CHAPTER 1

INTRODUCTION

1.1 Introduction

Medical X-rays are images are generally used to diagnose some sensitive human body parts such
as bones, chest, teeth, skull, etc. Medical experts have used this technique for several decades to
explore and visualize fractures or abnormalities in body organs (Er et al., 2010). This is due to
the fact that X-rays are very effective diagnostic tools in revealing the pathological alterations, in
addition to its non-invasive characteristics and economic considerations. Chest diseases can be
shown in CXR images in the form of cavitations, consolidations, infiltrates, blunted costophrenic
angles, and small broadly distributed nodules. The interpretation of a chest X-ray can diagnose
many conditions and diseases such as pleurisy, effusion, pneumonia, bronchitis, infiltration,
nodule, atelectasis, pericarditis, cardiomegaly, pneumothorax, fractures and many others (Er et
al., 2010).

Classifying the chest x-ray abnormalities is considered a tough task for radiologists. Hence, over
the past decades, computer aided diagnosis (CAD) systems have been developed to extract useful
information from X-rays to help doctors in having a quantitative insight about an X-ray.
However, those CAD systems haven’t achieved a significance level to make decisions on the
type of conditions of diseases in an X-ray (El-Solh et al., 1999). Thus, the role of them was left
as visualization functionality that helps doctors in making decisions.

Recently, accurate images classification has been achieved by deep learning based systems.
Those deep networks showed superhuman accuracies in performing such tasks. This success
motivated the researchers to apply those networks on medical images for diseases classification
tasks and the results showed that deep networks can efficiently extract useful features that
distinguish different images classes (Ashizawa et al., 2005). Convolutional neural networks have
been applied to various medical images diagnosis and classification due to its power of
extracting different level features from images.

Traditional networks have been also used in classifying medical diseases, however, their
performance was not as efficient as the deep networks in terms of accuracy, computation time,
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and minimum square error achieved. In this work, deep learning based networks are employed to
classify most common thoracic diseases. Two Region based Convolutional Neural Network are
examined in this study to classify the chest X-rays into two common classes: normal and
abnormal which may have different types of diseases that may be found in chest X-ray, i.e,
Atelectasis, Cardiomegaly, Effusion, Infiltration, Mass, Nodule, Pneumonia, Pneumothorax,
Consolidation, Edema, Emphysema, Fibrosis. In this work, we aim to train the deep network
on the same number of chest X-ray images and evaluate their performances in classifying
different chest X-rays. The data used in obtained from two public databases which are the
Shenzhen Hospital X-ray Set / China data set: X-ray images in this data set (Fushman et al.,
2005), and the Montgomery County X-ray Set (Fushman et al., 2016).

1.2 Aims of Thesis

Doctors and radiologists are still categorizing the chest X-rays in a manual manner based on
some visual examinations. Therefore, There is a need for an automatic and intelligent systems
that has the capability of accurate classification of chest X-rays into normal and abnormal
images. Thus, in this work we aim to use a powerful deep network in such classification tasks.
The deep network that is selected to be used in called the Region based Convolutional Neural
Network which showed a great efficacy in different classification tasks in the medial field.
Furthermore, the network is also examined on enhanced and unenhanced images, which aims
to demonstrate the effects of medical image processing and enhancement on the performance of
neural network.

1.3 Significance of the Study

As most of the previous work are conducted using convolutional neural networks (CNN) and
support vector machine (SVM), this work is ought to investigate the performance of other types
of deep networks in classifying the abnormality of chest X-rays. Thus, a deep network named as
Region based Convolutional Neural Network is selected to be used as the brain behind this
study. This network is expected to well perform since it has been applied to various medical
classification tasks where it achieved high accuracies and because the data available are enough
for training it and achieving a small error.

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 CHAPTER 2

LITERATURE SURVEY

2.1 Introduction

In this chapter, a brief review of radiography, its application in medical imaging, and diagnosis is
presented. Also, the applied approach to the classification of the segmented images, pattern
recognition, is introduced. Furthermore, background on related image processing and feature
extraction techniques as are considered in this thesis are discussed sufficiently. Artificial neural
networks, the backbone of machine learning, and which has also been used extensively in this
work for the classification phase are introduced; including the particular algorithms for the
supervised and unsupervised learning.

2.2 Related Works

In a past work, (Cernazanu and Holban, 2012), described the segmentation of chest X-ray using
convolutional neural network. In their work, they introduced image segmentation into bone
tissue and non-bone tissue. The aim of their work was to develop an automatic or an intelligent
segmentation system for chest X-rays. The system was established to have the capability to
segment bone tissues from the rest of the image.

They were able to achieve the aim of the research by using a convolutional neural network,
which was tasked with examining raw image pixels and hence classifying them into “bone
tissue” or “non-bone tissue”. The convolutional neural networks were trained on the image
patches collected from the chest X-ray images. It was recorded in their work that the automatic
segmentation of chest X-rays using the convolutional neural networks, and approaches
suggested in their research produced plausible performance.

In another recent research, “lung Cancer Classification using Image Processing”, presented the
application of some image processing techniques in the classification of patients chest X-rays
into whether cancer is present or not (benign or malignant). In this work, it was shown that by

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extracting some geometric features that are essential to the classification of the images such area,
perimeter, diameter, and irregularity; an automatic classification system was developed.
Furthermore, in the same research, texture features were considered for a parallel comparison of
results on the classification accuracy. The texture features used in the work are average gray
level, standard deviation, smoothness, third moment, uniformity, and entropy. The back
propagation neural network was used as the classifier, and an accuracy of 83% was recorded in
the work (Patil and Kuchanur, 2012).

In this thesis the classification of chest X-ray radiographs into two classes has been achieved
using artificial neural networks. The two classes are the normal one which has no disease or
conditions, and the abnormal one which may have any types of diseases that may encounter the
chest organs including heart, lungs. Chest etc… A deep network called Region based
Convolutional Neural Network is used for (RCNN), which relies on a supervised and
unsupervised learning algorithms was used to train the network on the images collected for the
research.

2.3 Features Extraction in Medicine

Pattern recognition is the process of developing systems that have the capability to identify
patterns; while patterns can be seen as a collection of descriptive attributes that distinguishes one
pattern or object from the other. It is the study of how machines perceive their environment, and
therefore capable of making logical decisions through learning or experience. During the
development of pattern recognition systems, we are interested in the manner in which patterns
are modeled and hence knowledge represented in such systems. Several advances in machine
vision have helped revamp the field of pattern recognition by suggesting novel and more
sophisticated approaches to representing knowledge in recognition systems; building on more
appreciable understanding of pattern recognition as achieved in the human visual processing.
Typical pattern recognition as the following important phases for the realization of its purpose
for decision making or identification.

• Data acquisition: This is the stage in which the data relevant to the recognition task are
collected.

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 • Pre-processing: It is at this stage that the data received in the data acquisition stage is
manipulated into a form suitable for the next phase of the system. Also, noise is removed
in this stage, and pattern segmentation may be carried out.
• Feature extraction/selection: This stage is where the system designer determines which
features are significant and therefore important to the learning of the classification task.
• Features: The attributes which describe the patterns.
• Model learning/ estimation: This is the phase where the appropriate model for the
recognition problem is determined based on the nature of the application. The selected
model learns the mapping of pattern features to their corresponding classes.
• Model: This is the particular selected model for learning the problem, the model is tuned
using the features extracted from the preceding phase.
• Classification: This is the phase where the developed model is simulated with patterns for
decision making. The performance parameters used for accessing such models include
recognition rate, specificity, accuracy, and achieved mean squared error (MSE).
• Post-processing: The outputs of the model are sometimes required to be processed into a
form suitable for the decision making phase stage. Confidence in decision can be
evaluated at this stage, and performance augmentation may be achieved.
• Decision: This is the stage in which the system supplies the identification predicted by
the developed model.

There exist several approaches to the problem of pattern recognition such as syntactic analysis,
statistical analysis, template matching, and machine learning using artificial neural networks.

Syntactic approach uses a set of feature or attribute descriptors to define a pattern, common
feature descriptors include horizontal and vertical strokes, term stroke analysis; more compact
descriptors such as curves, edges, junctions, corners, etc., which is termed geometric features
analysis. Generally, it is the job of the system designer to craft such rules that distinguish one
pattern or object from another. The designer is meant to explore attribute descriptors which are
unique to identify each pattern, and where there seems to a conflict of identification rules such as
can be observed in identifying Figure 6 and 9; they have same geometric feature descriptors save
that one is the inverted form of the other, the system designer is meant to explore other
techniques of resolving such issues (Yumusak and Temurtas, 2010).
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Statistical pattern analysis uses probability theory and decision to infer the suitable model for the
recognition tasks.

Template pattern matching uses the technique of collecting perfect or standard examples for each
distinct pattern or object considered in the recognition task. It is with these perfect examples that
the test patterns are compared. It is usually the work of the system designer to craft the
techniques with which pattern variations or dissimilarities from the templates are measured, and
hence determine decision boundaries as to accept or reject a pattern being a member of a
particular class. Euclidean distance is a common used function to measure the distance between
two vectors in n-dimensional space.

Template matching can either be considered as global or local depending on the approach and
aim for which the recognition system is designed. In global template matching, the whole pattern
for recognition is used to compare the whole perfect example pattern; whereas in local template
matching, a region of the pattern for classification is used to compare a corresponding region in
the perfect template.

Artificial neural networks, on the other hand, are considered intelligent pattern recognition
systems due to their capability to learn from examples in a phase known as training. These
systems have sufficed in lots of pattern recognition systems; the ease with which same learning
algorithms can be applied to various recognition tasks is motivating.

In this approach, the designer is allowed to focus on determining features to be extracted for
learning by the designed systems, rather than expending a huge amount of time, resources, and
labour in understanding the whole details of the application domain; instead, the system learns
relevant features that distinguish one pattern from the other (Yumusak and Temurtas, 2010).

2.4 Image Processing

An image can be considered as a visual perception of a collection of pixels; where, a pixel can be
seen as the intensity value at a particular coordinate in an image. Generally, pixels are described
in 2D, such as f(x,y).

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The pixel values can vary in an image depending on the number gray levels used in the image.
The range of pixels can be expressed as 0 to 2m, for an image with gray level of m. Image
processing is a very important of computer vision, as image data can be suitably conditioned
before machine learning.

2.4.1 Image enhancement

Image processing has been extensively used in medicine. Image enhancement is always the most
common process needed in this field. A medial image contains many parts and may have lot of
noise. This makes it very tough for doctors to find the correct diagnosis of it. Image processing
can be useful tool in this case as it helps in detecting and enhancing the images since all parts in
image including noise differ from each other’s in terms of brightness and intensities. Thus, in
this work, image processing tools are used in order to enhance the chest X-ray images and
remove the noise that may be found in them. This is done by using many techniques for image
enhancement such as filtering, histogram equalization, and intensity adjustment. An example of
the working principle of the proposed algorithm is shown in Figure 1 (Yumusak and Temurtas,
2010).

In case of filtering, many filters can be used such as median, mean, Gaussian filters. For median
filters, the images are filtered as some of them have noise artifacts which should be removed to
enhance the quality of images. Median filter is a good technique for removing noise as it
provides good rejection of the Salt and Pepper noise which is found in some medical images.

Moreover, image intensities adjustment can be also used for enhancing the quality of images.
This technique involves the mapping of the pixels intensity distribution form one level to another
level. To highlight the images more and more, the intensities of pixels are increased by mapping
them into other values. This ended up with brighter images where the cells are clearer; including
the cancerous cells.

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 Figure 1: Medical Image Enhancement (Yumusak and Temurtas, 2010)

2.5 Artificial Neural Network (ANN)

Artificial neural systems are structure that originated from the cerebrum of the human brain that
is used for reasoning. The structure has been used to deal with troublesome issues in science. The
vast majority of the structures of neural systems are like the organic mind in the requirement for
preparing before having the capacity to complete a required assignment (Yumusak and
Temurtas, 2010). Like the standard of the human neuron, neural system processes the aggregate
of every one of its data sources.

On the off chance that that aggregate is more than a decided level, the journalist yield would then
be able to be enacted. Something else, the yield isn't going to the actuation work. Figure 2
illustrates the principal assembly of the neural system where the source of the weight and info on
summation of work is shown. The quantity of neuron that is find in a structure can is referred to
as the yield work. The equation that is used in the calculation of initial work is precisely
explained in (Santos et al., 2004):

(2.1)

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 Figure 2: Artificial Neural Network's Basic Structure (Santos et al., 2004)

2.6 Structure of ANN

The ANNs structure contains three layers despite the learning technique. These angles are the
layers, weights, and initiation capacities. Every last one of these three sections play an
imperative lead in the ANN limit. The three sections or segment works collectively to ensure
proper working of the system (Santos et al., 2004).

2.6.1 ANN Layers

The mutual relationship that occurs between the layers of ANN is the major derivative to its
creations. The layers interact by sending information between each other using the synaptic
weight. The Ann structure can be subdivided into three layers that is listed in the subsequent
section below.

1. Input layer: This is the first layer that is found in the neural system of ANN. This layers
is major that send information or data to other layers in the neural system. It can be
regarded as sensors because it doesn’t process later but only pass information processed
by other layers.

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 2. Hidden layers: this can be regard as the central bit of the neural system. It involves no
less than one of the layers which is the input layer and the neural layer. This layer
transmits the data to the output layers. The Hidden layer can be regards as the
intermediate layers or as a principal layer because the synaptic weights found in it are
reliable.

3. Output layer: This layer is regard as the output layers because its last contact where the
results of the neural system are gotten, the output layer got its information that is
processed from the Hidden layer.

Figure 3: The figure below shows the neural system and the interactions that occurs between its
three layers. The first layer which is the input layers is the source of the data that is passed to the
hidden layer and later to the output layer. The yield or result of the neural system is gotten from
the output layer.

Figure 3: The ANNs structure showing the three layers (Santos et al., 2004)

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2.7 Supervised and Unsupervised Learning

The phase of building knowledge into neural networks is called learning or training. The three
basic types of learning paradigms are:

-Supervised learning: The network is given examples and con-currently supplied the desired
outputs; the network is generally meant to minimize a cost function in order to achieve this,
usually an accumulated error between desired outputs and the actual outputs.

• Training data includes both the input and the desired results.

• For some examples the correct results (targets) are known and are given in input to the model
during the learning process.

• These methods are usually fast and accurate.

• Have to be able to generalize: give the correct results when new data are given in input without
knowing a priori the target.

Error per training pattern = desired output - actual output

Accumulated error= ∑(error of training patterns)

-Unsupervised learning: The network is given examples but not supplied with the
corresponding outputs; the network is meant to determine patterns between the input attributes
(examples) according to some criteria and therefore group the examples thus.

• The model is not provided with the correct results during the training.

• Can be used to cluster the input data in classes on the basis of their statistical properties only.

• Cluster significance and labeling.

• The labeling can be carried out even if the labels are only available for a small number of
objects representative of the desired classes.

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2.7.1 Supervised learning rules

• Perceptron learning rule

There are several different models of supervised learning that have been implemented in
artificial neural networks (Santos et al., 2004).

T .P =  wji xi
i =1 (2.2)

If T .P   , then y = 1
else T .P   , then y = 0 (2.3)

Where T.P is known as the total potential of the neuron, ϴ is the threshold value, wji is the
weight connection from input xi to neuron j, m is the number of inputs, and y is the output of the
neuron. If the total potential is greater than or equal to the threshold value, then the neuron fires;
if otherwise, then the neuron does not fire.

The perceptron learning rule is given below; the weights of the network are updated using the
equation.

wj = wj (t) +(d − y)x

(2.4)

Training patterns are presented to the network's inputs; the output is computed. Then the
connection weights wj are modified by an amount that is proportional to the product of the
difference between the actual output, y, and the desired output, d, and the input pattern, x.

• Delta learning rule

An alternative but related approach to the perceptron learning rule is known as the delta rule.
While the perceptron training rule is based on the idea of modifying weights according to some
fraction of the difference between the output and target, the delta rule is based on the more
general idea of "gradient descent". For example, consider the task of training a single TLU with a
set of input patterns p, each with a desired target output tp. The global error E is a function of the
weights w. That is, as weights change, the error changes. The goal is to move in "weight space"
12
down the slope of the error function with respect to each weight. The size of the step should be
proportional to the magnitude of the slope. How is the slope calculated? Using calculus the slope
may be expressed as the partial derivative of the error with respect to the weight:
E
= −
wj w
j
(2.5)

where α is the learning rate

If ep is the error produced by a network processing a particular pattern p, then the global error E
is the mean error produced over all the different patterns in the training set:

E = 1 ep
N

N p=1
(2.6)

where N is the number of patterns in the training set.

The simplest way of determining the pattern error ep is simply the target output minus the actual
output:

ep = t p − yp (2.7)

where y is the neuron output and t is the target for training pattern p.

However, the above equation has several problems. First the subtraction means that the term may
be either positive or negative rather than a simple magnitude and may therefore complicate
further calculations. This issue is managed by squaring the term:

e p = (t p − y p )2 (2.8)

The second problem we encounter is more subtle. In order to perform gradient descent values
must be continuous. This can be remedied by substituting activation a rather than the output y.
Though when doing this the target should be carefully defined - if the threshold is set to 0 then
one target should be set as positive and the other negative e.g. -1 and 1.

e p = 1 (t p − y p )2
2 (2.9)
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The final modification is to divide the entire term by 2 simply to make differentiation easier.

Since E is the mean of all patterns one cannot technically calculate dE/dwi until the entire set of
patterns is available. However, this is very computationally intensive, so de/dwi is usually
performed individually with each training pattern as an approximation as shown below.

ep = −(t p − y p )x p
wi (2.10)

2.8 Learning Parameters for the Back Propagation Algorithm

• Learning rate

The learning rate is a very important parameter in supervised learning; it is used to control how
fast the network learns the training examples. The value of this parameter varies between 0 to 1.
Learning rate determines the step size with which network weights are updated during training.
If the value set for the learning rate is too high, the network runs a high risk of only memorizing
the training data, as learning is completed in fewer epochs (possible that the network weights
have not been properly tuned to the examples); a situation referred to as over-fitting. If the value
set for the learning rate is too low, then the network runs a risk of not insufficient learning of the
training data by the time the set number of maximum epochs is reached. It there follows that
using a value that is too small for the learning rate makes the learning much slower, and the
network may not converge to the set MSE goal before training is stopped. Generally, the suitable
value for the learning rate is determined heuristically (through a trial and error method). Low
values are usually preferred (Santos et al., 2004).

• Momentum rate

The momentum parameter is often optional for supervised learning, its sole purpose is to help
reduce the possibility of the network getting trapped in a poor local minimum during training. Its
value also ranges between 0 to 1. The momentum rate parameter can be seen as kind of inertia
being introduced into the network. It helps push the learning past poor local minima during
network training; and also dampens oscillations that may occur during learning, hence the
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learning curve is usually smoother compared to when the momentum rate parameter is not used
in the learning algorithm.

• Goal of cost function (MSE)

Generally, for any supervised learning algorithm, since a cost function relating the deviation of
the actual response of the network from the desired is to be minimized, it then follows that there
should be a specified value for the goal of the cost function being minimized.

When the network reaches this specified value for the MSE goal, the training of the network is
stopped ().

• Maximum epochs

Since neural networks learn by examples, the forward pass of an example from the input and the
back pass of the computed error constitute what is referred to as an epoch. This process is
repeated for each training example till all the examples have been propagated through the
network; after which the process repeats in such manner, while the set value for the MSE goal is
monitored. When training neural networks, it is very important to specify the maximum number
of iterations allowed in the training. This has the effect of not allowing the network to continue
training indefinitely in a situation where the learning has not converged to the set MSE goal,
hence is used as an important stopping criterion in training.

• Number of hidden neurons

For the back propagation neural network and most other networks, the network is made of at
least three layers, which are the input layer, hidden layer, and output layer. The input layer is
where the training examples are supplied to the network, the hidden layer learns the features
represent in the input, and the output layer allows the actual output of the network to be
obtained. Also, the input layer neurons are non-processing, they basically serve to supply the
input features to the network.

The output layer in a supervised learning, allows the computation of the error between the
desired output and actual output of the network; and therefore back propagation of errors into the
network for weights adjustment or tuning (Patil and Kuchanur, 2012).
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The hidden layer is very important, considering that it is where the main knowledge
representation of the features present in the training examples is achieved. Hence, it is very
crucial that a suitable number of neurons are used at the input layer of neural networks to ensure
proper learning of a task.

If the number of hidden neurons is too few, then the network may not have enough power to
accommodate the feature representation present in the training examples; a situation also referred
to as low degree of freedom.

Conversely, if the number of neurons used is too many, then the network develops a far more
complex model to the training examples than is required, the network has too much
representation power, such that it may begin to model features that too peculiar to the training
examples, hence the network is likely to over-fit. A situation also referred to as too high degree
of learning freedom.

It is therefore desirable that the number of neurons used in the hidden layer should not be too few
or too many. Generally, during training, the number of suitable hidden neurons is determined
through a trial and error approach.

• Activation function

Activation functions are used to squash the output of artificial neurons to within a certain range
of values. It is conceived that the output of neurons should not be infinite. The weighted sum of
the inputs to a neuron is computed, the value referred to as the total potential, which is then
passed through an activation function.

Common activation functions used in neural networks include the Signum, linear, Log-Sigmoid,
and the Tan-Sigmoid.

During the design of neural networks, the type of application determines the activation function
to be used in each layer of the network. The layer that is so application specific is the output
layer. The type of activation used in the output layer depends on the range or type of values
expected at the output.

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For real values problems such as regression tasks, the linear activation function is used, for
classification tasks, output values are generally integers, and hence the Log-Sigmoid or Tan-
Sigmoid can be used.

2.9 Deep Learning

Deep Learning is another and progressed documented of Machine Learning. It has been
produced and enhanced keeping in mind the end goal to move the moving Machine Learning to
be nearer its primary and unique objective Artificial Intelligence (Glavan, Holban, 2012).

Deep Learning is called "Deep" because of its structure of the neural systems. Prior, neural
systems used to have two layers deep on the grounds that it was not computationally plausible to
assemble bigger systems. These days, a neural system with in excess of 10 layers and
considerably more layers are being started and constructed. These sorts of systems are called
deep neural systems. Figure 4 shows engineering of a deep neural system. It demonstrates that
the system comprises of numerous layers which makes it deep (Deng, 2014).

Figure 4: Deep network structure (Glavan, Holban, 2012)

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2.9.1 Region based Convolutional Neural Network

Region based Convolutional Neural Network is one sort of deep systems that is prepared
utilizing another calculation called covetous layer wise training. The eager layer wise approach
for pre-training a deep system works via training each layer thus. In this page, you will
discover how auto-encoders can be "stacked" in an insatiable layer wise design for pre-
training (instating) the weights of a deep system (Glavan and Holban, 2012).

A Region based Convolutional Neural Network is a neural system comprising of different

layers of meager auto- encoders in which the outputs of each layer are wired to the inputs
of the progressive layer. Formally, consider a Region based Convolutional Neural Network with
n layers. Utilizing documentation from the auto- encoder area, let W(k,1),W(k,2),b(k,1),b(k,2)
signify the parameters W(1),W(2),b(1),b(2) for kth auto-encoder. At that point the encoding
venture for the Region based Convolutional Neural Network is given by running the
encoding advance of each layer in forward request:

The decoding step is given by running the decoding stack of each auto-encoder in reverse order:

The data of intrigue is contained inside a(n), which is the actuation of the deepest layer of hidden
units. This vector gives us a representation of the input as far as higher-arrange highlights.

The highlights from the Region based Convolutional Neural Network can be utilized for
classification issues by nourishing a(n) to a Softmax classifier.

To give a solid illustration, assume you wished to prepare a Region based Convolutional Neural
Network with 2 hidden layers for classification of MNIST digits, First, you would prepare a
scanty auto-encoder on the crude inputs x(k) to learn essential highlights h(1)(k) on the crude
input.

18
 Figure 5: Auto-encoder step 1

Next, you would encourage the crude input into this trained auto-encoder, getting the essential
element initiations h(1)(k) for every one of the inputs x(k). You would then utilize these essential
features as the "crude input" to another meager auto-encoder to learn optional features h(2)(k) on
these essential features.

19
 Figure 6: Auto-encoder step 2 (Glavan, Holban, 2012)

Following this, you would feed the primary features into the second sparse auto-encoder to
obtain the secondary feature activations h(2)(k) for each of the primary features h(1)(k)(which
correspond to the primary features of the corresponding inputs x(k)). You would then treat these
secondary features as "raw input" to a Softmax classifier, training it to map secondary features to
digit labels.

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 Figure 7: Softmax classifier (Glavan, Holban, 2012)

At long last, you would join every one of the three layers together to frame a stacked auto-
encoder with 2 hidden layers and a last Softmax classifier layer equipped for ordering the
MNIST digits as wanted.

Figure 8: Region based Convolutional Neural Networks (Glavan, Holban,

2012)
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2.9.2 Training

A decent method to acquire great parameters for a Region based Convolutional Neural
Network is to utilize ravenous layer-wise training. To do this, first prepare the primary layer
on crude input to get parameters W(1,1),W(1,2),b(1,1),b(1,2). Utilize the primary layer to
change the crude input into a vector comprising of enactment of the hidden units, A.
Prepare the second layer on this vector to acquire parameters W(2,1),W(2,2),b(2,1),b(2,2).
Rehash for ensuing layers, utilizing the output of each layer as input for the resulting layer
(Albarqoun et al., 2016).

This strategy prepares the parameters of each layer exclusively while solidifying parameters for
the rest of the model. To create better outcomes, after this period of training is finished, fine-
tuning utilizing backpropagation can be utilized to enhance the outcomes by tuning the
parameters of all layers are changed in the meantime (Bengio et al., 2007).

On the off chance that one is just intrigued by fine-tuning for the reasons for classification, the
normal practice is to then dispose of the "disentangling" layers of the Region based
Convolutional Neural Network and connection the last hidden layer a(n) to the Softmax
classifier. The angles from the (Softmax) classification error will then be backpropagated into
the encoding layers.

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 CHAPTER 3

EXISTING SYSTEM

3.1 Introduction

In the territory of human services diagnostics, therapeutic image preparing has assumed a
contributory part. From the different scopes of accessible radiological images created from
ultrasound, x-beams, attractive Resonance imaging, Computed Tomography, Positron Emission
Tomography and so forth, every has its own particular technique for catching the images. Be that
as it may, even in the wake of narrowing the focal point of the image catch, just a couple of
segments of the radiological images are of clinical significance to the counseling doctor
(Fushman et al., 2015). Be that as it may, there are different purposes behind which the
pathologist and also radiologist trusted that image produced by such radiological test doesn't
yield 100% exact data. For less minor types of the perilous ailment, such blunders may not make
any difference much, but rather it does conceivably make a difference generally. In any case,
presenting the patient to destructive radiological beams is restoratively not prudent and might be
a significant costly issue for both specialist and patient. Consequently, from the previous decades
utilization of image handling is progressively used to recognize the issues and settle it. The initial
phase in such issue distinguishing proof is to perform image improvement. As though the image
with clinical significance isn't upgraded it might possibly prompt exceptions in cutting edge
investigation of medicinal information (Fushman et al., 2012).Henceforth, image upgrade
assumes a pivotal part in uncovering the malady with more data to the specialist or to the
procedure of further investigation of the illness. This paper talks about the chest x-beam images
and proposed an answer with greater activity and lower computational cost for improving the
chest x-beams. The radiological images particularly chest x-beam images experiences following
issues i.e. I) numerous outline, ii) nearness of rib confines (bones), iii) shadows of bosom in
female subjects, iv) stomach and so on. In spite of the fact that there are propelled adaptations of
radiological images however chest x-beam image is thought to be essential finding factor by the
clinicians. Subsequently, if the chest x-beam images are covered with different relics or issues,
post diagnosis will dependably prompt anomalies. Subsequently, it
23
is vital that chest x-beam images ought to be appropriately pre-prepared even before subjecting it
to propel investigation.

Therefore, this paper presents a very simple and cost effective chest X-rays classification system
using deep networks for chest x-ray images with and without operations of enhancements.

3.2 Chest X-rays

A chest X-beam test is an extremely normal, non-obtrusive radiology test that creates an image
of the chest and the inward organs. To deliver a chest X-beam test, the chest is quickly presented
to radiation from a X-beam machine and an image is created on a film or into a computerized
computer (Jaeger et al., 2014).

Chest X-beam is additionally alluded to as a chest radiograph, chest roentgenogram, or CXR.

Contingent upon its thickness, every organ inside the chest pit retains fluctuating degrees of
radiation, creating distinctive shadows on the film. Chest X-beam images are highly contrasting
with just the brilliance or haziness characterizing the different structures. For instance, bones of
the chest divider (ribs and vertebrae) may assimilate a greater amount of the radiation and along
these lines, seem more white on the film.

Then again, the lung tissue, which is for the most part made out of air, will enable the majority of
the radiation to go through, building up the film to a darker appearance. The heart and the aorta
will seem whitish, however typically less brilliant than the bones, which are denser.

Chest X-beams tests are requested by doctors for an assortment of reasons. Numerous clinical
conditions can be assessed by this basic radiology test. A portion of the basic conditions
recognized on a chest X-beam include:

• pneumonia,
• enlarged heart,
• congestive heart disappointment,
• lung mass,
• rib cracks,
24
 • fluid around the lung (pleural radiation), and
• air around the lung (pneumothorax).

All in all, a chest X-beam test is a straightforward, brisk, economical, and moderately innocuous
system with insignificant danger of radiation. It is additionally broadly accessible.

3.3 Chest Abnormalities

3.3.1 Pleural disease

• The pleura and pleural spaces are just noticeable when abnormal

• There ought to be no noticeable space between the instinctive and parietal pleura

• Check for pleural thickening and pleural emanations

• If you miss a strain pneumothorax you hazard your patient's life – and in addition your
outcome at finals!

• The pleura just wind up noticeable when there is an abnormality show. Pleural
abnormalities can be unpretentious and it is critical to check precisely around the edge of
every lung where pleural abnormalities are normally more effortlessly observed (Figure
9). A few illnesses of the pleura cause pleural thickening, and others prompt liquid or air
assembling in the pleural spaces (Xue et al., 2015).

Figure 9: Pleural thickening (Xue et al., 2015)

25
3.3.2 Pneumothorax

A pneumothorax shapes when there is air caught in the pleural space. This may happen
precipitously, or because of hidden lung illness. The most widely recognized reason is injury,
with slash of the instinctive pleura by a broken rib (Figure 10).

On the off chance that the lung edge measures in excess of 2 cm from the inward chest divider at
the level of the hilum, it is said to be 'substantial. If there is tracheal or mediastinal move far
from the pneumothorax, the pneumothorax is said to be under 'pressure.' This is a restorative
crisis! Missing a pressure pneumothorax may not just mischief your patient; it is likewise the
snappiest method to fizzle the radiology OSCE at finals!

Figure 10: Pneumothorax (Xue et al., 2015)

26
3.3.3 Asbestos plaques

Calcified asbestos related pleural plaques have a trademark appearance, and are for the most part
thought to be favorable. They are sporadic, all around characterized, and traditionally said to
look like holly takes off (Candemir, et al., 2014).

Figure 11: Asbestos related pleural plaques (Candemir, et al., 2014)

3.3.4 Pleural effusions

A pleural emission or effusion is a gathering of liquid in the pleural space. Liquid accumulates in
the most minimal piece of the chest, as per the patient's position. In the event that the patient is
upright when the X-beam is taken, at that point liquid will encompass the lung base framing a
'meniscus' – a sunken line clouding the costophrenic edge and part or the majority of the
hemidiaphragm (Figure 12).

27
On the off chance that a patient is recumbent, at that point a pleura radiation layers along the
back part of the chest pit and ends up hard to see on a chest X-beam(Shiraishi et al., 2000).

Figure 12: Pleural effusion (Shiraishi et al., 2000)

28
 CHAPTER 4

PROPOSED SYSTEM

4.1 Methodology

This study presents an original research for the diagnosis of chest X-rays using deep learning. A
deep network named as Region based Convolutional Neural Network (RCNN) is selected to be
used as the brain this work. This selection came from the few researches that were conducted
for the chest X-rays classification using this kind of networks. Thus, there is a need to
investigate the effectiveness and performance of Region based Convolutional Neural Network
in classifying the chest X-rays and detecting whether a radiograph has a disease or it is normal
(healthy).

Two auto-encoder networks were used to build the proposed Region based Convolutional
Neural Network that is then used to be as the intelligent classifier of the chest X-ray images.
The auto-encoder was first trained layer by layer using greedy layer wise training until a
network of two hidden layer, one input, and one output network is formed. Therefore, these
trained auto-encoders were all stacked together and the proposed Region based Convolutional
Neural Network is formed.

The proposed network is trained to classify chest images into normal which have no
abnormalities or diseased images regardless of the type of the disease. A sample of the database
normal and abnormal chest X-rays is shown in Figure 14.

Note that in this work, two deep models are employed. Both models are Region based
Convolutional Neural Networks with the same learning parameters, however, for the first
model, which we call RCNN1, the chest X-rays are fed directly into network, without
processing and enhancement. The second network model, which is called RCNN2, was trained
on images that are processed and enhanced before being fed into network. The aim of the
use of two models is to investigate the effects of processing and image enhancement on the auto-
encoder training and testing performance.

29
 Figure 13: Flowchart of the proposed methodology

Figure 13 shows the workflow of the proposed methodology. As seen, the network model is
trained first on the chest images without enhancement and the network is then tested and the
performance is evaluated. Same network is then trained and tested on same images but here they
are enhanced using image Histogram equalization and similarly, the network is also evaluated
and tested in order to investigate the one that outperforms in terms of accuracy and less error
achieved.

4.2 Database

A deep network an intelligent classifier that is hungry for data. The more data it is trained on the
more intelligent it will be. Therefore, there is need for a good database that has good number of
normal and abnormal images to train and test the developed network. Therefore, the images in
this work are all obtained from two public and well-known databases. The first one is Shenzhen
Hospital X-ray Set / China data set: X-ray images in this data set (Fushman et al., 2005), while
the other database is the Montgomery County X-ray Set. The first database contains chest X-rays
of both normal and abnormal cases and they were acquired as part of the routine care at
Shenzhen Hospital. The images are of JPEG format and there 340 normal x-rays and 275

30
abnormal x-rays showing various aspects of tuberculosis. The second database contains 58
abnormal x-rays and 80 normal images.

Figure 14: A sample of the database images

31
 Figure 14 shows a sample of the chest X-rays found in the database used for training and testing
the employed models. Note that the figure shows the two classes of the database images: the
normal and the abnormal.
Table 1 shows the number of images found in the database in addition to the training and testing
ratios used.

Table 1: Dataset 1 and data division

Image sets Number of Normal images Abnormal
images Images
Training 400 200 200
set
Testing set 215 140 75
Both sets 615 340 275

Table 2 shows the number of X-rays in the dataset 2 and its data division.

Table 2: Dataset 2 and data division

Image sets Number of Normal images Abnormal
images Images
Training 70 40 30
set
Testing set 68 40 28
Both sets 138 80 58

4.3 Training the Deep Models

In this section the training of the two deep models which are RCNN1 and RCNN 2 is discussed.
Note that the RCNN1 is the Region based Convolutional Neural Network network that uses X-ray
images without enhancement
32
while RCNN2 is the same network but with enhanced images as inputs. It is important to
mention that RCNN1 and RCNN2 are both trained on the same number of images which is
470 images; among them 240 are normal and 230 are abnormal.

For output classes coding it was considered as the following:

• Abnormal output class [1 0],

• Normal output class [0 1]

Note that the networks are first pre-trained as they are deep networks. Pre-training means that the
networks are first trained layer by layer using Greedy-layer wise training (Hinton, 2006). In this
phase there is no output labeling because the network is trained here to reconstruct its input from
the extracted features in the hidden layer, which is why the number of output neurons is equal to
the number of input neurons which is 4096.

Once the networks finish pre-training, it is then fine-tuned using the conventional
backpropagation algorithm. Here, the input images are labeled therefore, output neurons are two
which means that network is being trained to classify the images into two classes: normal and
abnormal.

Table 3 shows the training and testing data from the two datasets. It is seen that the network is
trained on 470 images and tested on 283 chest X-rays.

Table 3: Training and testing data from the two databases

Image sets Number of Training Testing
images
Dataset 1 615 400 215
Dataset 2 138 70 68
Both sets 753 470 283

33
4.3.1 RCNN1 Training

RCNN1 is a Region based Convolutional Neural Network that is trained on 470 images that
are fed into it without any processing or enhancement technique. This deep model is composed
of one input layer of 4096 neurons since the input images size is 64*64 pixels; two hidden
layers of 100 and 65 neurons, respectively. Also, it has an output layer of two neurons as the
output classes are only two.

Figure 15 shows the architecture of the RCNN1. Table 4 shows the values of the learning
parameters of the RCNN1 when it is trained on 200 images.

Figure 15: The deep network model 1 (RCNN1) structure

34
 CHAPTER 5

RESULT

5.1 WEB APPLICATION DESIGNED

Figure 16: web application designed for Tuberculosis

5.2 TESTING PAGE

Figure 17: website for Tuberculosis testing page

35
5.3 POSITIVE CASE

Figure 18: Positive result from CXR Image

5.4 NEGATIVE CASE

Figure 19: Negative result from CXR image

36
5.5 ACCURACY PLOT

Figure 20: Accuracy plot for Tuberculosis prediction

37
 CHAPTER 6

CONCLUSION

6.1 Conclusion

This thesis presents the employment of deep network in particular Region based
Convolutional Neural Network in a medical field challenging task which is the classification
of chest X-rays into normal and abnormal images. Such a classification medical system is
needed as it makes the radiologist’s job faster and easier.

A Region based Convolutional Neural Network is employed in this work and it was trained and
tested on 470 and 283 images, respectively. The network is first trained on images taken
directly from the database, without processing and enhancing. Then same network was tested
and performance was evaluated in terms of training time, error, and accuracy. The same
network was trained again on the same images but here the images were enhanced using
histogram equalization. Also, this network was tested and an evaluation of its performance was
carried out.The performance of both networks was discussed and a comparison of the two
network performance was shown, in terms of accuracy, error reached, training time, and number
of iterations needed. After this comparison it was seen that the network that uses enhanced
images outperformed the one that used unprocessed images as it achieved a higher recognition
rate during testing.

In conclusion, the testing of Region based Convolutional Neural Network showed that it
gained a good capability of diagnosing the new unseen chest X-rays and correctly classifying
them into normal or abnormal images. Thus, it can be stated that the RCNN can be a
good classifier for the chest X-rays classification with a small margin of errors. Moreover, it
is seen that the enhancement of chest X-rays using histogram equalization has a good role in
improving the learning of the Region based Convolutional Neural Network, which results in a
better accuracy during the testing of the network.

38
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