on unknown samples. The training procedure itself consisted of
two processes involving feed-forwarding the input data followed by back
propagation of error by adjusting weights to minimize error on each training epoch
[24]. Following research paper presents the effectiveness of MLP for diagnosis and
prognosis of breast cancer-
An expert system for detection of breast cancer based on association rules
and neural network, Author: M. Karabatak and M. C. Ince [93]
This paper presents an automatic diagnosis system for detecting breast cancer based
on association rules (AR) and neural network (NN). In this study, AR is used for
reducing the dimension of breast cancer database and NN is used for intelligent
classification. The proposed AR + NN system performance is compared with NN
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model. The dimension of input feature space is reduced from nine to four by using
AR. In test stage, 3-fold cross validation method was applied to the Wisconsin breast
cancer database to evaluate the proposed system performances. The correct
classification rate of proposed system is 95.6%. This research demonstrated that the
AR can be used for reducing the dimension of feature space and proposed AR + NN
model can be used to obtain fast automatic diagnostic systems for other diseases.

Cross Validation Evaluation for Breast Cancer Prediction Using Multilayer
Perceptron Neural Networks, Author: Shirin A. Mojarad, Satnam S. Dlay, Wai L.
Woo and Gajanan V. Sherbet [25]
Abstract:
The aim of this study is to investigate the effectiveness of a Multilayer Perceptron
(MLP) for predicting breast cancer progression using a set of four biomarkers of
breast tumors. The biomarkers include DNA ploidy, cell cycle distribution
(G0G1/G2M), steroid receptors (ER/PR) and S-Phase Fraction (SPF). A further
objective of the study is to explore the predictive potential of these markers in
defining the state of nodal involvement in breast cancer. Two methods of outcome
evaluation viz. stratified and simple k-fold Cross Validation (CV) are studied in order
to assess their accuracy and reliability for neural network validation. Criteria such as
output accuracy, sensitivity and specificity are used for selecting the best validation
technique besides evaluating the network outcome for different combinations of
markers.
Comments:
The presence of metastasis in the regional lymph nodes is the most important factor
in predicting prognosis in breast cancer. Many biomarkers have been identified that
appear to relate to the aggressive behaviour of cancer. However, the nonlinear
relation of these markers to nodal status and also the existence of complex interaction
between markers have prohibited an accurate prognosis. The results show that
stratified 2-fold CV is more accurate and reliable compared to simple k-fold CV as it
obtains a higher accuracy and specificity and also provides a more stable network
validation in terms of sensitivity. Best prediction results are obtained by using an
individual marker-SPF which obtains an accuracy of 65%. The authors suggest that
XXVI

MLP-based analysis provides an accurate and reliable platform for breast cancer
prediction given that an appropriate design and validation method is employed.

WBCD breast cancer database classification applying artificial
metaplasticity neural network, Author: A. Marcano-Cedeo , J. Quintanilla-
Domnguez and D. Andina [26]
Abstract:
The correct diagnosis of breast cancer is one of the major problems in the medical
field. From the literature it has been found that different pattern recognition
techniques can help them to improve in this domain. These techniques can help
doctors form a second opinion and make a better diagnosis. In this paper we present a
novel improvement in neural network training for pattern classification. The
proposed training algorithm is inspired by the biological metaplasticity property of
neurons and Shannons information theory. During the training phase the Artificial
metaplasticity Multilayer Perceptron (AMMLP) algorithm gives priority to updating
the weights for the less frequent activations over the more frequent ones. In this way
metaplasticity is modeled artificially. AMMLP achieves a more effcient training,
while maintaining MLP performance. To test the proposed algorithm we used the
Wisconsin Breast Cancer Database (WBCD). AMMLP performance is tested using
classification accuracy, sensitivity and specificity analysis, and confusion matrix.
The obtained AMMLP classification accuracy of 99.26%, a very promising result
compared to the Backpropagation Algorithm (BPA) and recent classification
techniques applied to the same database.
Comments:
In this study, a Artificial Neural Network for Classification Breast Cancer based on
the biological metaplasticity property was presented. The proposed AMMLP
algorithm was compared with the classic MLP with Backpropagation, applied to the
Wisconsin Breast Cancer Database. The AMMLP classifier shows a great
performance obtaining the following results average for 100 networks: 97.89% in
specificity, 100% in sensitivity and the total classification accuracy of 99.26%, the
ROC curve to show the AMMPL superiority over the classic MLP with
Backpropagation and finally the results obtained after calculating the AUC in this
XXVII

case were as follows for AMMLP is 0.989 while the AUC for BP is 0.928, this
indicates one more time the AMMLP superiority over the BP, in this particular case.
From the above results, we conclude that the AMMLP obtains very promising results
in classifying the possible breast cancer. We believe that the proposed system can be
very helpful to the physicians for their as a second opinion for their final decision. By
using such an efficient tool, they can make very accurate decisions. Our AMMLP,
proved to be equal or superior to the state-of-the-art algorithms applied to the
Wisconsin Breast Cancer Database, and shows that it can be an interesting
alternative.

Classification of breast cancer by comparing back propagation training
algorithms Author: F. Paulin and A. Santhakumaran [27]
Abstract:
Breast cancer diagnosis has been approached by various machine learning techniques
for many years. This paper presents a study on classification of Breast cancer using
Feed Forward Artificial Neural Networks. Back propagation algorithm is used to
train this network. The performance of the network is evaluated using Wisconsin
breast cancer data set for various training algorithms. The highest accuracy of
99.28% is achieved when using levenberg marquardt algorithm.
Comments:
The Back-propagation algorithm and supervised training method are used in this
project. The aim of training is to adjust the weights until the error measured between
the desired output and the actual output is reduced. The training stops when this
reaches a sufficiently low value. To analyze the data neural network tool box which
is available in MATLAB software is used. In this research a feed forward neural
network is constructed and the Back propagation algorithm is used to train the
network. The proposed algorithm is tested on a real life problem, the Wisconsin
Breast Cancer Diagnosis problem. In this paper six training algorithms are used,
among these six methods, Levenberg Marquardt method gave the good result of
99.28%. Preprocessing using min-max normalization is used in this diagnosis.
Further work is needed to increase the accuracy of classification of breast cancer
diagnosis.
XXVIII


Radial Basis Function Neural Network (RBFNN)

RBFNN is trained to perform a mapping from an m-dimensional input space to an n-
dimensional output space. An RBFNN consists of the m-dimensional input x being
passed directly to a hidden layer. Suppose there are c neurons in the hidden layer.
Each of the c neurons in the hidden layer applies an activation function, which is a
function of the Euclidean distance between the input and an m-dimensional prototype
vector. Each hidden neuron contains its own prototype vector as a parameter. The
output of each hidden neuron is then weighted and passed to the output layer. The
outputs of the network consist of sums of the weighted hidden layer neurons [28].
The transformation from the input space to the hidden-unit space is nonlinear where
as the transformation from the hidden-unit space to the output space is linear [29].
The performance of an RBFNN depends on the number and location (in the input
space) of the centers, the shape of the RBFNN functions at the hidden neurons, and
the method used for determining the network weights. Some researchers have trained
RBFNN networks by selecting the centers randomly from the training data [30].
Following research paper describes the application of RBFNN in breast cancer
prediction-
Breast Cancer Detection using Recursive Least Square and Modified Radial
Basis Functional Neural Network, Author: M. R. Senapati, P. K .Routray, P. K.
Dask [31]
Abstract:
A new approach for classification has been presented in this paper. The proposed
technique, Modified Radial Basis Functional Neural Network (MRBFNN) consists of
assigning weights between the input layer and the hidden layer of Radial Basis
functional Neural Network (RBFNN). The centers of MRBFNN are initialized using
Particle swarm Optimization (PSO) and variance and centers are updated using back
propagation and both the sets of weights are updated using Recursive Least Square
(RLS). Our simulation result is carried out on Wisconsin Breast Cancer (WBC) data
set. The results are compared with RBFNN, where the variance and centers are
updated using back propagation and weights are updated using Recursive Least
XXIX

Square (RLS) and Kalman Filter. It is found the proposed method provides more
accurate result and better classification.
Comments:
Modified Radial Basis Functional Neural Network is same as that of RBFNN with an
exception that weights are assigned between neurons in the input layer and the
neurons in the hidden layer. An efficient Pattern Recognition and rule extraction
technique using Recursive Least square approximation and Modified Radial Basis
Functional Neural Networks (MRBFNN) is presented in this paper. The weights
between input layer and the hidden layer as well as hidden layer and output layer of
the RBFNN classifier can be trained using the linear recursive least square (RLS)
algorithm. The RLS has a much faster rate of convergence compared to gradient
search and least mean square (LMS) algorithms.

Probabilistic Neural Networks (PNN):
PNN is a kind of RBFNN suitable for classification problems. It has three layers. The
network contains an input layer, which has as many elements as there are separable
parameters needed to describe the objects to be classified. It has a pattern layer,
which organizes the training set such that an individual processing element represents
each input vector. And finally, the network contains an output layer, called the
summation layer, which has as many processing elements as there are classes to be
recognized [32]. For detection of breast cancer output layer should have 2 neurons
(one for benign class, and another for malignant class). Each element in this layer
combines via processing elements within the pattern layer which relate to the same
class and prepares that category for output [32].


Fig. 2.2 Probabilistic neural network for breast cancer diagnosis

PNN used in [33] has a multilayer structures consisting of a single RBF hidden layer
of locally tuned units which are fully interconnected to an output layer (competitive
XXX

layer) of two units, as shown in Fig. 2.2. In this system, real valued input vector is
features vector, and two outputs are index of two classes. All hidden units
simultaneously receive the eight-dimensional real valued input vector. The input
vector to the network is passed to the hidden layer nodes via unit connection weights.
The hidden layer consists of a set of radial basis functions. Associated with jth
hidden unit is a parameter vector, called (C_j ) a center. The hidden layer node
calculates the Euclidean distance between the center and the network input vector
and then passes the result to the radial basis function. All the radial basis functions
are of Gaussian type. Equations which used in the neural network model are as
follows-

X_j=(f -c _j * b^ih)
2.1
(X)=exp(-X^2 )
2.2
b^ih= 0.833/s
2.3
S_i=_(j=1)^hW_ji^ho* X_j
2.4
1, if Si max of { S_1,S_2 }
Y_i= 2.5
0, else
where i = 1,2, j = 1,2,. . . ,h, Y_i is the ith output (classification index), (f ) is the
eight-dimensional real valued input vector, W_ji^ho is the weight between the jth
hidden node and the ith output node, (C _j) is the center vector of the jth hidden
node, s is the real constant known as spread factor, bih is the biasing term of radial
basis layer, and (.) is the nonlinear RBF (Gaussian). PNN provides a general
solution to pattern classification problems by following an approach developed in
statistics, called Bayesian classifiers [34][35]. PNN combines the Bays decision
strategy with the Parzen non-parametric estimator of the probability density functions
XXXI

of different classes [36]. Following research papers present the application of PNN in
breast cancer diagnosis and prognosis-

The Wisconsin Breast Cancer Problem: Diagnosis and DFS time prognosis
using probabilistic and generalised regression neural classifiers Author: Ioannis
Anagnostopoulos, Christos Anagnostopoulos, Angelos Rouskas, George
Kormentzas and Dimitrios Vergados [37].
Abstract:
This papers deals with the breast cancer diagnosis and prognosis problem employing
two proposed neural network architectures over the Wisconsin Diagnostic and
Prognostic Breast Cancer (WDBC/WPBC) datasets. A probabilistic approach is
dedicated to solve the diagnosis problem, detecting malignancy among instances
derived from the Fine Needle Aspirate (FNA) test, while the second architecture
estimates the time interval that possibly contain the right end-point of the patients
Disease-Free Survival (DFS) time. The accuracy of the neural classifiers reaches
nearly 98% for the diagnosis and 92% for the prognosis problem. Furthermore, the
prognostic recurrence predictions were further evaluated using survival analysis
through the Kaplan-Meier approximation method and compared with other
techniques from the literature.
Comments:
In this paper PNN is used to solve the diagnosis problem because this kind of
networks present high-generalization ability and do not require large amount of
training data. PNN is used to detect malignancy among instances derived from the
Fine Needle Aspirate (FNA) test. The accuracy of the neural classifiers reaches
nearly 98%.
Generalized Regression Neural Networks (GRNN):
GRNN is the paradigm of RBFNN, often used for function approximations [38].
GRNN consists of four layers: The first layer is responsible for reception of
information, the input neurons present the data to the second layer (pattern neurons),
the output of the pattern neurons are forwarded to the third layer (summation
neurons), summation neurons are sent to the fourth layer (output neuron)[39]. If f(x)
XXXII

is the probability density function of the vector random variable x and its scalar
random variable z, then the GRNN calculates the conditional mean E(z\x) of the
output vector. The joint probability density function f(x, z) is required to compute the
above conditional mean. GRNN approximates the probability density function from
the training vectors using Parzen windows estimation [40]. GRNNs do not require
iterative training; the hidden- to-output weights are just the target values tk, so the
output y(x), is simply a weighted average of the target values tk of training cases xk
close to the given input case x. It can be viewed as a normalized RBF network in
which there is a hidden unit centered at every training case. These RBF units are
called kernels and are usually probability density functions such as the Gaussians.
The only weights that need to be learned are the widths of the RBF units h. These
widths (often a single width is used) are called smoothing parameters or bandwidths
and are usually chosen by cross validation [38]. Following research paper gives
breast cancer diagnosis and prognosis results by GRNN-
The Wisconsin Breast Cancer Problem: Diagnosis and DFS time prognosis
using probabilistic and generalised regression neural classifiers, Author: Ioannis
Anagnostopoulos and Christos Anagnostopoulos, Angelos Rouskas, George
Kormentzas, and Dimitrios Vergados [37].
Abstract:
This papers deals with the breast cancer diagnosis and prognosis problem
employing two proposed neural network architectures over the Wisconsin Diagnostic
and Prognostic Breast Cancer (WDBC/WPBC) datasets. A probabilistic approach is
dedicated to solve the diagnosis problem, detecting malignancy among instances
derived from the Fine Needle Aspirate (FNA) test, while the second architecture
estimates the time interval that possibly contain the right end-point of the patients
Disease-Free Survival (DFS) time. The accuracy of the neural classifiers reaches
nearly 98% for the diagnosis and 92% for the prognosis problem. Furthermore, the
prognostic recurrence predictions were further evaluated using survival analysis
through the Kaplan-Meier approximation method and compared with other
techniques from the literature.
Comments:
XXXIII

Generalised Regression Neural Network architecture (GRNNs) is used for
breast cancer prognosis in this paper. These neural networks have the special ability
to deal with sparse and non-stationary data where non-linear relationships exist
among inputs and outputs. In the problem addressed, the network calculates a time
interval that corresponds to a possible right end-point of the patients disease-free
survival time. Thus, if f(x,z) is the probability density function of the vector random
variable x and its scalar random variable z, then the GRNN calculates the conditional
mean E(x\z)of the output vector. The joint probability density function f(x,z) is
required to compute the above conditional mean. GRNN approximates the pdf from
the training vectors using Parzen windows estimation, which is a non-parametric
technique approximating a function by constructing it out of many simple parametric
probability density functions. Parzen windows are considered as Gaussian functions
with a constant diagonal covariance matrix. The accuracy of the neural classifiers
reaches 92% for prognosis problem.

Fuzzy- Neuro System:
Fuzzy-Neuro system uses a learning procedure to find a set of fuzzy membership
functions which can be expressed in the form of if-then rules[41]-[43]. A fuzzy
inference system uses fuzzy logic, rather than Boolean logic, to reason about data
[44]. Its basic structure includes four main components- a fuzzifier, which translates
crisp (real-valued) inputs into fuzzy values; an inference engine that applies a fuzzy
reasoning mechanism to obtain a fuzzy output; a defuzzifier, which translates this
latter output into a crisp value; and a knowledge base, which contains both an
ensemble of fuzzy rules, known as the rule base, and an ensemble of membership
functions, known as the database. The decision-making process is performed by the
inference engine using the rules contained in the rule base[45].The fuzzy logic
procedure can be summarized in following steps: Determination of the input and
output variables that describe the observed phenomenon together with the selection
of their variation interval, defining a set of linguistic values together with their
associated membership functions that map/cover the numerical range of the fuzzy
variable, and defining a set of fuzzy inference rules between input and output fuzzy
XXXIV

variables[46]. Following research papers uses fuzzy logic approach for breast cancer
diagnosis-

A fuzzy-genetic approach to breast cancer diagnosis, Author: Carlos
Andres Pena-Reyes, Moshe Sipper [47].
Abstract:
The automatic diagnosis of breast cancer is an important, real-world medical
problem. In this paper we focus on the Wisconsin breast cancer diagnosis (WBCD)
problem, combining two methodologiesfuzzy systems and evolutionary
algorithmsso as to automatically produce diagnostic systems. We find that our
fuzzy-genetic approach produces systems exhibiting two prime characteristics: first,
they attain high classification performance (the best shown to date), with the
possibility of attributing a confidence measure to the output diagnosis; second, the
resulting systems involve a few simple rules, and are therefore (human-)
interpretable.
Comments:
A good computerized diagnostic tool should possess two characteristics, which are
often in conflict. First, the tool must attain the highest possible performance, i.e.
diagnose the presented cases correctly as being either benign or malignant.
Moreover, it would be highly desirable to be in possession of a so-called degree of
confidence: the system not only provides a binary diagnosis (benign or malignant),
but also outputs a numeric value that represents the degree to which the system is
confident about its response. Second, it would be highly beneficial for such a
diagnostic system to be human-friendly, exhibiting so-called interpretability. This
means that the physician is not faced with a black box that simply spouts answers
(albeit correct) with no explanation; rather, we would like for the system to provide
some insight as to how it derives its outputs. In this paper we combine two
methodologiesfuzzy systems and evolutionary algorithmsso as to automatically
produce systems for breast cancer diagnosis. The major advantage of fuzzy systems
is that they favour interpretability, however, finding good fuzzy systems can be quite
an arduous task. This is where evolutionary algorithms step in, enabling the
automatic production of fuzzy systems, based on a database of training cases.
XXXV

Cancer Diagnosis Using Modified Fuzzy Network, Author: Essam Al-
Daoud [48]
Abstract:
In this study, a modified fuzzy c-means (MFCM) radial basis function (RBF)
network is proposed. The main purposes of the suggested model are to diagnose the
cancer diseases by using fuzzy rules with relatively small number of linguistic labels,
reduce the similarity of the membership functions and preserve the meaning of the
linguistic labels. The modified model is implemented and compared with adaptive
neuro-fuzzy inference system (ANFIS). The both models are applied on "Wisconsin
Breast Cancer" data set. Three rules are needed to obtain the classification rate 97%
by using the modified model (3 out of 114 is classified wrongly). On the contrary,
more rules are needed to get the same accuracy by using ANFIS. Moreover, the
results indicate that the new model is more accurate than the state-of-art prediction
methods. The suggested neuro-fuzzy inference system can be re-applied to many
applications such as data approximation, human behavior representation, forecasting
urban water demand and identifying DNA splice sites.

Comments:
ANFIS works with different activation functions and uses un-weighted connections
in each layer. ANFIS consists from five layers and can be adapted by a supervised
learning algorithm. In this paper ANFIS and the modified Fuzzy RBF (MFRBF) are
applied on Wisconsin Breast Cancer data set. The main purposes of the suggested
model are to diagnose the cancer diseases by using fuzzy rules with relatively small
number of linguistic labels, reduce the similarity of the membership functions and
preserve the meaning of the linguistic labels. The standard fuzzy c-means has various
well-known problems, namely the number of the clusters must be specified in
advanced, the output membership functions have high similarity, and FCM is
unsupervised method and cannot preserve the meaning of the linguistic labels. On the
contrary, the grid partitions method solves some of the previous matters, but it has
very high number of the output clusters. The basic idea of the suggested MFCM
algorithm is to combine the advantages of the two methods, such that, if more than
one cluster's center exist in one partition then merge them and calculate the
XXXVI

membership values again, but if there is no cluster's center in a partition then delete it
and redefined the other clusters. The experimental results show that MFRBF can be
used to get high accuracy with fewer and unambiguous rules. The classificati-on rate
is 97% by using only three rules. On the contrary, more rules are needed to get the
same accuracy by using ANFIS. Moreover the features projected partition in ANFIS
is amb-iguous and cant preserve the meaning of the linguistic labels.
Genetic Algorithm (GA):
The standard GA proceeds as follows: an initial population of individuals is
generated at random or heuristically. Every evolutionary step, known as a generation,
the individuals in the current population are decoded and evaluated according to
some predefined quality criterion. To form a new population (the next generation),
individuals are selected according to their fitness. Many selection procedures are
currently in use, one of the simplest being fitness-proportionate selection, where
individuals are selected with a probability proportional to their relative fitness. This
ensures that the expected number of times an individual is chosen is approximately
proportional to its relative performance in the population. Thus, high-fitness or good
individuals stand a better chance of reproducing, while low-fitness ones are more
likely to disappear [45]. Genetic algorithms can be used to determine the
interconnecting weights of the ANN. During training of the network, the BP requires
approximately two ANN evaluations (i.e., one forward propagation and one
backward error propagation) for each iteration, while the GA required only one ANN
evaluation (i.e., forward propagation) for each generation and each chromosome. In
comparison to the conventional BP training algorithm, the GA has shown to provide
some benefit in evolving the inter-connecting weights for the ANNs. In [49] although
the GA trained ANN didnt outperform the BP-trained ANN at all numbers of ANN
evaluations in the test set, the GA trained ANN was found to converge faster than the
BP trained ANN in the training set.
Computer-aided diagnosis of breast cancer using artificial neural networks:
Comparison of Back propagation and Genetic Algorithms Author: Yuan-Hsiang
Chang, Bin Zheng, Xiao-Hui Wang, abd Walter F. Good [49].
Abstract:
XXXVII

The authors investigated computer-aided diagnosis (CAD) schemes to determine the
probabilio for the presence of breast cancer using artificial neural networks (ANN)
that were trained by a Backpropagation (BP) algorithm or by a Genetic Algorithm
(GA). A clinical database of 418 previously verified patient cases was employed and
randomly pariitioned into two independent sets for CAD training and testing. During
training, the BP and the GA were independenti'y applied to optimize, or to evolve the
inter-connecting weights of the ANN . Both the BP-trained and the GA-trained CAD
performances were then compared using receiver-operating characteristics (ROC)
analysis. In the training set, the BP-trained and the GA-trained CAD schemes yielded
the areas under ROC curves of 0.91 and 0.93, respectively. In the testing set, both the
BP-trained and the GA-trained ANN, yielded the areas under ROC curves of
approximately 0.83. These results demonstrated that the GA performed slightly
better, although not significantly, than BP for the training of the CAD schemes.

Comments:
In this paper it is found that although the GA trained ANN didnt outperform the BP-
trained ANN at all numbers of ANN evaluations in the test set, the GA trained ANN
was found to converge faster than the BP trained ANN in the training set.
2.3 Comparison of neural network techniques for breast cancer diagnosis and
prognosis
NN techniques for breast cancer diagnosis are compared for WBC data. It is
concluded that the MLP, RBFNN, PNN, GRNN, GA, Fuzzy- neuro -system, SANE,
IGANIFS, Xcyct system, ANFIS, SIANN may be used for the classification problem.
Almost all intelligent computational learning algorithms use supervised learning. The
accuracy of different methods is compared in table 2.1.
Table 2.1 Accuracy comparison for test data classification
Type of Network Accuracy References
Radial Basis Function Neural Network (RBFNN) 96.18% [18]
Probabilistic Neural Network (PNN) 97.0% [18]
Multilayer Perceptorn (MLP) 95.74% [18]
XXXVIII

Generalized Regression Neural Network (GRNN) 98.8% [18]
Symbiotic Adaptive Neuro-Evolution (SANE) 98.7% [50]
Information Gain and Adaptive Neuro-Fuzzy Inference System (IGANIFS)
98.24% [51]
Xcyct system using leave one out method 90 to 91% [52]
Adaptive Neuro-Fuzzy Inference System (ANFIS) 59.90% [53]
Fuzzy 96.71% [54]
Shunting Inhibitory Artificial Neural Networks (SIANN) 100% [55]
XXXIX





Chapter 4
Matlab





4.1 Introduction
MATLAB is a powerful computing system for handling the calculations involved in
scientific and engineering problems. The name MATLAB stands for MATrix
LABoratory, because the system was designed to make matrix computations
particularly easy[87]. Matlab program and script files always have filenames ending
with ".m". Script files contain a sequence of usual MATLAB commands, that are
executed (in order) once the script is called within MATLAB. In MATLAB almost
every data object is assumed to be an array. A good source of information related to
MATLAB, the creator company THE MATHWORKS INC and their other products
is their Web Page at www.mathworks.com [88]. There are two essential requirements
for successful MATLAB programming [87]-
a) We need to learn the exact rules for writing MATLAB statements.
b) We need to develop a logical plan of attack for solving particular problems.
The MATLAB program implements the MATLAB programming language, and
provides a very extensive library of predefined functions to make technical
programming task easier and more efficient.

XL

4.2 Advantages of MATLAB [89]
MATLAB has many advantages compared to conventional computer languages for
technical problem solving. Among them are-
1. Ease of use:
MATLAB is an interpreted language like Basic, it is very easy to use. Programs may
be easily written and modified with the built-in integrated development environment
and debugged with the MATLAB debugger. Because the language is so easy to use,
it is ideal for the rapid prototyping of new programs. Many program development
tools are provided to make the program easy to use. They include an integrated
editor/debugger, on-line documentation and manuals, a workspace browser, and
extensive demos.
2. Platform Independence:
In MATLAB programs written on any platform will run on all of the other platforms,
and data files written on any platform may be read transparently on any other
platform. As a result, programs written in MATLAB can migrate to new platforms
when the needs of user changes.
3. Predefined functions:
MATLAB has extensive library of predefined functions that provide tested
and pre-packaged solutions to many basic technical tasks. There are many special
purpose toolboxes available to solve complex problems in specific areas. Toolboxes
are libraries of MATLAB functions used to customize MATLAB for solving
particular class of problem. Toolboxes are a result of some of the worlds top
researchers in specialized fields. They are equivalent to pre-packaged of-the-
shelfsoftware for particular class of problem. These are the collection of special files
called M files that extend the functionality of the base program. Such files are called
m-files because they must have the filename extension .m. This extension is
required in order for these files to be interpreted by MATLAB. Each toolbox is
purchased separately. If an evaluation license is requested, the MathWorks sales
department requires detailed information about the project for which MATLAB is to
be evaluated. Overall the process of acquiring a license is expensive in terms of
XLI

money and time. If granted (which it often is), the evaluation license is valid for two
to four weeks. The various toolboxes are-
a. Control Systems
b. Signal Processing
c. Communications
d. System Identification
e. Robust Control
f. Simulink
g. Image processing
h. neural networks
i. fuzzy logic
j. Analysis
k. Optimization
l. Spline
m. Symbolic
n. User interface utility
4. Device- Independent plotting
MATLAB has many integral plotting and imaging commands. The plots and images
can be displayed on any graphical output device supported by the computer on which
MATLAB is running. This capability makes MATLAB an outstanding tool for
visualizing technical data.
5. Graphical User Interface:
MATLAB include tools that allow a programmer to interactively construct a
graphical user interface (GUI) for his/her own program. With this capability, the
programmer can design sophisticated data-analysis programs that can be operated by
relatively inexperienced users.
6. MATLAB Compiler:
XLII

MATLAB code interpreted rather than compiled. A separate compiler is available.
This compiler can compile a MATLAB program into a true executable code that runs
faster than the interpreted code. Its a great way to convert a prototype MATLAB
program into an executable and suitable for sale and distribution to users.
MATLAB is an efficient tool to develop applications based on neural network.
Therefore it is used in proposed result for breast cancer diagnosis and prognosis
using polynomial neural network.
4.3 Limitations of MATLAB [89]
Following are some limitations of using MATLAB-
1. It is an interpreted language and therefore can execute more slowly than
compiled languages.
This problem can be mitigated by properly structuring the MATLAB program and by
the use of MATLAB compiler to compile the final MATLAB program before
distribution and general use.
2. A full copy of MATLAB is 5-10 times more expensive than a conventional
than C or FORTRAN compiler. There is also an inexpensive student edition for
MATLAB which is a great tool for students. The student edition of MATLAB is
essentially identical to the full edition.

4.4 Neural Network Toolbox [90]
Neural network toolbox is equivalent to pre-packaged of-the-shelf software for
neural network class of problem. The Neural Network Toolbox software uses the
network object to store all of the information that defines a neural network. There are
four different levels at which the Neural Network Toolbox software can be used-

1. The first level is represented by the GUIs that are described in Getting
Started with Neural Network Toolbox. These provide a quick way to access the
power of the toolbox for many problems of function fitting, pattern recognition,
clustering and time series analysis.
XLIII

2. The second level of toolbox use is through basic command-line operations.
The command-line functions use simple argument lists with intelligent default
settings for function parameters. (You can override all of the default settings, for
increased functionality.) This topic, and the ones that follow, concentrate on
command-line operations. The GUIs described in Getting Started can automatically
generate MATLAB code files with the command-line implementation of the GUI
operations. This provides a nice introduction to the use of the command-line
functionality.
3. A third level of toolbox use is customization of the toolbox. This advanced
capability allows you to create your own custom neural networks, while still having
access to the full functionality of the toolbox.
4. The fourth level of toolbox usage is the ability to modify any of the M-files
contained in the toolbox. Every computational component is written in MATLAB
code and is fully accessible.

4.5 Neural Network Design using Neural Network Toolbox[90]
The multilayer feed forward neural network is the workhorse of the Neural Network
Toolbox software. It can be used for both function fitting and pattern recognition
problems. With the addition of a tapped delay line, it can also be used for prediction
problems. The work flow for the neural network design process has seven primary
steps:
Collecting the data
Creating the network
Configuring the network
Initializing the weights and biases
Training the network
Validating the network
Using the network
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The first step might happen outside the framework of Neural Network Toolbox
software, but this step is critical to the success of the design process.
4.5.1 Collecting the data
We need to collect and prepare sample data that cover the range of inputs for which
the network will be used. After the data have been collected, there are two steps that
need to be performed before the data are used to train the network: the data need to
be pre-processed, and they need to be divided into subsets.

4.5.1.1 Pre-processing and post-processing the data
The most common pre-processing routines are provided automatically when we
create a network, and they become part of the network object, so that whenever the
network is used, the data coming into the network is pre-processed in the same way.
It is easiest to think of the neural network as having a pre-processing block that
appears between the input and the first layer of the network and a post-processing
block that appears between the last layer of the network and the output, as shown in
the fig. 4.1.


Input Output

Fig 4.1 Pre-processing and post-processing
Most of the network creation functions in the toolbox, including the multilayer
network creation functions, such as feedforwardnet, automatically assign processing
functions to network inputs and outputs. These functions transform the input and
target values you provide into values that are better suited for network training. Some
common pre-processing and post-processing functions are shown in table 4.1.
Table 4.1 Pre-processing and post-processing functions
Function Algotithm
Mapminmax Normalize inputs/targets to fall in the range [1, 1]
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processpca Extract principal components from the input vector
fixunknowns Process unknown inputs

Generally, the normalization step is applied to both the input vectors and the target
vectors in the data set. In this way, the network output always falls into a normalized
range. The network output can then be reverse transformed back into the units of the
original target data when the network is put to use in the field.
4.5.1.2 Representing Unknown or Dont Care Targets
Unknown or dont care targets can be represented with NaN values. All the
performance functions of the toolbox will ignore those targets for purposes of
calculating performance and derivatives of performance.
4.5.1.3 Dividing the Data
When training multilayer networks, the general practice is to first divide
the data into three subsets- trining, validation and testing. The function dividerand
is a default function that divide the data randomly into three subsets.
4.5.2 Creating and configuring the network
Basic components of a neural network are created and stored in the network object.
As an example, the dataset file contains a predefined set of input and target vectors.
We Load the dataset using the load command. Loading the dataset file creates two
variables. The input matrix and The target matrix. The function
feedforwardnetcreates a multilayer feedforward network.The resulting network can
then be configured with the configure command.
4.5.3 Initializing weights and biases
The configure command automatically initializes the weights, but we might want to
reinitialize them. You do this with the init command. This function takes a network
object as input and returns a network object with all weights and biases initialized.
4.5.4 Train the network
Once the network weights and biases are initialized, the network is ready for training.
The multilayer feed forward network can be trained for function approximation
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(nonlinear regression) or pattern recognition. The training process requires a set of
examples of proper network behaviour- network inputs pand target outputs t. The
process of training a neural network involves tuning the values of the weights and
biases of the network to optimize network performance, as defined by the network
performance function net.performfcn. The default performance function for feed
forward networks is mean square error (mse). For training multilayer feedforward
networks, any standard numerical optimization algorithm like gradient descent can be
used to optimize the performance function. Gradient descent algorithm updates the
network weights and biases in the direction in which the performance function
decreases most rapidly, the negative of the gradient. Training function traingd is
used for gradient descent algorithm. The gradient is calculated using a technique
called the back propagation algorithm, which involves performing computations
backward through the network. Properly trained multilayer networks tend to give
reasonable answers when presented with inputs that they have never seen. This
property is called generalization. The default generalization feature for the multilayer
feed forward network is early stopping. Data are automatically divided into training,
validation and test sets. The error on the validation set is monitored during training,
and the training is stopped when the validation increases over
net.trainParam.max_fail iterations.
4.5.5Validation of network
When the training is complete, we check the network performance and determine if
any changes need to be made to the training process, the network architecture or the
data sets. The first thing to do is to check the training record, tr, which was the
second argument returned from the training function. For example, tr.trainInd,
tr.valInd and tr.testInd contain the indices of the data points that were used in the
training, validation and test sets, respectively. If we want to retrain the network using
the same division of data, we can set net.divideFcn to 'divideInd',
net.divideParam.trainInd to tr.trainInd, net.divideParam-.valInd to tr.valInd,
net.divideParam.testInd to tr.testInd. We can use the training record to plot the
performance progress by using the plotperf command. The next step in validating
the network is to create a regression plot, which shows the relationship between the
outputs of the network and the targets. If the training were perfect, the network
outputs and the targets would be exactly equal, but the relationship is rarely perfect in
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practice. If the network is not sufficiently accurate, we can try initializing the
network and the training again. Each time your initialize a feed forward network, the
network parameters are different and might produce different solutions.
4.5.6 Use the network
After the network is trained and validated, the network object can be used to
calculate the network response to any input.
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Chapter 5
Simulation and Results






5.1 Introduction
For simulation three different datasets named Wisconsin Breast Cancer original
(WBC) dataset, Wisconsin diagnosis Breast Cancer (WBCD) dataset and Wisconsin
Prognosis Breast Cancer (WPBC) dataset are downloaded from the UCI Machine
Learning Repository website [91] and saved as a text file. A brief description of
Wisconsin dataset is given in table 5.1. Detaied decription of dataset is provided in
next section.
Table 5.1 A brief description of Breast Cancer datasets
Dataset name No of attributes No of instances No. of classes
Wisconsin Breast Cancer (WBC) 11 699 2
Wisconsin Diagnosis Breast Cancer (WDBC) 32 569 2
Wisconsin Prognosis Breast Cancer (WPBC) 34 198 2

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After downloading we have got three separate files; one for each dataset. These files
are then imported into Excel spreadsheets and the values are saved with the
corresponding attributes as column headers. The ID of the patient cases does not
contribute to the classifier performance. Hence it is removed and the outcome
attribute defines the target or dependant variable. We preprocessed the data using
principal component analysis described in chapter 3[34]. After pre processing the
WBC data is applied to PNN described in chapter 3[29-31] which classifies the data
into two sets. The overall classification involves training and testing as shown in fig
5.1. Implementation is done with help of MATLAB 7.0 using neural network toolbox
described in chapter 4 [40-41].




Fig. 5.1 Flow chart of ANN process

5.2 Description of dataset
Detailed description of the three datasets used in the proposed research is as follows
[83]-
Wisconsin Breast Cancer (WBC) Dataset :
This database has 699 instances and 10 attributes including the class attribute.
Attribute 1 through 9 are used to represent instances. Each instance has one of two
possible classes: benign or malignant. According to the class distribution 458 or
65.5% instances are Benign and 241 or 34.5% instances are malignant. Table 5.2
provides the attribute information.
Table 5.2 Attribute information of WBC dataset
S.no Attribute Domain
1 Clump thickness 1-10
2 Uniformity of cell size 1-10
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3 Uniformity of cell shape 1-10
4 Marginal adhesion 1-10
5 Single epithelial cell size 1-10
6 Bare nuclei 1-10
7 Bland chromatin 1-10
8 Normal nucleoli 1-10
9 Mitosis 1-10
Class 2 for benign, 4 for malignant












In the Clump thickness benign cells tend to be grouped in monolayer, while
cancerous cells are often grouped in multilayer. While in the Uniformity of cell
size/shape the cancer cells tend to vary in size and shape. That is why these
parameters are valuable in determining whether the cells are cancerous or not. In the
case of Marginal adhesion the normal cells tend to stick together, where cancer cells
tend to lose this ability. So loss of adhesion is a sign of malignancy. In the Single
epithelial cell size the size is related to the uniformity mentioned above. Epithelial
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cells that are significantly enlarged may be a malignant cell. The Bare nuclei is a
term used for nuclei that is not surrounded by cytoplasm (the rest of the cell). Those
are typically seen in benign tumors. The Bland Chromatin describes a uniform
texture of the nucleus seen in benign cells. In cancer cells the chromatin tends to be
coarser. The Normal nucleoli are small structures seen in the nucleus. In normal cells
the nucleolus is usually very small if visible. In cancer cells the nucleoli become
more prominent, and sometimes there are more of them. Finally, Mitoses is nuclear
division plus cytokines and produce two identical daughter cells during prophase. It
is the process in which the cell divides and replicates. Pathologists can determine the
grade of cancer by counting the number of mitoses.
Wisconsin Diagnosis Breast Cancer (WDBC) Dataset :
This database has 569 instances and 32 attributes including the class attribute.
Attribute 2 is class attribute. Other attributes are used to represent instances. Each
instance has one of two possible classes: benign or malignant. According to the class
distribution 357 instances are Benign and 212 instances are Malignant. Table 5.3
provides the attribute information of WDBC dataset.
Table 5.3 Attribute information of WDBC dataset
Attribute name Significance Attribute ID
ID Unique ID of patient 1
Outcome Diagnosis ( B- Benign / M- Malingnant) 2
Radius 1,2,3 Mean of distances from centre to points on the perimeter 3, 13, 23
Texture 1, 2,3 Standard deviation of gray scale values 4, 14, 24
Perimeter 1,2,3 Perimeter of the cell nucleolus 5, 15,25
Area 1,2,3 Area of the cell nucleolus 6, 16, 26
Smoothness 1,2,3 Local variation in radius lengths 7, 17,27
Compactness 1,2,3 Perimeter2 / area - 1.0 8, 18, 28
Concavity 1,2,3 Severity of concave portions of the contour 9, 19,29
Concave points 1,2,3 Number of concave portions of the contour 10, 20, 30
Symmetry 1,2,3 Symmetry of the cell nuclei 11,21, 31
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12, 22, 32
Fractal dimension 1,2,3 Coastline approximation 1 12, 22, 32

The details of the attributes found in WDBC dataset are : ID number, Diagnosis
(M = malignant, B = benign) and ten real-valued features are computed for each cell
nucleus: Radius, Texture, Perimeter, Area, Smoothness, Compactness, Concavity,
Concave points, Symmetry and Fractal dimension [92]. These features are computed
from a digitized image of a fine needle aspirate (FNA) of a breast mass. Where the
radius of an individual nucleus is measured by averaging the length of the radial line
segments defined by the centroid of the snake and the individual snake points. The
total distance between consecutive snake points constitutes the nuclear perimeter.The
area is measured by counting the number of pixels on the interior of the snake and
adding one-half of the pixels on the perimeter. The perimeter and area are combined
to give a measure of the compactness of the cell nuclei using the formula
perimeter2/area. Smoothness is quantified by measuring the difference between the
length of a radial line and the mean length of the lines surrounding it. This is similar
to the curvature energy computation in the snakes. Concavity is captured by
measuring the size of the indentation (concavities) in the boundary of the cell
nucleus. Chords between non-adjacent snake points are drawn and measure the
extent to which the actual boundary of the nucleus lies on the inside of each chord.
Concave Points feature is similar to concavity but counted only the number of
boundary point lying on the concave regions of the boundary. In order to measure
symmetry, the major axis, or longest chord through the center, is found. Then the
length difference between lines perpendicular to the major axis to the nuclear
boundary in both directions is measured. The fractal dimension of a nuclear boundary
is approximated using the coastline approximation described by Mandelbrot. The
perimeter of the nucleus is measured using increasingly larger rulers. As the ruler
size increases, decreasing the precision of the measurement, the observed perimeter
decreases. Plotting log of observed perimeter against log of ruler size and measuring
the downward slope gives (the negative of) an approximation to the fractal
dimension. With all the shape features, a higher value corresponds to a less regular
contour and thus to a higher probability of malignancy. The texture of the cell
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nucleus is measured by finding the variance of the gray scale intensities in the
component pixels.

Wisconsin Prognosis Breast Cancer (WPBC) Dataset:
This database has 198 instances and 35 attributes including the class attribute.
Attribute 2 is class attribute. other attributes are used to represent instances. Each
instance has one of two possible classes: R (recur) or N (non-recur). According to the
class distribution 151 instances belongs to non-recur class and 47 instances belong to
recur class. Table 5.4 provides the attribute information of WPBC dataset.
Table 5.4 Attribute information of WPBC dataset
Attribute name Significance Attribute ID

ID Unique ID of patient 1

Outcome Nature of the case ( R- recurrent/ N- Non- recurrent) 2

Time TTR (Time to recur)/ DFS (Disease free survival) 3

Radius 1,2,3 Mean of distances from centre to points on the perimeter 4, 14, 24

Texture 1, 2,3 Standard deviation of gray scale values 5, 15, 25

Perimeter 1,2,3 Perimeter of the cell nucleolus 6, 16, 26

Area 1,2,3 Area of the cell nucleolus 7, 17,27

Smoothness 1,2,3 Local variation in radius lengths 8, 18, 28
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Compactness 1,2,3 Perimeter2 / area - 1.0 9, 19,29

Concavity 1,2,3 Severity of concave portions of the contour 10, 20, 30

Concave points 1,2,3 Number of concave portions of the contour 11,21, 31

Symmetry 1,2,3 Symmetry of the cell nuclei 12, 22, 32

Fractal dimension 1,2,3 Coastline approximation 1 13, 23, 33

Tumour size Size of the tumour 34

Lumph node status Status of the lymph node 35


The details of the attributes found in WPBC dataset are: ID number, Outcome (R
= recur, N = non-recur), Time (R => recurrence time, N => disease-free time), from 3
to 33 ten real-valued features are computed for each cell nucleus: Radius, Texture,
Perimeter, Area, Smoothness, Compactness, Concavity, Concave points, Symmetry
and Fractal dimension. These features computed for each cell nucleus from a
digitized image of a fine needle aspirate (FNA) of a breast mass. The mean, standard
error, and/or largest (worst case-mean of the three largest values) of these features
were computed for each image, resulting in 30 features. The thirty four is Tumor size
and the thirty five is the Lymph node status. Its known from the previous lines that
the diagnosis and prognosis has the same features yet the prognosis has two
additional features as follows: Tumor Size is the diameter of the excised tumor in
centimeters. Tumor Size is divided into four classes: T-1 is from 0 - 2 centimeters. T-
2 is from 2 - 5 cm. T-3 is greater than 5cm. T-4 is a tumor of any size that has broken
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through (ulcerated) the skin, or is attached to the chest wall. Lymph node status is the
number of positive auxiliary lymph nodes observed at time of surgery. The lymph
nodes in the armpit (the auxillary lymph nodes) are the first place breast cancer is
likely to spread. Lymph node status is highly related to prognosis. Lymph node-
negative means the lymph nodes do not contain cancer. And Lymph node-positive
means the lymph nodes contain cancer.


According to the attributes in WDBC and WPBC datasets, these attributes have
following 3 values with 3 columns in the data set.

The mean calculated as :
Mean=_(i=1)^nx_i
5.1
The standard error calculated as:
S_e= s/n 5.2
Where refers to Standard error parameter, s refers to Standard deviation and n
refers to sample size.
Worst mean or largest mean.

5.3 Results and Discussion
5.3.1 Diagnosis Results
Diagnosis results divides the whole data into two sets- malignant (cancerous) and
benign (non-cancerous). WBC and WDB databases are used for taining and testing
the neural network. We have got different results which are shown below-
Result using WBC dataset:
PCA data preprocessing is used in this dataset to deal with missing data. PNN
architecture has 10 input nodes 2 nodes in the hidden layer 1, 2 nodes in the hidden
layer 2 and 1 output node. The MSE performance for normalized WBC data and
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WBC data after applying PCA is compared in Table 5.5. We observed that MSE is
substantially reduced for PCA processed data even when 400 instances are used for
training. The testing error is compared in table 5.6.
Table 5.5 Training performance for WBC dataset
Number of Training Patterns MSE for Normalization MSE for PCA
100 0.0050 0.0011
200 0.0025 6.6408e-04
300 0.0017 4.1121e-04
400 0.0013 3.0468e-04

Table 5.6 Testing performance for WBC dataset
Number of Testing Patterns MSE for Normalization MSE for PCA
100 0.0076 3.3319e-04
200 9.7617e-05 4.1995e-04
300 3.6278e-04 1.5611e-04
400 1.4996e-04 3.0486e-04
500 1.6873e-04 9.5419e-05
600 1.0297e-04 3.8735e-05
699 1.0078e-05 2.2117e-05

Results using WDBC dataset:
WDBC data do not have missing values so there is no need to preprocess the data.
The PNN architecture has 31 inputs nodes, 2 nodes in the hidden layer 1, 2 nodes in
the hidden layer 2 and 1 output node. The MSE performance for normalized WDBC
data is given in Table 5.7. The testing error is compared in Table 5.8.
Table 5.7 Training performance for WDBC dataset
Number of Training Patterns MSE for Normalization
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100 0.0050
200 0.0026
300 0.0017
400 0.0013
Table 5.8 Testing performance for WDBC dataset
Number of Testing Patterns MSE for Normalization
100 0.0340
200 0.0016
300 7.6359e-04
400 5.7702e-04
500 1.9828e-04
569 8.8298e-05

5.3.2 Prognosis Results
Prognosis results divides the whole data into two sets- recurred and non-recurred
.WPBC dataset is used for prognosis prediction. PCA data preprocessing is used in
this dataset to deal with missing data. The MSE for normalized and PCA
preprocessed WPBC data are compared in Table 5.9 and 5.10. The corresponding
graphs are given in fig. 5.3 (a) and 5.3 (b) We observed that MSE is substantially
reduced for PCA processed data.
Table 5.9 Training performance for WPBC dataset
Number of Training Patterns MSE for Normalization MSE for PCA
100 0.0050 3.5910e-08
198 0.0025 2.1737e-08

Table 5.10 Testing performance for WPBC dataset
Number of Testing Patterns MSE for Normalization MSE for PCA
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100 0.0022 6.9075e-08
198 0.0019 4.6077e-11


Fig 5.2 Comparision of the Convergence performance for WPBC dataset
(50 iterations)

Fig 5.3 (a) Testing error for normalization and PCA data for WPBC dataset over 100
data

Fig 5. 3(b) Testing error for normalization and PCA for WPBC dataset over 198 data.


Chapter 3
Artificial Neural Network
and
Principal Component Analysis







3.1 Overview of Artificial Neural Network
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Neural networks are an emergent technology with an increasing number of real-
world applications [56]. Neural networks are a form of artificial intelligence that
have found application in a wide range of problems [57]-[59] and have given, in
many cases, superior results to standard statistical models [60].Artificial Neural
Networks perform various tasks such pattern matching and classification,
optimization function and data clustering. These tasks are very difficult for
traditional computers, which are faster in algorithmic computational tasks and precise
arithmetic operations [61].Originally inspired by biological models of mammalian
brains, ANN have emerged as a powerful technique for data analysis [62].Neural
Network is able to solve highly complex problems due to the non linear processing
capabilities of its neurons. In addition, the inherent modularity of the neural network
structure makes it adaptable to a wide range of applications [63].Following are the
main characteristics of ANN [64]-
The NNs exibit mapping capabilities, that is, they can map input patterns to
their associated output patterns.
The NNs learn by examples. Thus NN architectures can be trained with
known examples of a problem before they are tested for their inference capability
of unknown instances of the problem. They can, therefore, identify new objects
previously untrained.
The NNs posses the capability to generalize. Thus they can predict new
outcomes from the past trends.
The NNs are robust systems and are fault tolerant. They can, therefore, recall
full patterns from incomplete, partial or noisy patterns.
The NNs can process information in parallel, at high speed, and in distributed
manner.
3.2 Basic concepts of ANN
The terminology of ANNs has developed from a biological model of brain [64].
There are three aspects involved in the construction of a Neural Networks [63]-
Structure : The architecture and topology of Neural Networks.
Encoding : The method of changing weights ( Training ).
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Recall : The method and capacity to retrieve information.

A NN consists of a set of connected cells: The neurons. The neuron or unit processes
inputs of NN to create an output[64]. The network consists of a number of input
units, one or more output units, together with internal units. The outputs of the
network correspond to the variables we require to predict: the inputs to the variables
on which we base the prediction. Adjustable weights are associated with the
interconnections between the units [65]. Fig 3.1[64] shows the structure of a single
neuron. Artificial neuron performs the following- Receives signal from other
neurons, multiplies each signal by the corresponding connection strength, that is
weight, sums up the weighted signals and pass them through an activation function
and feeds output to other neurons[66].

Fig 3.1 A single neuron

3.3 Feed Forward Neural Network with Back propagation

Various Neural Networks models exist and among Feed Forward Neural Network.
Feed forward neural network model, besides being popular and simple, is easy to
implement and appropriate for classification applications [63]. The feed forward
backpropagation network does not have feedback connections, but the errors are back
propagated during training. Fig.3. 2 shows the feed forward NN for breast cancer
diagnosis. The Network consists an input layer, one or more hidden layers and an
output layer. It takes the predictive attributes as input and produces the output that is
the class attribute {benign or Malingnant}.

Fig 3.2: Feed Forward NN model for Breast Cancer diagnosis
The neurons present in the hidden and output layer have biases, which are the
connections from the units whose activation is always 1. The bias terms also acts as
weights. Backpropagation learning consists of two passes through the different layers
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of the network: a forward pass and backward pass. In forward pass, input vector is
applied to the sensory nodes of the network and its effect propagates through the
network layer by layer. Finally, a set of outputs is produced as the actual response of
the network. During the forward pass the synaptic weights of the network are all
fixed. During the backward pass, the synaptic weights are all adjusted in accordance
with an error correction rule. The actual response of the network is subtracted from a
desired (target) response to produce an error signal. This error signal is then
backpropogated through the network, against the direction of synaptic connections
[67]. Propagation of errors is done beginning at the output layer, through the hidden
layer, and so on, to the input layer, in backward direction. The weights are therefore
updated at each layer, beginning at the output layer. The changes in weights are
proportional to the derivative of the errors with respect to incoming weights [68]. For
a given set of training input-output pair, A BP learning algorithm provides a
procedure for changing the weights in a BPNN to classify the given input patterns
correctly. The error is the difference between the actual (calculated) and desired
(target) output [69].The input and output of the neuron, i, (except for the input layer
according to the BP algorithm [70] is formulated in 3.1 and 3.2.
Input X_i= W_(ij ) O_j+b_i 3.1
Output O_i=f(X_i) 3.2
where Wij is the weight of the connection from neuron i to node j, bi is the numerical
value called the bias and f is the activation function. The sum in (1) is over all
neurons, j, in the previous layer. The output function is a nonlinear function, which
allows a network to solve problems that a linear network cannot [71].The training
algorithm and various parameters used for training BPNN is as follows [61]-

A. Various Parameters:
Input training vector x = (x_1,,x_i,x_n )
Output target vector t =(t_(1,.) t_(k..,) t_m)
_k= error at the output unit y_k
_j=error at the hidden unit z_j
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= learning rate
V_oj= bias on hidden unit j
z_j=hidden unit at j
w_oj=bias on output unit k
y_k=output unit k.

B. Training Algorithm:
Step 1: Initialize weight to small random values.
Step 2: While stopping condition is false, do steps 3-10.
Step 3: For each training pair do Steps 4-9.
Step 4: Each input unit receives the input signal x_i and transmit to all units in the
hidden layer.
Step 5: Each hidden unit (z_(j,)j=1p) sums its weighted input signals
z_inj=v_oj+_(i=1)^nx_i v_ij , applying activation functionZ_j=f(z_inj) and
sends this signal to all units in the output layer.
Step 6: Each output unit (y_(k,) k=1 m) sums its weighted input signals
y_ink=w_ok+_(j=1)^pz_j w_jk, and applies its activation function to calculate
the output signal Y_k=f(y_ink).
Step 7: Each output unit (y_(k,) k=1 m) receives a target pattern corresponding to
an input pattern. Error information term is calculated as _k=(t_k-y_k )f(y_ink).
Step 8: Each hidden unit (z_j, j=1 n) sums its delta inputs from units in the layer
above _inj= _(k=1)^m_j w_jk .
The error information term is calculated as _j =_inj f(z_inj).
Step 9: Each output unit (y_k, k=1 m) updates its bias and weights (j = 0 p) the
weight correction term is given by w_jk=_k z_k and the bias correction
term is given byW_ok=_k. Therefore,
W_jk (new) = W_jk(old) +W_jk , W_ok(new) =W_ok+W_ok. Each
hidden unit (z_j,j=1,p) updates its bias and weights (i=0n). The weight
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correction term V_ij=_j x_i.The bias correction term V_oj=_j.
Therefore V_jk(new) = V_jk(old) +V_ij , V_oj(new) =V_oj+V_oj
Step 10: Test the stopping condition.
Steps 1 to 3 initializes the weights, steps 4-6 are called feed forward steps,
steps 7-8 are called BP steps, step 9 updates weight and biases, and finally step 10 is
stopping condition which may be the minimization of the errors, number of epochs
etc. Back propagation algorithm can be improved by considering momentum and
variable learning rate. Momentum allows a network to respond not only to the local
gradient, but also to the recent trends in error surface. Acting like a low pass filter,
momentum allows the network to ignore small features in the error surface. Without
momentum, a network may get struck in a shallow local minimum. In
backpropagation with momentum, the weight change is in a direction that is a
combination of the current and previous gradients. This is a modification of gradient
descent whose advantages arise chiefly when some training data are very different
from the majority of the data. Convergence is sometimes faster if a momentum term
is added to the weight update formulas. The performance of algorithm is very
sensitive to the proper setting of the learning rate. If the learning rate is set too high,
the algorithm may oscillate and become unstable. If the learning rate too small, the
algorithm will take too long to converge. It is not practical to determine the optimal
setting for the learning rate before training and in fact the optimal learning rate
changes during the training process, as the algorithm moves across the performance
surface. Performance of the backpropogation can be improved by allowing the
learning rate to change during the training process. An adaptive learning rate will
attempt to keep the learning step size as large as possible while keeping the learning
process stable. The learning rate is made responsive to the complexity of the local
error surface [63].

3.4 Higher order or polynomial neural network

Higher order or Polynomial neural networks ( PNNs) were first introduced by [72]
and further analyzed by [73] who referred to them as 'tensor networks' and regarded
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them as a special case of his functional-link models. PNNs use joint activations
between inputs, thus removing the task of establishing relationships between them
during training. PNN is faster to train and execute when compared to other neural
networks [73]. An error back propagation based learning using a norm-squared error
function is described as follows [74].The aggregation function is considered as a
product of linear functions in different dimensions of space. A bipolar sigmoidal
activation function is used at each node. This kind of neuron itself looks complex in
the first instance but when used to solve a complicated problem needs less number of
parameters as compared to the existing conventional models. PNN is a type of feed
forward NN. Fig. 3.4 shows a feed forward NN for breast cancer diagnosis. Fig.
3.3[75] shows a schematic diagram of a generalized single multiplicative or
polynomial neuron. The operator is a multiplicative operation as in (1) and (2) with
shows an architecture of PNN.

Figure 3.3 Node Structure of PNN

Fig. 3.4 Polynomial Neural Network
Aggregation u before applying activation function is given by:
u= 3.3
3.4
The output at the node y is given by
3.5
The mean square error is given by
3.6
Where, is the number of input patterns.
The weight update equation for the split complex back propagation algorithm is
given by
3.7
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Where, is the learning rate and is the desired signal.
The bias is updated as-
3.8
3.9
3.10
The weights are updated after the entire training sequence has been presented to the
network once. This is called learning by epoch. The algorithm is extended to train
PNN.
3.5 Advantages of neural network
Neural network, with their remarkable ability to derive meaning from complicated or
imprecise data, could be used to extract patterns and detect trends that are too
complex to be noticed by either humans or other computer technique. Advantages of
neural network include their high tolerance to noises data as well as their ability to
classify patterns on which they have not been trained. Other advantages of working
with ANN include [61]:
Adaptive Learning: An ANN is endowed with the ability to learn how to do
tasks based on the data given for training or initial experience.
Self-Organization: An ANN can create its own organization or representation
of the information it receives during learning time.
Real time operation: ANN computation may be carried out in parallel. Special
hardware devices are being designed and manufactured to take advantage of this
capability of ANNs.
Fault tolerance: Partial destruction of a neural network leads to the
corresponding degradation of performance. However, some network capabilities may
be retrained even after major network damage.
3.6 Medical applications
Baxt [76] demonstrated the predictive reliability of an artificial neural networks
model in medical diagnosis. In this case, we utilise the ability of neural networks to
recognise complex and highly non-linear relationships, such as are likely to
LXVI

characterise medical circumstances. Owing to their wide range of applicability and
their ability to learn complex and non linear relationships including noisy or less
precise information Neural Networks are very well suited to solve problems in
biomedical engineering. By their nature, Neural Networks are capable of high-speed
parallel signal processing in real time. They have an advantage over conventional
technologies because they can solve problems that are too complex-problems that do
not have an algorithmic solution or for which an algorithmic solution is too complex.
Neural Networks are trained by examples instead of rules and are automated. This is
one of the major advantages of neural networks over traditional expert systems [77]-
[78]. When NN is used in medical diagnosis they are not affected by factors such as
human fatigue, emotional states and habituation. They are capable of rapid
identification, analyses of conditions, and diagnosis in real time. With the spread of
Neural Networks in almost all fields of science and engineering, it has found
extensive application in biomedical engineering field also. The applications of neural
networks in biomedical computing are numerous. Various applications of ANN
techniques in medical field are [79]-
Cardiology
Oncology
Neurology
Radiology
Pathology
Genetics
Clinical chemistry
Biochemistry etc.
3.7 Overview of data Preprocessing
Pre-processing is the process of transforming data into simpler, more effective, and
in accordance with user needs [80]. If a training data set contains irrelevant attributes
classification analysis may produce less accurate results. The problem of missing
data poses difficulty in the analysis and decision-making processes and the missing
data is replaced before applying it to NN model. Without this pre-processing, training
LXVII

the neural networks would have been very slow. Data preprocessing is required to
improve the predictive accuracy. It can be used to scale the data in the same range of
values for each input feature in order to minimize bias within the neural network for
one feature to another. Data pre-processing speeds up training time by starting the
training process for each feature within the same scale. It is especially useful for
modeling application where the inputs are generally on widely different scales.
Therefore Neural networks learn faster and give better performance if the input
variables are pre-processed before being used to train the network. Preprocessing for
neural network involves feature selection and feature extraction.
3.7.1 Feature selection
Feature selection is the process of finding a subset of the original variables, with the
aim to reduce and eliminate the noise dimension. The main idea of feature selection
is to choose a subset of input variables by eliminating features with little or no
predictive information. Feature selection can significantly improve the
comprehensibility of the resulting classifier models and often build a model that
generalizes better to unseen points [81].
3.7.2 Feature extraction
Feature extraction is a technique to transform high-dimensional data into lower
dimensions. When the input data to an algorithm is too large to be processed and it is
suspected to be notoriously redundant (much data, but not much information) then
the input data will be transformed into a reduced representation set of features (also
named features vector). If the features extracted are carefully chosen it is expected
that the features set will extract the relevant information from the input data in order
to perform the desired task using this reduced representation instead of the full size
input. By reducing, the dimensionality of the input set correlated information is
eliminated at the cost of a loss of accuracy. Dimensionality reduction can be
achieved by either eliminating data closely related with other data in the set, or
combining data to make a smaller set of features. The identification of a reduced set
of features that are predictive of outcomes can be very useful from a knowledge
discovery perspective. For many learning algorithms, the training and/or
classification time increases directly with the number of features, which is efficiently
reduced by dimension reduction methods Noisy or irrelevant features can have the
LXVIII

same influence on classification as predictive features so they will impact negatively
on accuracy, by using dimension reduction methods noisy or irrelevant features can
also be removed [82]. Two popular methods for feature extraction are linear
discriminant analysis (LDA) and principal Component analysis (PCA). Linear
Discriminant Analysis (LDA) is a supervised learning algorithm and Principal
Component Analysis (PCA) is unsupervised learning, algorithms for data
preprocessing[80]. Linear Discriminant Analysis (LDA) is a widely used technique
for pattern classification. It seeks the linear projection of the data to a low
dimensional subspace where the data features can be modeled with maximal
discriminative power. The main computation involved in LDA is the dot product
between LDA base vector and the data which is costly element-wise floating point
multiplications [86].
3.8 Principal Component Analysis
PCA uses an orthogonal transformation to convert a set of observations of possibly
correlated variables into a set of values of linearly uncorrelated variables called
principal components. The number of principal components is less than or equal to
the number of original variables [83]. PCA finds linear transformations of data that
retain the maximal amount of variance [84]. The PCA can be used as a features
reduction transformation method in which combines a set of correlated features [83].
Fig. 3.5 shows data preprocessing using PCA. PCA reduces the dimensions of the
data while retaining as much as possible of the variation present in the original
dataset. The best low-dimensional space can be determined by the best eigenvectors
of the covariance matrix of M. The eigenvectors corresponding to the highest eigen
values are also called principal components.

Fig 3.5 Data Pre-processing using PCA

3.8.1 Dimensionality reduction
The goal of PCA is to reduce the dimensionality of the data while retaining as much
as possible of the variation present in the original dataset.

LXIX


[(b_1@b_2@@b_K )]
PCA allows us to compute a linear transformation that maps data from a high
dimensional space to a lower dimensional space.
y=Tx where T=[(((T_11& T_12 T_1N @T_21&T_22
T_2N ) @ ) @ (&) @T_(K1 ) T_K2 T_KN )]

3.8.2 Lower dimensionality basis
Approximate the vectors by finding a basis in an appropriate lower dimensional
Space.
(1) Higher-dimensional space representation:
x = 10v1 + 11v2 + + aNvN
v1, v2... vN is a basis of the N-dimensional space
(2) Lower-dimensional space representation:
x = 12u1 + b2u2 + bKuK
u1, u2 uK is a basis of the K-dimensional space.

3.8.3 Selection of principal components
To choose K, use the following criterion.
(_(i=1)^K _i )/(_(i=1)^N _i ) > Threshold (e.g., 0.9 or 0.95)
3.8.4 Selecting best lower dimensional space
The best low-dimensional space can be determined by the "best" eigenvectors of the
covariance matrix of x (i.e., the eigenvectors corresponding to the "largest"
eigenvalues also called "principal components").

3.8.5 Linear transformation implied
The linear transformation RN ->RK that performs the dimensionality reduction is:
LXX

[(b_1@b_2@@b_K )]= [(u_1^T@u_2^T@@u_K^T )](x-x) =
UT( x-x)
3.9 Advantages of Principal Component Analysis
Principal components capture most of the variability in data by using fewer
dimension that where the data exists. Hence the principal components lie in the same
space as data.
The principal eigenvectors are orthogonal and represent the directions where
the signals have maximum variation. This property will speed up the convergence of
model training and improve the system performance [85].
The feature space having reduced features that truly contributes to
classification that cuts pre-processing costs [85].
LXXI





Chapter 6
Conclusion and
Future Work

6.1 Conclusion
The last decade has witnessed major advancements in the method of diagnosis and
prognosis of breast cancer. Soft Computing techniques can be used for breast cancer
diagnosis and prognosis. The use of ANN increases the accuracy of most methods
and decreases the need of human expert. The neural network based clinical support
system proposed in this research provides the medical experts with a second opinion
thus removing the need for biopsy, excitation and reduce the unnecessary
expenditure. We believe that the results presented here are interesting and will leads
to further research on how the technique can be more efficiently used for diagnosis of
other diseases. The neural network works depending on the data being train to the
network. If more data being trained in the network, it will make the network more
intelligent. From the diagnosis results, determination can be made weather the
women having cancerous tumor or not. Prognosis results will help in taking treatment
decision for women having cancerous tumor.
6.2 Future work
For future work Neural Network Classification with on Fuzzy Inference System can
be applied to the task of diagnosis and prognosis. So that we can give results with a
percentage of confidence that the women is having cancerous breast tumor or non-
cancerous breast tumor. Prognosis results can also be given with a confidence
measure that the cancer is re-occurred or not. More accurate learning methods may
be evaluated. It is believed that the fuzzy system along with polynomial neural
network can be very helpful to the physicians for their final decision for diagnosis
LXXII

and prognosis on their patients. The physicians can perform very accurate with a
confidence by using such an efficient tool. It can assist in diagnosis and prognosis of
breast cancer.
We can also use genetic algorithm to generate the optimum weights for our network.
There are three methods where GA can be used in NN. The first is threshold hybrid
where the fitness function uses standard deviation that is less than 0.0001. Secondly
is basic hybrid of GA and BP when iteration is less than 2000 or using basic error
rate is less than 0.01. And the third is adaptation hybrid of GA and BP where error
square root is decreases by 30% until it reaches 0.01. All the three methods have
helped NN from trapped in the local minimum. In addition, GA is also a stochastic
method, it can works well with BPNN as the generated weight might be changed
several times during the learning process.
LXXIII







List of Publications

International Journal
1. Shweta Saxena, Kavita Burse,A Survey on Neural Network Techniques for
Classification of Breast Cancer Data, Int. J. of Eng. and adv. Tech. (IJEAT), ISSN:
2249 8958 , vol. 2, no. 1, pp. 234-237, October 30, 2012.
International Conferences
1. Shweta Saxena, Kavita Burse,Classification of Wisconsin Breast Cancer
(Original) Database and Wisconsin Breast Cancer (Diagnostic) Database using
Polynomial Neural Network, in proc. of Int. Conf. of Elect. and Electron. Eng.,
December 9, 2012, Bhopal, India.
2. Shweta Saxena, Vishnu Pratap Sing Kirar, Kavita Burse, A Polynomial
Neural Network Model for Prognostic Breast Cancer Prediction, in proc. of Int.
Conf. on Advances in Comput. Sci. and Eng., Jan 2013, Hydrabad, India.
LXXIV






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