MEDICAL IMAGE CLASSIFICATION AND SYMPTOMS DETECTION USING NEURO FUZZY

MOHD ARIFFANAN BIN MOHD BASRI

A project report submitted in partial fulfillment of the requirements for the award of the degree of Master of Engineering (Electrical Mechatronics and Automatic Control)

Faculty of Electrical Engineering Universiti Teknologi Malaysia

NOVEMBER 2008

iii

Specially..

To my beloved mother and late father, My kind brothers and sisters And not forgetting to all my friends For their Love, Sacrifice, Encouragement, and Best Prayers

iv

ACKNOWLEDGEMENTS

Praise be to Allah S.W.T to Whom we seek help and guidance and under His benevolence we exist and without His help this project could not have been accomplished.

I would like to express my sincere thanks and appreciation to Dr. Hj. Mohd. Fauzi bin Othman for his supervision, advice, guidance, encouragement and insightful comments given throughout the course of completing this project.

I am also indebted to the Universiti Teknologi Malaysia for their encouragement and financial support during my study. Not forgetting to all my fellow postgraduate students and friends for their moral support and given throughout the entire masters programme. Without their continued support and interest, this project would not have been realized.

Last but not least, my gratitude also goes to all my family members for their continuous encouragement and support. Thank you all.

ABSTRACT

The conventional method in medicine for brain MR images classification and tumor detection is by human inspection. Operator-assisted classification methods are impractical for large amounts of data and are also non-reproducible. MR images also always contain a noise caused by operator performance which can lead to serious inaccuracies classification. The use of artificial intelligent techniques, for instance, neural networks, fuzzy logic, neuro fuzzy have shown great potential in this field. Hence, in this project the neuro fuzzy system or ANFIS was applied for classification and detection purposes. Decision making was performed in two stages: feature extraction using the principal component analysis (PCA) and the ANFIS trained with the backpropagation gradient descent method in combination with the least squares method. The performance of the ANFIS classifier was evaluated in terms of training performance and classification accuracies and the results confirmed that the proposed ANFIS classifier has potential in detecting the tumors.

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ABSTRAK

Teknik konvensional di dalam perubatan untuk pengkelasan dan pengesanan barah untuk imej magnetik resonan otak adalah dilakukan secara pemeriksaan manual. Teknik pengkelasan yang dibantu oleh operator adalah tidak praktikal untuk jumlah data yang besar dan juga tidak dapat dihasilkan. Imej magnetic resonan juga lazimnya mengandungi hingar yang berpunca daripada mutu kerja operator yang mana boleh menjurus kepada ketidaktepatan pengkelasan yang serius. Penggunaan teknik kecerdikan buatan contohnya, neural network, fuzzy logic dan juga neuro fuzzy telah menunjukkan potensi yang besar di dalam bidang ini. Oleh yang demikian, di dalam projek ini sistem neuro fuzzy atau juga dikenali sebagai ANFIS telah diaplikasikan untuk tujuan pengkelasan dan pengesanan. Pengambilan

keputusan telah dilakukan secara dua peringkat: pengekstrakan sifat menggunakan prinsip analisis komponen dan ANFIS terlatih dengan penggabungan teknik backpropagation gradient descent dan juga least squares. Prestasi pengkelas ANFIS berkenaan dengan prestasi latihan dan ketepatan pengkelasan telah diuji dan hasilnya telah menunjukkan bahawa pengkelas ANFIS yang dicadangkan mempunyai potensi untuk mengesan barah.

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TABLE OF CONTENTS

CHAPTER

TITLE

PAGE

DECLARATION DEDICATION ACKNOWLEDGMENTS ABSTRACT ABSTRAK TABLE OF CONTENTS LIST OF TABLES LIST OF FIGURES LIST OF ABBREVIATIONS LIST OF SYMBOLS LIST OF APPENDICES

ii iii iv v vi vii x xi xiii xiv xv

INTRODUCTION 1.1 1.2 1.3 1.4 1.5 1.6 Project Background Magnetic Resonance Imaging Problem Statement Objectives Scope of Work and Methodology Thesis Outline

1 1 2 5 5 6 7

LITERATURE REVIEW 2.1 2.2 Related Works Artificial Neural Networks 2.2.1 2.2.2 Learning from Biology Generic Model of Neural Network

8 8 11 11 13

viii 2.2.3 2.2.4 2.2.5 2.2.6 2.3 Bias and Threshold Activation Functions Network Learning Phase 14 15 15 16 17 18 19 20 21 21

Fuzzy Logic Systems 2.3.1 2.3.2 2.3.3 2.3.4 2.3.5 2.3.6 Advantages of Fuzzy Logic Disadvantages of Fuzzy Logic Fuzzy Sets Membership functions Components of a fuzzy system Fuzzy Logic Graphical User Interface (GUI)

24 25

2.4

Principal Component Analysis (PCA)

RESEARCH METHODOLOGY 3.1 3.2 3.3 3.4 3.5 3.6 Methodology Proposed Method Transformation of Image to Data Form Pixels Labeling Region of Interest Extraction Feature Extraction using Principal Component Analysis (PCA) 3.7 3.8 Data Modeling System developing 3.8.1 3.8.2 3.8.3 3.8.4 3.8.5 3.8.6 Data Management and Preparation Data Mining Input Phase FIS Phase ANFIS modeling phase Output phase

27 27 27 28 30 31

32 34 37 37 38 38 39 40 42

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NEURO FUZZY MODELING AND SOFTWARE IMPLEMENTATION 4.1 4.2 Neuro Fuzzy Model Adaptive neuro fuzzy inference system (ANFIS) 4.2.1 4.2.2 4.2.3 4.3 4.4 4.5 4.6 4.7 4.8 4.9 4.10 ANFIS Architecture Learning algorithm of ANFIS ANFIS Classifier

43 43

44 45 49 51 52 53 54 55 56 57 58

ANFIS editor GUI FIS Editor Membership Functions Editor Rule Editor Rule Viewer ANFIS Model Structure Modeling Data through ANFIS Model Validation (Checking and Testing Data)

60

RESULTS AND DISCUSSIONS 5.1 5.2 5.3 5.4 Result Performance Analysis Noise Consideration Comparisons of Result

62 62 64 66 70

CONCLUSIONS AND FUTURE WORKS 6.1 6.2 Conclusions Future Works

72 72 74

REFERENCES Appendices A-K

77 80 - 99

LIST OF TABLES

TABLE NO. 4.1 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9

TITLE Two passes in the hybrid learning procedure for ANFIS The ANFIS errors The ANFIS test results The values of statistical parameters Testing data set with 1% noise Testing data set with 2% noise Testing data set with 3% noise The ANFIS test results with noise consideration PNN target results Comparison between PNN and ANFIS

PAGE

51 63 66 66 67 67 68 70 70 71

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LIST OF FIGURES

FIGURE NO. 1.1 1.2 1.3 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10 3.11 3.12 3.13 4.1 MRI machine

TITLE

PAGE 3 4 4 13 14 16 21 21 22 24 28 30 30 31 32 34 36 37 39 40 41 41 42 46

Schematic diagram of MRI machine Brain MRI Biology neuron Generic model of artificial neural network Feedforward Network Membership functions of a crisp set and a fuzzy set Membership grades of a fuzzy set Components of a fuzzy logic system Fuzzy Logic Graphical User Interface (GUI) The proposed system Convert brain image to binary image Pixel coordinate system Advanced coordinate system for matrix 16 by 16 Location of tumor Schematic diagram of a MR image recognizer Training Data Set Basic flow diagram of computations in ANFIS Partial of input phase FIS generated thru genfis1 Information of the ANFIS model ANFIS training errors and total time training Sample of classification results A two-input first-order Sugeno fuzzy model with two rules

xii 4.2 4.3 4.4 4.5 4.6 4.7 4.8 4.9 4.10 4.11 4.12 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 6.1 6.2 ANFIS architecture. Two-input first-order Sugeno fuzzy model with nine rules The input space that are partitioned into nine fuzzy regions ANFIS editor GUI FIS editor Membership function editor Rule editor Rule viewer ANFIS model structure Training error Output of ANFIS Training and checking data ANFIS errors The misclassified output of ANFIS classifier a)Membership function before training b)Membership function after training The misclassified output of ANFIS classifier with 1% noise The misclassified output of ANFIS classifier with 2% noise The misclassified output of ANFIS classifier with 3% noise Chart comparison Different slice of brain medical image Block Diagram of the neuro fuzzy approach 46 49 49 53 54 55 56 57 58 59 60 62 63 64 65 68 69 69 71 75 76

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LIST OF ABBREVIATIONS

AFLC ANFIS ANN CAT COG COS CT FCM FIS GUI MF MLP MR MRI NMR NN PCA PET PNN RF RGB ROI

Adaptive Fuzzy Leader Clustering Adaptive Neuro Fuzzy Inference System Artificial Neural Network Computed Axial Tomography Centre of Gravity Centre of Singleton Computed Tomography Fuzzy C-Means Fuzzy Inference System Graphical User Interface Membership Function Multi Layer Perceptron Magnetic Resonance Magnetic Resonance Image Nuclear Magnetic Resonance Neural Network Principal Component Analysis Positron Emission Tomography Probabilistic Neural Network Radio Frequency Red Green Blue Region of Interest

xiv

LIST OF SYMBOLS

i w b O x e E A(x)

threshold Input signals Weight the neurons Bias signal Output signals Summation of all incoming signals Product of all the incoming signals Universal sets error total error Subset Membership functions of A Intersection @ AND logic operation Complement @ OR logic operation activation function Rows x columns training image of image i pixel vector feature vectors

f MxN
i

xv

LIST OF APPENDICES

APPENDIX A B C D E F G H I J K

TITLE MATLAB source code for transformation image to data PCA Algorithm code CreateDatabase function code EigenMRICore function code TumorRecognition function code Neuro Fuzzy Algorithm code Brain MR Image for Class 1 Brain MR Image for Class 2 Brain MR Image for Class 3 Brain MR Image for Class 4 Brain MR Image for Class 5

PAGE

80 83 85 87 89 91 95 96 97 98 99

CHAPTER 1

INTRODUCTION

1.1

Project Background

Automated classification and detection of tumors in different medical images demands high accuracy since it deals with human life. Also, computer assistance is highly sought in medical institutions due to the fact that it could improve the results of humans in such a domain where the false negative cases must be at a very low rate. It has been proven that double reading of medical images could lead to better tumor detection. But the cost incurred in double reading is very high, therefore good software to assist humans in medical institutions is of great interest nowadays.

Different approaches that can produce medical images must be studied. Also, the technique that produces those images is very important in order to know what to apply to a certain medical image in order to get better results. A lot of methods have been proposed in the literature for CT (Computed Tomography), such as scans, different types of X-rays, MRI images and other radiological techniques. With all this effort done in the research field, there is still a lot of place for improvements and the medical image processing is a domain in continuous expansion. Why is this domain in continues expansion and without and good accepted method? This is due to the fact that in such an important domain, the accuracy must be very high and the false negative rate must be low. The problem is that it is not very easy to obtain such results. The idea is to reduce human error as much as possible by assisting

2 physicians and radiologists with some software that could lead to better results. This is important since it involve saving human lives.

In this project the automated classification of brain magnetic resonance images by using some prior knowledge like pixel intensity and some anatomical features is proposed. Since currently there are no widely accepted methods, therefore automatic and reliable methods for tumor detection are of great need and interest. The application of neuro fuzzy systems in the classification and detection of data for MR images problems are not fully utilized yet. These include the clustering and classification techniques especially for MR images problems with huge scale of data which consumes time and energy if done manually. Thus, fully understanding the detection, classification or clustering techniques is essential to the developments of neuro fuzzy systems particularly in medical-related problems. Furthermore, fuzzy set theory plays an important role in dealing with uncertainty when making decisions in medical applications [1]. Neuro fuzzy systems are fuzzy systems which use ANNs theory in order to determine their properties (fuzzy sets and fuzzy rules) by processing data samples. A specific approach in neuro fuzzy development is the adaptive neuro fuzzy inference system (ANFIS), which has shown significant results in modelling nonlinear functions. The ANFIS learns features in the data set and adjusts the system parameters according to a given error criterion [2]. Successful implementations of ANFIS in biomedical engineering have been reported, for classification [3] and data analysis [4].

1.2

Magnetic Resonance Imaging

Magnetic resonance imaging (MRI) is a procedure used to produce high resolution images of the inside of the body, including the brain. MRI is a type of nuclear magnetic resonance (NMR), which is used by chemists to study the properties of molecules. The technique is called magnetic resonance imaging rather than nuclear magnetic resonance imaging because of the public's negative associations with the word nuclear in the late 1970's. MRI, like other imaging techniques such as CAT and PET, is primarily a tomography imaging technique

3 ("tomo" means slice). This means that it produces an image in a thin slice through the body. This form of imaging is, in some respects, very much like a real anatomical slice through the body. In fact, to the untrained eye, an MRI image may be indistinguishable from a slice taken from a post-mortem body. However, unlike a post-mortem slice, the MRI is formed by an MRI camera or scanner and the slices are composed of groups of picture elements or pixels displayed on a computer monitor. In MRI the subject or patient is placed inside the scanner which is made up of a moveable bed-like structure and a large hollow tube. The tube contains a thick coil of wire that generates a very intense magnetic field (between 1.5 and 4 Tesla) which is strong enough to accelerate a paper clip to near lethal velocities across the distance of a small room. In order to generate a magnetic field of this strength the coil is cooled to near absolute zero with liquid helium. This very strong magnetic field is then used to align the hydrogen nuclei of the tissue to be imaged. Also placed near the tissue to be imaged is another coil of wire called an RF coil (RF because it generates/reads radio frequency fields). The RF coil is used to both change the energy state of the hydrogen nuclei and to record the RF output of these perturbations. The latter are the raw data of an MRI which are recorded by the computer, transformed and then displayed [5]. Figure 1.1 shows a picture of an MRI machine and Figure 1.2 shows the schematic of an MRI machine.

Figure 1.1: MRI machine

Figure 1.2: Schematic diagram of MRI machine

In MRI, water molecules give off radio signals which are converted into high resolution images that look like a picture shown in figure 1.3.

Figure 1.3: Brain MRI

5 1.3 Problem Statement

The conventional method in medicine for brain MR images classification and tumor detection is human inspection. Operator-assisted classification methods are impractical for large amounts of data and are also non-reproducible. MR images also always contain a noise caused by operator performance which can lead to serious inaccuracies classification. The MR images data is by nature, a huge, complex and cognitive process. Accurate diagnosis of MR images data is not an easy task and is always time consuming. In some extreme scenario, diagnosis with wrong result and delay in delivery of a correct diagnosis decision could occur due to the complexity and cognitive process of which it is involved.

The use of artificial intelligent techniques for instance, neural networks, fuzzy logic, neuro fuzzy has shown great potential in this field. With the

involvement of soft computing, the pattern matching, classification and detection of algorithms which have direct applications in many medical problems have become much easier to be implemented and diagnosed.

Hence, this project tries to find out how the neuro fuzzy system or the hybrid combination of neural network and fuzzy logic techniques can be applied in the classification and detection purposes, particularly on the medical field.

1.4

Objectives

The main objective of this project is to propose an efficient classification technique for magnetic resonance (MR) images using neuro fuzzy. Hence, the study on the fundamental theory of neuro fuzzy system have to be done. This includes the neuro fuzzy architecture and the adaptation algorithm for the neuro fuzzy structure itself. The neuro fuzzy models hereby refer to the ANFIS (Adaptive Neuro Fuzzy Inference System). Besides, a sample medical image will be tested on the model to observe the classification and detection performance and subsequently optimization

6 of the chosen technique will be carried out. As the ultimate goal of this project, hopefully an automated system that provides high accuracy of brain medical images classification and symptoms detection that probably can replace the current human visual inspection methods is achieved.

1.5

Scope of Work and Methodology

The scope of the project is as follows:i. Convert the brain medical images into a form of data using MATLAB. ii. iii. iv. Process the brain medical images using PCA. Develop the neuro fuzzy algorithm for classification using MATLAB. The neuro fuzzy model considered hereby refers to ANFIS (Adaptive Neuro Fuzzy Inference System). v. vi. Deal only with the same size of the brain medical images slice. Distinguish between normal and abnormal of the brain medical images. vii. Extract the region of abnormal tissues using image processing tool in MATLAB. viii. ix. Training, testing and tuning or optimization parameters. Analyzing the neuro fuzzy model performance accuracy.

The methodologies of project are as follows: i. Involves the neuro fuzzy model coding, simulation, adaptation and training of the neuron using the MATLAB. ii. This project starts with converting the brain medical images into a form of data using MATLAB. iii. The brain medical images also have to be pre-processed using PCA to reduce the dimensionality of the data. iv. Classify the abnormal brain medical images based on the region of abnormal tissues using neuro fuzzy.

7 v. Then, this proposed technique will be coded in MATLAB and subsequently to be trained and tested with the brain medical images data. vi. Finally, optimize the performance of the proposed technique.

1.6

Thesis Outline

This thesis is organized as follows. In Chapter 1, some overview including the background, problem statement, objectives, scope of work and methodology are presented. Some literature reviews, related works and also theories regarding this project are included in Chapter 2. Chapter 3 contains a research methodology of the proposed method, the extraction of a region of interest, transformation of image into a form of data and also data and ANFIS modelling. The neuro fuzzy architecture and software development and implementation for classification are discussed in Chapter 4. Chapter 5 presents the result from the simulation and discusses the performance analysis. Lastly, the conclusion of this project and some recommendations for future work are discussed in Chapter 6.

CHAPTER 2

LITERATURE REVIEW

2.1

Related Works

This section will present some approaches that have been developed and used in MRI images. Rami J.Oweis et al., (2005) present the pixel classification of biomedical image using neuro fuzzy approach, where it uses neural networks ability to learn, and membership degrees and functions of fuzzy logic, respectively. The method is based on the spatial properties of the image features and makes use of multi-scaled representations of the image. A training set is used to create and train the classifier system. The classes are represented as fuzzy sets with degrees of memberships. Each pixel is assigned a degree of membership for each of the three fuzzy subsets. Classified pixels are finally shown as three separate images each representing a set. The method showed high quality classification for images of simple components.

N.Benamrane et al., (2006) has proposed an approach for detection and specification of anomalies present in medical images. The idea is to combine three metaphors: Neural Networks, Fuzzy Logic and Genetic Algorithms in a hybrid system. The Neural Networks and Fuzzy Logic metaphors are coupled in one system called Fuzzy Neural Networks. The Genetic Algorithm adds to this hybridizing the property of total research like an initialization of the Fuzzy Neural Networks training algorithm which is based on an adapted version of the back propagation algorithm. After applying the growing region algorithm to extract regions, the Fuzzy Neural

9 Network detects the suspect regions, which are interpreted by the Fuzzy Neural Network of specification.

Ian Middleton et al., (2003) reports on the combined use of a neural network(a multi layer perceptron, MLP) and active contour model (snake) to segment structures in magnetic resonance (MR) images. The perceptron is trained to produce a binary classification of each pixel as either a boundary or a non-boundary point. Subsequently, the resulting binary (edge-point) image forms the external energy function for a snake, used to link the candidate boundary points into a continuous, closed contour. The inputs to the MLP are limited to normalized intensity values of the pixels from a (7 7) window scanned across the image. The use of spatial coordinates as additional inputs to the MLP is then shown to provide an improvement in segmentation performance as quantified using the effectiveness measure (a weighted product of precision and recall). Training sets are first developed using a lengthy iterative process. Thereafter, a novel cost function based on effectiveness is proposed for training that allows us to achieve dramatic improvements in segmentation performance, as well as faster, non-iterative selection of training examples. The classifications produced using this cost function are sufficiently good since the binary image produced by the MLP can be post-processed using an active contour model to provide an accurate segmentation.

Ramiro Castellanos et al., (2000) have evaluated a segmentation technique for magnetic resonance (MR) images of the brain based on the adaptive fuzzy leader clustering (AFLC) algorithm. This approach performs vector quantization by updating the winning prototype of a competitive network through an unsupervised learning process. Segmentation of MR images is formulated as an unsupervised vector quantization process, where the value of a vigilance parameter restricts the number of prototypes representing the feature vectors.

Chin-Ming Hong et al., (2006) propose a novel neuro fuzzy network which can efficiently reason fuzzy rules based on training data to solve the medical diagnosis problems. This study proposes a refined K-means clustering algorithm and a gradient-based learning rule to logically determine and adaptively tune the fuzzy

10 membership functions for the employed neuro fuzzy network. In the meanwhile, this study also presents a feature reduction scheme based on the grey-relational analysis to simplify the fuzzy rules obtained from the employed neuro fuzzy network. Experimental results indicate that the proposed neuro fuzzy network with feature reduction can discover very simplified and easily interpretable fuzzy rules to support medical diagnosis.

S. Shen et al., (2003) show the neighborhood attraction based on the traditional fuzzy c-means (FCM) clustering algorithm to improve the segmentation performance. In this algorithm, two factors of neighborhood attraction are considered; one is the feature difference between neighboring pixels in the image, the other is the relative location of neighboring pixels. A histogram specification technique is applied on brain MR images before segmentation. The method can enhance the contrast between different brain tissues. Non-brain regions of all the MR images used in this paper have already been removed.

Yue Wang et al., (1997) present a probabilistic neural network based technique for unsupervised quantification and segmentation of the brain tissues from magnetic resonance image. The problem is formulated as distribution learning and relaxation labeling that may be particularly useful in quantifying and segmenting abnormal brain tissues where the distribution of each tissue type heavily overlaps. The new technique utilizes suitable statistical models for both the pixel and context images. The quantification is achieved by model-histogram fitting of probabilistic self-organizing mixtures and the segmentation by global consistency labeling through a probabilistic constraint relaxation network.

Clarke et al., (1995) has surveyed and presented some segmentation methods that have been proposed in medical image community. The image techniques used for brain segmentation could be divided in the following groups: threshold-based segmentation, statistical methods for brain segmentation and region growing methods. For all these groups many methods have been proposed in the literature but no one has been widely accepted in order to be used as a general method in clinics. In the category of threshold-based segmentation, use of: iterative thresholding,

11 histogram analysis and morphological operations are proposed. Some of these techniques are followed by some refinement of the segmented zones. Statistical methods represent another important category in the segmentation process and most of the approaches proposed in this category use some statistical classifications combined with different image processing techniques in order to segment the MR images. Also, the use of statistical methods in texture analysis has been proposed.

The segmentation problem widely encountered by researchers is the noise introduced with the acquisition of the image, the overlapping intensities (different brain structures have different tissue characteristics which results in various signal intensities and these intensities could overlap), the partial volume effect (when a pixel represents more than one kind of tissue type) and also some anatomical changes from one person to another. The blood vessels could also influence image that is taken and could introduce some noise. So, there are a lot of problems that researchers have to deal with in order to build an accurate segmentation system.

Since all these techniques have their advantages and drawbacks, more research is demanded in this domain and maybe some combination of the already existing methods or some new image processing techniques will lead to better results.

2.2

Artificial Neural Networks

2.2.1

Learning from Biology

A small neuron is a small cell that receives electrochemical stimuli from multiple sources and responds by generating electrical impulses that are transmitted to other neurons or effectors cells. There is something like 1010 to 1012 neurons in the human nervous system and each is capable of storing several bits of information. The total weight of an average brain is 1.5kg, so an average neuron weighs something less than 1.5 X 10-9 g.

12 Neurons receive input from sensory or other types of cells and send outputs to other neurons or effectors organs such as muscles and glands. About 10% of neurons are input (afferent) and output (efferent). The remaining 90% are interconnected with other neurons which store information or perform various transformations on the signals being propagated through the networks. Although many different types of neurons have been identified, they all share some common characteristics.

Neurons are complex cells that respond to electrochemical signals. They are composed of nucleus, a cell body, numerous dendrite links providing input connections from other neurons through synapses, and an axon trunk that carries an action potential output to other neurons through terminal links and synapses.

A single neuron may be connected to hundreds or even tens of thousands of other neurons. The connections are made through two general types of synapses, excitatory and inhibitory. Neural activity is related to the creation of an internal electric potential called a membrane potential. This potential may be increased or decreased by the input activity received from other cells through the synapses.

When the cumulative inputs raise the potential above a threshold value, the neuron fires by propagating a sequence of action potential spikes down the axon to either excite or inhibit other neurons. The pulses cause a chemical neurotransmitter substance to be released at the terminating synapses which, in turn, can excite or inhibit other neurons. The rate of pulse propagation ranges from about 5 to 125 ms-1, and the time required for a stimulus to traverse a synapse is about 10ms during which the neuron cannot fire again. The activity of a neuron is measured by the firing frequency of the potential analogue spikes which it generates. They range from about 50 to a few hundred spikes per second. Figure 2.1 below shows a simplified biological neuron.

13

Figure 2.1: Biology Neuron

Artificial Neural Networks (ANNs) are imitation of simplified models of the central nervous system. They are networks of highly interconnected neural

computing elements that have the ability to respond to input stimuli and to learn to adapt to the environment. Biological neurons or networks are able to process

millions of input stimuli in milliseconds even though the processes are electrochemical in nature and propagate at relatively slow milliseconds rates.

ANNs have been shown to be effective as computational processors for various tasks including pattern recognition in speech and visual image recognition, associative recall, classification, data compression, modeling and forecasting, combinational problem solving, adaptive control, multi sensor data fusion and noise filtering.

2.2.2

Generic Model of Neural Network

Although ANN architectures differ in several characteristic ways, a typical ANN neuron or computing element is basically a comparator that produces an output when the cumulative effect of the input stimuli exceeds a threshold value. Each input link i has an associated external input signal or stimulus xi and a corresponding weight wi, a sort of filter which is part of the linkage connecting the input to the

14 neuron. The xi values can be real (+ or -), binary (0, 1), or bipolar (-1, 1). This is shown in Figure 2.2.

Figure 2.2: Generic model of Artificial Neural Network

The weights, which model the synaptic neural connections in biological nets, act to either increase (excitatory) or decrease (inhibitory) the input signals to the neuron. The weights can also be binary or real-valued, but are usually assumed to be real (positive for excitatory and negative for inhibitory links). The outputs from the ANN can also be real-valued or binary or bipolar.

The neuron behaves as an activation or mapping function f(.) producing an output y = f(net), where net is the cumulative input stimuli to the neuron and f is typically a nonlinear function of net. Normally, net is often taken as the weighted sum of the inputs and f is typically a monotonic non-decreasing function of net and this can be summarized in the equation below.
net = x1 w1 + x 2 w2 + x3 w3 = xi wi
i =1 3

(2.1)

2.2.3

Bias and Threshold

A bias acts exactly like a weight and it is considered as a connection and its activation function is always 1. It is adapted similar to the way a weight is adapted according to the learning rule of the neural network. A bias is often used to increase

15 the signal levels in neural network, such as to improve convergence. However, some models of neural network do not use any bias signals.

A threshold or normally symbolized as , is a value that is used to make some form of decisions in an artificial neural network such that the neural network will fire or unfire. It is quite similar to a bias but not adaptable.

2.2.4

Activation Functions

In most neural network models, one of the above mentioned activation functions is used. The choice of the activation function strongly depends on the neural network model. In thermodynamic models a linear threshold function is normally used, and the activation values are chosen from {0,1} or {-1,1}. Multilayered models generally use a sigmoid activation function, and therefore have continuous activations, mostly chosen from [0, 1] or [-1, 1].

2.2.5

Network

A neural network is formed when we place units at the vertices of the directed graph, with the arcs of the digraph representing the flows of signals between units. Some of the units are termed input units: these receive signals not from other units, but instead they take their signals from the outside environment. Units that do not transmit signals to other units are termed output units. The network is said to be a feed-forward network when the units can be labeled with integers in such a way that there is a connection from the computation unit labeled i to the computation unit labeled j, then i < j and it also can be in multilayer networks. This is illustrated in the Figure 2.3 below.

16

Figure 2.3: Feedforward Network

2.2.6

Learning Phase

Basically, there are two ways of learning in artificial neural network which are supervised and unsupervised learning. The overall concept of learning is to

change the weights in the neuron in such a way that the error value is minimized for each pair of patterns of the fixed learning problem. As a stop criterion for the learning process, generally a total error E is used that is usually chosen to be the sum of the single error values. This total error is calculated anew after each epoch. An epoch is a complete run through the learning problem such that each pair of input / output patterns is processed once by the network using the learning algorithm. The learning process stops when the total error E is close enough to 0, or when the network is obviously not able to solve the learning problem.

A supervised learning algorithm can be divided into five steps: i. A pair of patterns of the learning problem is chosen and the input i presented to the neural network. ii. The input is then, propagated through the network, until it has reached its inoperative mode. iii. The output determined by the network is compared to the target pattern. The error value (e) is determined and added to the total error E. iv. If e 0, then the weights are changed in a way that a reduction of the absolute value of error.

17 v. When an epoch is over, total error, E is checked and when the stop condition reached, then, the learning process has ended successfully. Else, it will repeat the general steps above until it converges or reaches the stop condition, If the current epoch is not yet over, then the procedure continues with step (i) and the value of E is kept.

The most common supervised learning algorithms involve approximation of a gradient descent method and try to reduce the total error E to zero. However, this learning procedure cannot always guarantee convergence, because it is equivalent to a local heuristic search procedure. The algorithm stops when it reaches a local minimum. There are however, some disadvantages of this technique as the local minimum is not the global minimum. This means that the minimized error is not

reached and the learning process has failed.

On the other hand, unsupervised learning algorithm works on a free learning problem which only contains input patterns. However, for this kind of learning procedure the network is also supposed to map similar input patterns to output that are similar to each other. In unsupervised learning algorithm, the units compete with each other and the principle of winner-takes-all applied. It is trained without teaching signals or targets and it is only supplied with examples of the input patterns that it will solve eventually. This type of learning usually has an auxiliary cost function which needs to be minimized and the weights are modified where a cost function is minimized. At the end of the learning phase, the weights would have been adapted in such a manner such that similar patterns are clustered into a particular node.

2.3

Fuzzy Logic Systems

The theory of Fuzzy Logic was first raised by the mathematician Lotfi A. Zadeh in 1965. This theory is a result of the insufficiency of Boolean Algebra to many problems of the real world. As most of the information in the real world is

18 imprecise, and one of humans' greatest abilities is to effectively process imprecise and "'fuzzy" information.

According to the Oxford English Dictionary, the word Fuzzy is defined as blurred, indistinct, imprecisely defined, confused or vague. Fuzzy systems are knowledge based or rule based systems. The heart of a fuzzy system is a knowledge base consisting of the so called fuzzy IF-THEN rules. A fuzzy IF-THEN rule is an IF-THEN statement in which some words are characterized by continuous membership functions.

2.3.1

Advantages of Fuzzy Logic

Below are some reasons why we need to use fuzzy logic rather than linear system:

Fuzzy logic is conceptually easy to understand. The mathematical concepts behind fuzzy reasoning are very simple. What makes fuzzy nice is the "naturalness" of its approach and not its far-reaching complexity. Fuzzy logic is flexible. With any given system, it's easy to massage it or layer more functionality on top of it without starting again from scratch. Fuzzy logic is tolerant of imprecise data. Everything is imprecise if you look closely enough, but more than that, most things are imprecise even on careful inspection. Fuzzy reasoning builds this understanding into the process rather than tacking it onto the end. Fuzzy logic can model nonlinear functions of arbitrary complexity. A fuzzy system can be created to match any set of input-output data. This process is made particularly easy by adaptive techniques like Adaptive Neuro-Fuzzy Inference Systems (ANFIS), which are available in the Fuzzy Logic Toolbox. Fuzzy logic can be built on top of the experience of experts.

19 In direct contrast to neural networks, which take training data and generate opaque, impenetrable models, fuzzy logic lets you rely on the experience of people who already understand your system. Fuzzy logic can be blended with conventional control techniques. Fuzzy systems don't necessarily replace conventional control methods. In many cases fuzzy systems augment them and simplify their implementation. Fuzzy logic is based on natural language. The basis for fuzzy logic is the basis for human communication. This observation underpins many of the other statements about fuzzy logic.

The last statement is perhaps the most important one and deserves more discussion. Natural language, that which is used by ordinary people on a daily basis, has been shaped by thousands of years of human history to be convenient and efficient. Sentences written in ordinary language represent a triumph of efficient communication. We are generally unaware of this because ordinary language is, of course, something we use every day. Since fuzzy logic is built atop the structures of qualitative description used in everyday language, fuzzy logic is easy to use. [Jang and Sun, 1997].

2.3.2

Disadvantages of Fuzzy Logic

Fuzzy logic is not a cure-all. When should you not use fuzzy logic? The safest statement is the first one made in this introduction: fuzzy logic is a convenient way to map an input space to an output space. If it's not convenient, try something else. If a simpler solution already exists, use it. Fuzzy logic is the modification of common sense - use common sense when it is implemented and the right decision will probably been made. Many controllers, for example, do a fine job without using fuzzy logic. However, if time is taken to become familiar with fuzzy logic, a very powerful tool can be proved for dealing quickly and efficiently with imprecision and nonlinearity.

20 2.3.3 Fuzzy Sets

In the classical set theory a set can be represented by enumerating all its elements using A = {a1 , a 2 , a3 ......., a n } (2.2)

If these elements ai (i = 1,.....,n) of A are together a subset of the universal base set X, the set A can be represented for all elements x X by its characteristic function

A (x) =

1 0

if x A otherwise

(2.3)

In classical set theory A(x) has only the values 0 (``false'') and 1 (``true''), so two values of truth. Such sets are also called crisp sets. Non-crisp sets are called fuzzy sets, for which also a characteristic function can be defined. This function is a generalization of that in equation 2.3 and called a membership function. The membership of a fuzzy set is described by this membership function A(x) of A which associates to each element xo = X a grade of membership A(xo). In contrast to classical set theory a membership function A(x) of a fuzzy set can have in the normalized closed interval [0 1]. Therefore, each membership function maps elements of a given universal base set X which is itself a crisp set, into real numbers in [0,1]. The notation for the membership function, A(x) of a fuzzy set A is as equation 2.4 below.

A : X [0,1]

(2.4)

Each fuzzy set is completely and uniquely defined by one particular membership function. Consequently symbols of membership functions are also used as labels of the associated fuzzy sets, such as big, small and others. Figure 2.4 shows the differences in the crisp and fuzzy sets.

21

x Figure 2.4: Membership functions of a crisp set and a fuzzy set

2.3.4 Membership functions

The membership function A(x) describes the membership of the elements x of the base set X in the fuzzy set A, whereby for A(x) a large class of functions can be taken. Reasonable functions often used are linear functions, such as triangular or trapezoidal functions. The grade of membership A(x) of a membership function describes which grade it belongs to in the fuzzy set A. This value is in the unit interval [0,1]. This is shown in Figure 2.5.

x Figure 2.5: Membership grades of a fuzzy set

2.3.5

Components of a fuzzy system

There are basically four components in the fuzzy logic system which is fuzzification, inference engine, rule base and defuzzification. In some cases, a fuzzy system is drawn as a black box with some inputs and an output. Figure 2.6 shows the components of a fuzzy system.

22

Figure 2.6: Components of a Fuzzy Logic System

The first block inside the controller is fuzzification. Fuzzification is used to convert each piece of input data to degrees of membership by a lookup in one or several membership functions. The fuzzification block thus matches the input data with the conditions of the rules to determine how well the condition of each rule matches that particular input instance. There is a degree of membership for each linguistic term that applies to that input variable.

A fuzzy rule base consists of a set of fuzzy IF-THEN rules. It is the heart of the fuzzy system in the sense that all other components are used to implement these rules in a reasonable and efficient manner. Inference engine simply implies the combination of certain rules into a mapping from a fuzzy rule base to get some output corresponding to the inferred rules. There are two ways to infer with a set of rules which are composition based inference and individual rule based inference. In composition based inference, all rules in the fuzzy rule base is combined into a single fuzzy relation which is then viewed as a single fuzzy IF-THEN rule. Most common type of inference used is shown below:-

The fuzzy intersection operator (fuzzy AND connective) applied to two fuzzy sets A and B with the membership functions A(x) and B(x) is

A B ( x) = min{ A ( x), B ( x)},

x X

(2.5)

23 The fuzzy union operator (fuzzy OR connective) applied to two fuzzy sets A and B with the membership functions A(x) and B(x) is

A B ( x) = max{ A ( x), B ( x)},

x X

(2.6)

The fuzzy complement operator (fuzzy NOT operation) applied to the fuzzy sets A with the membership functions A(x) is

A ( x) = 1 A ( x),

x X

(2.7)

In individual rule base inference, each rule in the fuzzy rule base determines an output fuzzy set and the output of the whole fuzzy inference engine is the combination of many individual fuzzy sets. The combination can be taken either by union or by intersection. In general, there are three criteria of choosing the inference methods which are intuitive appeal, computational efficiency and special properties. For intuitive appeal, the choice should make sense from an intuitive point of view. Simple computation of fuzzy inference system is also one of the issues that need to be considered besides the intuitive issue and some inference need special properties.

The value inferred by the fuzzy rule base is in the fuzzy value or in other words, for every possible value , one gets a grade of membership that describes to what extent this value is reasonable to use. Defuzzification is used to transform fuzzy information into a single value. It is not a unique operation as different methods are possible. The most common are centre of gravity (COG), centre of singleton (COS), maximum membership, weight average and mean-max membership method.

24 2.3.6 Fuzzy Logic Graphical User Interface (GUI)

There are five primary GUI tools for building, editing, and observing fuzzy inference systems in the Fuzzy Logic package: 1. 2. 3. 4. 5. Fuzzy Inference System (FIS) Editor Membership Function Editor Rule Editor Rule Viewer Surface Viewer

Figure 2.7: Fuzzy Logic Graphical User Interface (GUI)

25 The FIS Editor handles the high-level issues for the system. Fuzzy Logic Toolbox software does not limit the number of inputs. However, the number of inputs may be limited by the available memory of the machine. If the number of inputs is too large, or the number of membership functions is too big, then it may also be difficult to analyze the FIS using the other GUI tools. The Membership Function Editor is used to define the shapes of all the membership functions associated with each variable. The Rule Editor is for editing the list of rules that defines the behavior of the system. The Rule Viewer and the Surface Viewer are used for looking at, as opposed to editing, the FIS. They are strictly read-only tools. The Rule Viewer is a MATLAB technical computing environment based display of the fuzzy inference diagram shown at the end of the last section. Used as a diagnostic, it can show (for example) which rules are active, or how individual membership function shapes are influencing the results. The Surface Viewer is used to display the dependency of one of the outputs on any one or two of the inputs-that is, it generates and plots an output surface map for the system.

2.4

Principal Component Analysis (PCA)

Principal Components Analysis (PCA) is a multivariate procedure which rotates the data such that maximum variability is projected onto the axes. Essentially, a set of correlated variables are transformed into a set of uncorrelated variables which are ordered by reducing variability. The uncorrelated variables are linear combinations of the original variables, and the last of these variables can be removed with minimum loss of real data.

The main use of PCA is to reduce the dimensionality of a data set while retaining as much information as is possible. It computes a compact and optimal description of the data set.

The first principal component is the combination of variables that explains the greatest amount of variation. The second principal component defines the next

26 largest amount of variation and is independent to the first principal component. There can be as many possible principal components as there are variables.

It can be viewed as a rotation of the existing axes to new positions in the space defined by the original variables. In this new rotation, there will be no correlation between the new variables defined by the rotation. The first new variable contains the maximum amount of variation; the second new variable contains the maximum amount of variation unexplained by the first and orthogonal to the first, etc.

It can be viewed as finding a projection of the observations onto orthogonal axes contained in the space defined by the original variables. The criteria being that the first axis "contains" the maximum amount of variation, or "accounts" for the maximum amount of variation. The second axis contains the maximum amount of variation orthogonal to the first. The third axis contains the maximum amount of variation orthogonal to the first and second axis and so on until one has the last new axis which is the last amount of variation left.

CHAPTER 3

RESEARCH METHODOLOGY

3.1

Methodology

Basically, two main phases are employed in this project which is theoretical phase and practical phase. Theoretical phase involves the process of reading and understanding, reviewing of theories, studying and surveying the ANFIS model, classification and detection techniques on medical image fields.

On the other hand, the practical phase involves medical image processing, neuro fuzzy model coding, simulation, assumptions, adaptation and training of the neuron and etc by using MATLAB.

3.2

Proposed Method

There are 7 stages involved in the proposed model which starts from the data input to output. The first stage is the image processing system. Basically in image processing system, image acquisition and enhancement are steps that need to be done. In this project, these two steps are skipped and all the images are collected from available resources. The proposed model requires converting the image into a format capable of being manipulated by the computer. The MR images are converted into matrices form by using MATLAB. Then, the neuro fuzzy model is developed using MATLAB programming. After the neuro fuzzy model is successfully developed, the classification of the MR images starts.

28 Symptoms detection phase will follow once the output from the classification technique is done and lastly, performance based on the result will be analyzed at the end of the development phase. The proposed brain MR images classification and detection method is shown in Figure 3.1.

MR Image Input

MATLAB

Data Form

Neuro Fuzzy Model

Classification & Detection

Output

Performance Analysis Figure 3.1: The proposed system

3.3

Transformation of Image to Data Form

The MR image will obtain and convert it to data form (encoded information that can be stored, manipulated and transmitted by digital devices) in MATLAB environment such as basic arithmetic operations (addition, subtraction, and multiplication) and indexing, including logical indexing reshaping, reordering, and concatenating. The basic data structure in MATLAB is the array, an ordered set of real or complex elements. This object is naturally suited to the representation of images, real-valued ordered sets of color or intensity data. MATLAB stores most images as two-dimensional arrays (i.e., matrices), in which each element of the

29 matrix corresponds to a single pixel in the displayed image. (Pixel is derived from picture element and usually denotes a single dot on a computer display.) For example, an image composed of 200 rows and 300 columns of different colored dots would be stored in MATLAB as a 200-by-300 matrix. This convention makes working with images in MATLAB similar to working with any other type of matrix data, and makes the full power of MATLAB available for image processing applications. An intensity image is a data matrix, whose values represent intensities within some range. MATLAB stores an intensity image as a single matrix, with each element of the matrix corresponding to one image pixel. The matrix can be of class double, uint8, or uintl6.

A simple program (shown in Appendix) is created to transform images. dot of pixel labelling and also region of interest extraction. Initially, this program asked the user to insert normal brain image as the prior image and then insert an abnormal brain image as a diagnostic image. Both images are converted to matrix format automatically while the image being read in the MATLAB environment. Both images are obtained in the RGB format. An RGB image is stored in MATLAB as an m-by-n-by-3 data array that defines red, green, and blue color components for each individual pixel. If it is difficult to manipulate, it must be converted to intensity format. An intensity image is a data matrix, whose values represent intensities within some range. MATLAB stores an intensity image as a single matrix, with each element of the matrix corresponding to one image pixel. The elements in the intensity matrix represent various intensities, or gray levels, where the intensity 0 usually represents black and the intensity 1, 255 or 65535 usually represent full intensity, or white. Both intensity of normal brain and abnormal brain images are converted to binary images as shown in Figure 3.2.

The 'bwarea' function is used to convert the area to binary image. The area is a measure of the size of the foreground of the image. In other words, the area is the number of on pixels in the image. Comparison between the areas of the normal and the abnormal brain in a binary image is a technique used to make sure the size of both brain images are the same.

30

Figure 3.2: Convert brain image to binary image

3.4

Pixels Labeling

In succession, every dot of pixel will be labeled in different coordinates. Generally in the Matlab environment, the most convenient method for expressing locations in an image is to use pixel coordinates. Under this coordinate system, the image is treated as a grid of discrete elements, ordered from top to bottom and left to right, as illustrated in Figure 3.3.

Figure 3.3: Pixel coordinate system

For pixel coordinates, the first component r (the row) increases downwards, while the second component c (the column) increases to the right. Pixel coordinates are integer values and range between 1 and the length of the row or column. There is a one-to-one correspondence between pixel coordinates and the coordinates MATLAB uses for matrix subscripting. This correspondence makes the relationship

31 between an image's data matrix and the way the image is displayed easy to understand. For example, the data for the pixel in the fifth row, second column is stored in the matrix element (5, 2).

By using the existing pixel coordinate system, advanced coordinate system will be created. It means that, every dot of pixel coordinate in a single number. For instance, pixel in the first row, first column is stored in the single number 1; however pixel in the first row, second column is stored in the single number 2 and so on. Figure 3.4 shows the advanced coordinate system for matrix 16 by 16.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16

17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32

33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64

65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80

81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96

97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112

113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128

129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144

145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160

161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176

177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192

193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208

209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224

225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240

241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256

Figure 3.4: Advanced coordinate system for matrix 16 by 16

3.5

Region of Interest Extraction

The region of interest is determined by subtracting the normal brain image with abnormal image brain image as shown in Figure 3.5.

32 Normal Brain Abnormal Brain

Region of Interest

Figure 3.5: Location of tumor

The elements in the intensity matrix represent various intensities, or grey levels, where the intensity 0 usually represents black and the intensity 1, 255, or 65535 usually represents full intensity, or white.

3.6

Feature Extraction using Principal Component Analysis (PCA)

In this project, the principal component analysis (PCA) is used as a feature extraction algorithm. The principal component analysis (PCA) is one of the most successful techniques that have been used in image recognition and compression. The purpose of PCA is to reduce the large dimensionality of the data.

33 MR image recognition systems find the identity of a given test image according to their memory. The memory of an MR image recognizer is generally simulated by a training set. In this project, the training database consists of a set of MR images. Thus, the task of the MR image recognizer is to find the most similar feature vector among the training set to the feature vector of a given test image.

In the training phase, feature vectors are extracted for each image in the training set. Let
1

be a training image of image 1 which has a pixel resolution of M

1,

x N (M rows, N columns). In order to extract PCA features of

first convert the

image into a pixel vector 1 by concatenating each of the M rows into a single vector. The length (or, dimensionality) of the vector 1 will be M x N. In this project, the PCA algorithm is used as a dimensionality reduction technique which transforms the vector 1 to a vector 1 which has a dimensionality d where d << M x N. For each training image
i,

these feature vectors i are calculated and stored.

In the testing phase, the feature vector j of the test image using PCA. In order to identify the test image
j,

is computed

the similarities between j and all

of the feature vectors is in the training set are computed. The similarity between feature vectors is computed using Euclidean distance. The identity of the most similar i is the output of the image recognizer. If i = j, it means that the MR image j has correctly identified, otherwise if i j, it means that the MR image j has misclassified. Schematic diagram of the MR image recognition system that is implemented is shown in Figure 3.6.

34

Figure 3.6: Schematic diagram of a MR image recognizer.

3.7

Data Modeling

Eventually, a training data set that contains the desired input/output data pairs of the targeted system is modeled. The coordinated abnormal tissues which are in the matrix form are presented to ANFIS for training (estimating) membership function parameters. They fully represent the features of the data that the trained FIS intends to model. This project uses the ANFIS Editor GUI menu bar to load a FIS training initialization, and then save the trained FIS. From this GUI:

l. Load data (training) by selecting the appropriate radio buttons in the Load data portion of the GUI and then clicking Load Data. The loaded data is plotted on the plot region.

35 2. Generate an initial FIS model or load an initial FIS model using the options in the Generate FIS portion of the GUI. 3. View the FIS model structure once an initial FIS has been generated or loaded by clicking the Structure button. 4. Choose the FIS model parameter optimization method backpropagation or a mixture of backpropagation and least squares (hybrid method). This research uses the default hybrid method as the FIS model parameter optimization method. 5. Choose the number of training epochs and the training error tolerance. This research uses 0 as training epochs and 40 as training error tolerance. 6. Train the FIS model by clicking the Train Now button. This training adjusts the membership function parameters and plots the training error plot(s) in the plot region. 7. View the FIS model output versus the training, checking, and testing data output by clicking the Test Now button. This function plots the rest data against the FIS output in the plot region.

The training data is a required argument to the ANFIS Editor GUI. Each row of the training data is a desired input/output pair of the target system to be modeled. Each row starts with an input vector and is followed by an output value. Therefore, the number of rows of the training data is equal to the number of training data pairs, and, since there is only one output, the number of columns training data is equal to the number of inputs plus one. Figure 3.7 shows the training data set for this research.

36

Input vector

Output

Figure 3.7: Training Data Set

After data modeling by ANFIS, read this fuzzy inference system from an anfis.fis file on the disk and bring the resulting file into workspace. To evaluate the output of a fuzzy system for a given input, use the function evalfis. The evalfis has the following arguments.

Input: a number or a matrix specifying input values. If input is an M-by-N matrix, where N is a number of input variables, then evalfis takes each row of input as an input vector and returns the M-by-L matrix to the variable, output, where each row is an output vector and L is the number of output variables.

Fismat: a FIS structure to be evaluated. Output: the output matrix of size M-by-L, where M represents the number of input values specified above, and L is the number of output variables for the FIS.

Figure 3.8 shows the Basic flow diagram of computations or algorithm in ANFIS:

37

Initialize the fuzzy system Use genfis1 command

Give other parameters for learning Important are: Number of iterations (epochs) Tolerance (error)

Start learning process Use anfis command Stop when tolerance is achieved

Validation data Use evalfis command Figure 3.8: Basic flow diagram of computations in ANFIS

3.8

System developing

3.8.1

Data Management and Preparation

As this project fully use the MATLAB software, it is advisable to know its data management system. To work with m-files and data, all files are placed in a folder included in the MATLAB working path. The working path is a collection of folders where MATLAB searches files when these are called. Any file located outside this path will be invisible to MATLAB.

The working path is accessible by clicking the Path Browser button in the MATLAB command window, or typing path in the prompt. The most practical solution for beginners is to place files in the folder /MATLAB/Work, usually the

38 default current directory (i.e. the folder where MATLAB preferentially loads or saves data). An error will occur if m-files files are not in its directory. It means that the current directory is not in the folder.

The MATLAB working path is easily edited with the Path Browser tool. But we recommend beginners to work with the /MATLAB/Work folder as the working directory, and only edit the MATLAB working path if either this folder is absent or it is not the current directory. MATLAB is case sensitive. Thus, any data file or m-file should be named properly.

3.8.2

Data Mining

The data are provided from the transformation MR images into data form as explained before. It has a total of 50 data with 3 inputs and 1 output. The data is divided into 3 partition which are training, checking and application. Training data has 20 patterns, checking takes around 5 patterns and the rest which is 25 patterns are used for application purposes. Training data means that the data is used for ANFIS training and checking on the other hand, is used to check the model created. Application data is a collection of untrained data needed in testing the accuracy of the model.

The main program is developed in 4 phases which are input phase, classification and FIS phase, ANFIS phase, output phase (application and detection) and is explained in details below.

3.8.3

Input Phase

In this phase, the user is required to enter the files that have been partitioned accordingly by keying the file name in the space provided. In this package development, 4 main input files are needed. They are training data file, checking data

39 file, target data file and application data file including expected result data file. For the training data file, it is advisable to contain the data only and not combined together with training target. On the other hand, the checking file that is used for model checking and validation should contain data and training target together, arranged in rows and columns.

Application data purely contain the untrained data and is subjected to test the accuracy of the model. A convenient format to work with MATLAB is ASCII. It is always an easy way to paste data from a spreadsheet in the Windows Notepad and saving it under extension dat. User also is required to enter the total number of cluster and epochs required for training purposes. All data and m-files should be placed in a folder included in the MATLAB working path. Figure 3.9 shows a partial of the input phase and full coding can be accessed in Appendix.

Figure 3.9: Partial of input phase

3.8.4

FIS Phase

After the input phase, relevant data files will be loaded for Fuzzy Inference System (FIS) building. The fuzzy inference system is summarized in a function called genfis1. Genfis1 basically generates initial fuzzy inference system for ANFIS training by first applying classification technique on the data. Genfis1 function

40 requires 3 main inputs which are training data without target, target data and number of membership function required. Output from genfis1 is considered as initial information for building the fuzzy inference system which is useful for ANFIS training. This is accomplishes by extracting a set of rules that models the data behavior. Figure 3.10 shows a sample of generated fuzzy inference.

Figure 3.10: FIS generated thru genfis1

3.8.5

ANFIS modeling phase

This phase is fully the training of ANFIS model. The data such as number epoch and fuzzy inference system (FIS) is used to train and validate the ANFIS model. Information regarding the ANFIS model will prompt at the early of the process as shown in Figure 3.11. Result from training error and checking error will be calculated depending on the step size and is in matrix form. The second column shows the training error and third column indicates the checking error. Figure 3.12 shows the errors regarding to the number of epoch and the total time required for ANFIS training.

41

Figure 3.11: Information of the ANFIS model

Figure 3.12: ANFIS training errors and total time training

42

3.8.6

Output phase

The output phase involves the application of the model to observe how well the model reacts to the untrained data and also the detection of abnormal tissue based on the data itself. User is required to enter the application file name and also the expected result. By making comparison between the expected result and output from the ANFIS model, the class of the abnormal tissue can be determined. Figure 3.13 shows an example of the result.

Figure 3.13: Sample of classification results

CHAPTER 4

NEURO FUZZY MODELING AND SOFTWARE IMPLEMENTATION

4.1

Neuro Fuzzy Model

A neuro fuzzy system is a combination of neural network and fuzzy systems in such a way that neural network or neural network algorithms are used to determine the parameters of the fuzzy system. This means that the main intention of neuro fuzzy approach is to create or improve a fuzzy system automatically by means of neural network methods. An even more important aspect is that the system should always be interpretable in terms of fuzzy if-then rules, because it is based on a fuzzy system reflecting vague knowledge.

The idea of a neuro fuzzy system is to find the parameters of a fuzzy system by the means of learning methods obtained from neural network. A common way to apply a learning algorithm to a fuzzy system is to represent it in a special neuralnetwork-like architecture. Then a learning algorithm such as back propagation is used to train the system. However, neural network learning algorithms are usually gradient descent methods. This cannot be applied directly to a fuzzy system, because the functions used to realize the inference process are usually not differentiable. In order to realize the system, we need to replace the functions used in the fuzzy system (like min and max) by differentiable functions or do not use a gradient-based neural learning algorithm but a better-suited procedure.

44 Modern neuro fuzzy systems are often represented as multilayer feed forward neural network. A neuro fuzzy system is a fuzzy system that is trained by a learning algorithm (usually) derived from neural network theory. The (heuristic) learning procedure operates on local information, and causes only local modifications in the underlying fuzzy system. The learning process is not knowledge-based, but datadriven. Besides, a neural-fuzzy system can always be interpreted as a system of fuzzy rules. It is possible both to create the system out of training data from scratch, and to initialize it from prior knowledge in the form of fuzzy-rules.

The learning procedure of a neural-fuzzy system takes the semantical properties of the underlying fuzzy system into account. This results in constraints on the possible modification of the systems parameters. It also approximates an ndimensional (unknown) function that is partially given by the training data. The fuzzy rules encoded within the system represent vague samples, and can be viewed as vague prototypes of the training data.

Generally, a neuro fuzzy system should not be seen as a kind of (fuzzy) expert system, and it has nothing to do with fuzzy logic in the narrow sense. It can be viewed as a special kind of feed forward neural network. The units in this network use t-norms or t-conorms instead of the activation functions normally used in neural networks. Fuzzy sets are encoded as (fuzzy) connection weights.

4.2

Adaptive neuro-fuzzy inference system (ANFIS)

A neuro-fuzzy (ANFIS) system is a combination of neural network and fuzzy systems in such a way that neural network is used to determine the parameters of fuzzy system. ANFIS largely removes the requirement for manual optimization of the fuzzy system parameters. A neural network is used to automatically tune the system parameters, for example the membership functions bounds, leading to improved performance without operator invention.

45 The neuro fuzzy system with the learning capability of neural network and with the advantages of the rule-base fuzzy system can improve the performance significantly and can provide a mechanism to incorporate past observations into the classification process. In neural network the training essentially builds the system. However, using a neuro fuzzy scheme, the system is built by fuzzy logic definitions and is then refined using neural network training algorithms. Some advantages of ANFIS are: Refines fuzzy if-then rules to describe the behaviour of a complex system. Does not require prior human expertise o uses membership functions plus o desired dataset to approximate Greater choice of membership functions to use. Very fast convergence time.

4.2.1

ANFIS Architecture

The ANFIS is a fuzzy Sugeno model put in the framework of adaptive systems to facilitate learning and adaptation (Jang, 1992, 1993). Such framework makes the ANFIS modeling more systematic and less reliant on expert knowledge. To present the ANFIS architecture, two fuzzy if-then rules based on a first order Sugeno model are considered:

Rule 1: If (x is A1) and (y is B1) then (f1 = p1x + q1y + r1) Rule 2: If (x is A2) and (y is B2) then (f2 = p2x + q2y + r2)

where x and y are the inputs, Ai and Bi are the fuzzy sets, fi are the outputs within the fuzzy region specified by the fuzzy rule, pi, qi and ri are the design parameters that are determined during the training process. Figure 4.1 illustrates the reasoning mechanism for this Sugeno model where it is the basis of the ANFIS model.

46

Figure 4.1: A two-input first-order Sugeno fuzzy model with two rules

The ANFIS architecture to implement these two rules is shown in Figure 4.2, in which a circle indicates a fixed node, whereas a square indicates an adaptive node. Adaptive neuro fuzzy inference system basically has a 5 layer architectures and each of the function is explained in detail later.

Figure 4.2: ANFIS architecture.

In the first layer, all the nodes are adaptive nodes. The outputs of layer 1 are the fuzzy membership grade of the inputs, which are given by:

O1,i = Ai (x) O1,i = Bi2 (y)

i = 1, 2 i = 3, 4.

(4.1) (4.2)

47 where Ai(x), Bi2(y) can adopt any fuzzy membership function. For example, if the bell shaped membership function is employed, Ai (x) is given by:

A ( x) =

1 x ci 1+ ai
2b

(4.3)

where ai, bi and ci are the parameters of the membership function, governing the bell shaped functions accordingly.

In the second layer, the nodes are fixed nodes. They are labeled with , indicating that they perform as a simple multiplier. The outputs of this layer can be represented as:

O2,i = wi = Ai (x) Bi (y)

i = 1,2.

(4.4)

which are the so-called firing strengths of the rules.

In the third layer, the nodes are also fixed nodes labeled by N, to indicate that they play a normalization role to the firing strengths from the previous layer. The output of this layer can be represented as:

O3,i = wi =

wi , wi + w2

i = 1, 2.

(4.5)

which are the so-called normalized firing strengths.

In the fourth layer, the nodes are adaptive. The output of each node in this layer is simply the product of the normalized firing strength and a first order polynomial (for a first order Sugeno model). Thus, the output of this layer is given by: O4,i = wi f i = wi ( pi x + q i y + ri ) i = 1, 2 (4.6)

48 In the fifth layer, there is only one single fixed node labeled with . This node performs the summation of all incoming signals. Hence, the overall output of the model is given by:

O 5,i = wi f i =
i

wf w
i i i i

(4.7)

It can be observed that there are two adaptive layers in this ANFIS architecture, namely the first and the fourth layers. In the first layer, there are three modifiable parameters {ai, bi, ci}, which are related to the input membership functions. These parameters are the so-called premise parameters. In the fourth layer, there are also three modifiable parameters {pi, qi, ri}, pertaining to the first order polynomial. These parameters are the so-called consequent parameters (Jang, 1992, 1993).

Figure 4.3 shows the variation in the Sugeno model that is equivalent to a two-input first-order Sugeno fuzzy model with nine rules, where each input is assumed to have three associated MFs. Figure 4.4 illustrates how the two

dimensional input space is partitioned into nine overlapping fuzzy regions, each of which is governed by a fuzzy if-then rule. In other words, the premise part of a rule defines a fuzzy region, while the consequent part specifies the output within the region.

49

Figure 4.3: Two-input first-order Sugeno fuzzy model with nine rules

Figure 4.4: The input space that are partitioned into nine fuzzy regions

4.2.2

Learning algorithm of ANFIS

The task of the learning algorithm for this architecture is to tune all the modifiable parameters, namely {ai, bi, ci} and {pi, qi, ri}, to make the ANFIS output match the training data. When the premise parameters ai, bi and ci of the membership function are fixed, the output of the ANFIS model can be written as:

50

f =

w1 w2 f1 + f2 w1 + w2 w1 + w2

(4.8)

Substituting Eq. (5) into Eq. (4.8) yields:

f = w1 f 1 + w2 f 2

(4.9)

Substituting the fuzzy if-then rules into Eq. (4.9), it becomes:

f = w1 ( p1 x + q1 y + r1 ) + w2 ( p 2 x + q 2 y + r2 )

(4.10)

After rearrangement, the output can be expressed as: f = ( w1 x) p1 + ( w1 y )q1 + ( w1 )r1 + ( w2 x) p 2 + ( w2 y )q 2 + ( w2 )r2

(4.11)

which is a linear combination of the modifiable consequent parameters p1, q1, r1, p2,

q2 and r2. The least squares method can be used to identify the optimal values of
these parameters easily. When the premise parameters are not fixed, the search space becomes larger and the convergence of the training becomes slower. A hybrid algorithm combining the least squares method and the gradient descent method is adopted to solve this problem. The hybrid algorithm is composed of a forward and a backward pass. The least squares method (forward pass) is used to optimize the consequent parameters with the premise parameters fixed. Once the optimal consequent parameters are found, the backward pass starts immediately. The gradient descent method (backward pass) is used to adjust optimally the premise parameters corresponding to the fuzzy sets in the input domain. The output of the ANFIS is calculated by employing the consequent parameters found in the forward pass. Table 4.1 summarizes the activities in each pass. The output error is used to adapt the premise parameters by means of a standard backpropagation algorithm. It has been proven that this hybrid algorithm is highly efficient in training the ANFIS (Jang, 1992, 1993).

51
Forward pass Premise parameters Consequent parameters Signals Fixed Least-squares estimator Node outputs Backward pass Gradient descent Fixed Error signals

Table 4.1: Two Passes in the Hybrid Learning Procedure for ANFIS

4.2.3

ANFIS Classifier

Both neural network and fuzzy logic are universal estimators. They can approximate any function to any prescribed accuracy, provided that sufficient hidden neurons and fuzzy rules are available. Gradient descent and Backpropagation algorithms are used to adjust the parameters of membership functions (fuzzy sets) and the weights of defuzzification (neural networks) for fuzzy neural networks. ANFIS applies two techniques in updating parameters. The ANFIS is a FIS implemented in the framework of an adaptive fuzzy neural network. It combines the explicit knowledge representation of a FIS with the learning power of ANNs. The objective of ANFIS is to integrate the best features of fuzzy systems and neural network. The advantage of fuzzy is that prior knowledge is represented into a set of constraints to reduce the optimization research space. The adaptation of back propagation to structured network so as to automate fuzzy control parametric tuning is utilized from NN. For premise parameters that define membership functions, ANFIS employs gradient descent algorithm to fine-tune them. For consequent parameters that define the coefficients of each equation, ANFIS uses the leastsquares method to identify them. This approach is thus called hybrid learning method since it combines gradient descent algorithm and least-squares method. To achieve good generalization of unseen data, the size of the training data set should be at least as big as the number of modifiable parameters in ANFIS. Functionally there are almost no constrains on the node functions of an adaptive network except for the requirement of piecewise differentiability. The neurons in ANFIS have different structures.

52 The Membership function is defined by parameterized soft trapezoids (Generalized Bell Functions). The rules are differentiable T-norm usually product. The Normalization is by Sum and arithmetic division. Functions are linear regressions and multiplication with w , that is, normalized weights , and Output (Algebraic Sum).

4.3

ANFIS editor GUI

The ANFIS Editor GUI menu bar can be used to load a FIS training initialization, save the trained FIS, open a new Sugeno system or any of the other GUIs to interpret the trained FIS model. Any data set is loaded into the ANFIS Editor GUI, (or that is applied to the command-line function ANFIS) must be a matrix with the input data arranged as vectors in all but the last column. The output data must be in the last column. A sample of ANFIS Editor GUI with input is shown in Figure 4.5.

53

Figure 4.5: ANFIS Editor GUI

4.4

FIS Editor

The FIS Editor displays general information about a fuzzy inference system. There is a simple diagram at the top that shows the names of each input variable on the left, and those of each output variable on the right. The sample membership functions shown in the boxes are just icons and do not depict the actual shapes of the membership functions. This is shown in Figure 4.6.

54

Figure 4.6: FIS Editor

4.5

Membership Functions Editor

The Membership Function Editor shares some features with the FIS Editor. In fact, all of the five basic GUI tools have similar menu options, status lines, and Help and Close buttons. The Membership Function Editor is the tool that lets you display and edits all of the membership functions associated with all of the input and output variables for the entire fuzzy inference system. Figure 4.7 shows the membership function editor.

55

Figure 4.7: Membership Function Editor

4.6

Rule Editor

The Rule Editor allows user to construct the rule statements automatically, by clicking on and selecting one item in each input variable box, one item in each output box, and one connection item as in Figure 4.8. Choosing none as one of the variable qualities will exclude that variable from a given rule. Choosing not under any variable name will negate the associated quality. Rules may be changed, deleted, or added, by clicking the appropriate button.

56

Figure 4.8: Rule Editor

4.7

Rule Viewer

The Rule Viewer allows users to interpret the entire fuzzy inference process at once. The Rule Viewer also shows how the shape of certain membership functions influences the overall result. Since it plots every part of every rule, it can become unwieldy for particularly large systems, but, for a relatively small number of inputs and outputs, it performs well (depending on how much screen space we devote to it) with up to 30 rules and as many as 6 or 7 variables. The Rule Viewer shows one calculation at a time and in great detail. In this sense, it presents a sort of micro view of the fuzzy inference system.

57

Figure 4.9: Rule Viewer

4.8

ANFIS Model Structure

After the FIS is generated, the model structure can be viewed by clicking the Structure button in the middle of the right side of the GUI. A GUI can be seen in Figure 4.10. The branches in this graph are color coded. Color coding of branches characterize the rules and indicate whether or not and, not, or or are used in the rules. The input is represented by the left-most node and the output by the right-most node. The node represents a normalization factor for the rules. Clicking on the nodes indicates information about the structure.

58

Figure 4.10: ANFIS Model Structure

4.9

Modeling Data through ANFIS

The modeling approach used by ANFIS is similar to many system identification techniques. First, a parameterized model structure (relating inputs to membership functions to rules to outputs to membership functions, and so on) is hypothesized. Next, input/output data is collected in a form that will be usable by ANFIS for training. ANFIS can then be used to train the FIS model to emulate the training data presented to it by modifying the membership function parameters according to a chosen error criterion. Figures 4.11 and 4.12 show the example training error in ANFIS and output of the ANFIS.

In general, this type of modeling works well if the training data presented to ANFIS for training (estimating) membership function parameters is fully representative of the features of the data that the trained FIS intend to model. This is

59 not always the case, however. In some cases, data is collected using noisy measurements, and the training data cannot be representative of all the features of the data that will be presented to the model. This is where model validation comes into play. [Jang, 1993].

Figure 4.11: Training Error

60

Figure 4.12: Output of ANFIS

4.10

Model Validation (Checking and Testing Data)

Model validation is the process by which the input vectors from input/output data sets on which the FIS was not trained, are presented to the trained FIS model, to see how well the FIS model predicts the corresponding data set output values. This is accomplished with the ANFIS Editor GUI using the so-called testing data set, and its use is described in a subsection that follows.

Another type of data set can also be used for model validation in ANFIS. This other type of validation data set is referred to as the checking data set and it set is used to control the potential for the model over fitting the data. When the checking and training data are presented to ANFIS, the FIS model having parameters associated with the minimum checking data model error is then selected.

61 One problem with model validation for models constructed using adaptive techniques is selecting a data set that is both representative of the data the trained model intends to emulate, yet sufficiently distinct from the training data set so as not to render the validation process trivial. If a large amount of data has been collected, hopefully this data contains all the necessary representative features, so the process of selecting a data set for checking or testing purposes is made easier.

CHAPTER 5

RESULTS AND DISCUSSIONS

5.1

Result

Various experiments were performed and the sizes of the training and testing sets were determined by taking into consideration the classification accuracies. The data set was divided into two separate data sets the training data set (20 subjects) and the testing data set (15 subjects). The training data set was used to train the ANFIS, whereas the testing data set was used to verify the accuracy and the effectiveness of the trained ANFIS model for the detection of brain tumors. The partition of data used is shown in Figure 5.1 which is in the form of bar chart.

Figure 5.1: Training and Checking Data

63 The classifier is able to differentiate between normal and abnormal brain. There were a total of 27 fuzzy rules in the architecture of the ANFIS using a 3-type (generalized bell, triangular and pi) shaped membership function. The ANFIS was implemented by using MATLAB software package. The ANFIS used 20 training data in 40 training periods and the step size for parameter adaptation had an initial value of 0.01. At the end of 40 training periods, the final error convergence value is 2.5x10-3 as shown in Figure 5.2. The overall result regarding to the ANFIS errors can be seen in Table 5.1.

Figure 5.2: ANFIS Errors

Type of error Average Training Error 0.0038 Checking Error 0.1296 Global Error 0.0667 Table 5.1: The ANFIS Errors

64 5.2 Performance Analysis

In a real world domain, just like the one used in the present study, all of the features used in the descriptions of instances may have different levels of relevancy. Therefore, in the present study changes of the final (after training) membership functions with respect to the initial (before training) membership functions of the input parameters were examined. Membership function of each input parameter was divided into three regions, namely, small, medium, and large. The examination of initial and final membership functions indicates that there are considerable changes in the final membership functions but the change is very small due to less the number of data training. Figure 5.4 shows the initial and final membership function of inputs 1, 2 and 3 using the generalized bell, triangular and pi shaped membership function.

The outputs of ANFIS are shown in Figure 5.3. The proposed method gives a framework to detect more brain tumors using ANFIS method for the classification.

Figure 5.3: The misclassified output of ANFIS classifier

65

a)

b) Figure 5.4: a) Membership function before training b)Membership function after training.

66

After training, 15 testing data was used to validate the accuracy of the ANFIS classifier for the detection of brain tumors. The test results of the ANFIS are presented in Table 5.2. According to Table 5.2, 1 subject was classified incorrectly by the ANFIS. The test performance of the ANFIS was determined by the computation of the statistical parameters such as specificity, sensitivity and accuracy. The values of these statistical parameters are given in Table 5.3. As seen from that table, the ANFIS classified MRI and Iris subjects with the accuracy of 93.33% and 96%, respectively.

Type of Data MRI Iris

Number of subjects 15

Number of subjects classified correctly 14

25 24 Table 5.2: The ANFIS Test Results

Statistical parameters Specificity Sensitivity

Values 93.33% 96%

Accuracy 94.67% Table 5.3: The Values of Statistical Parameters

5.3

Noise Consideration

The training data set in this project is 0% noise implemented. The different percentage of noise which is 1%, 2% and 3% are implemented to the testing data set to look the performance of the ANFIS classifier with noise consideration. Tables 5.4, 5.5 and 5.6 show the testing data set with 1%, 2% and 3% noise respectively. Results from the ANFIS classifier are all displayed as a summary of the performance on the test data. An investigation is carried out to see the performance of this classifier when noise increases. The outputs of ANFIS are shown in Figure 5.5 to 5.7.

67

1237 1811 933 2403 1583 1176 1750 868 2344 1584 1177 1688 865 2470 1582

1238 1812 934 2404 1584 1177 1751 869 2345 1585 1179 1689 866 2471 1583

1251.37 1831.11 944.33 2429.03 1600.83 1189.76 1769.5 878.68 2369.44 1663.84 1191.77 1706.88 875.65 2557.7 1657.82

Table 5.4: Testing Data Set with 1% Noise

1237 1811 933 2403 1583 1176 1750 868 2344 1584 1177 1688 865 2470 1582

1238 1812 934 2404 1584 1177 1751 869 2345 1585 1179 1689 866 2471 1583

1263.74 1849.22 953.66 2453.06 1616.66 1201.52 1787 887.36 2392.88 1679.68 1203.54 1723.76 884.3 2582.4 1673.64

Table 5.5: Testing Data Set with 2% Noise

68

1237 1811 933 2403 1583 1176 1750 868 2344 1584 1177 1688 865 2470 1582

1238 1812 934 2404 1584 1177 1751 869 2345 1585 1179 1689 866 2471 1583

1276.11 1867.33 962.99 2477.09 1632.49 1213.28 1804.5 896.04 2416.32 1695.52 1215.31 1740.64 892.95 2607.1 1689.46

Table 5.6: Testing Data Set with 3% Noise

Figure 5.5: The misclassified output of ANFIS classifier with 1% noise

69

Figure 5.6: The misclassified output of ANFIS classifier with 2% noise

Figure 5.7: The misclassified output of ANFIS classifier with 3% noise

70

Percentage of Noise 1% 2% 3%

Number of Subjects 15 15 15

Number of subjects classified correctly 11 8 6

Table 5.7: The ANFIS Test Results with Noise Consideration

5.4

Comparisons of Result

Probabilistic Neural Network (PNN) is used as the border line or benchmark for this project in investigating the classification of data. Results from the PNN classifier are all displayed as a summary of the performance on both training and test data. By using the SPREAD value of 10 the PNN classifier has misclassified 2 out of 15 subjects. Performance from the PNN and ANFIS method is compared and it is summarized in Table 5.9.

1237 1811 933 2403 1583 1176 1750 868 2344 1584 1177 1688 865 2470 1582

Input Vector 1238 1239 1812 1813 934 935 2404 2405 1584 1585 1177 1178 1751 1752 869 870 2345 2346 1585 1648 1179 1180 1689 1690 866 867 2471 2533 1583 1642 Table 5.8: PNN Target Results

Target 1 2 3 4 5 1 2 3 4 5 1 5 3 1 5

71

Methods Application Data Overall Misclassified Performance Rating

PNN 15 2 86.67%

ANFIS 15 1 93.33%

Table 5.9: Comparison between PNN and ANFIS

Classification Results
100 86.67 80 60 40 20 0 2 PNN 1 ANFIS Performance Rating 93.33

Overall Misclassified

Figure 5.8: Chart Comparison

CHAPTER 6

CONCLUSIONS AND FUTURE WORKS

6.1

Conclusions

Medical image classification is an important thing in medicine. It allows for biological structures to be isolated non-invasively. Whether it is for diagnostic purposes or practically applied in image guided surgeries, image classification has many forms and uses. Unfortunately, currently there is no classification strategy that can accommodate all its applications.

The system that has been designed is used for classifying and detecting tumors in brain MR images. The system involves two major modules, one that performs classification and the other one that detects the tumors from the images. Neuro fuzzy is suitable and feasible to be used as supportive tools for medical problems. The combination of both, neural network and fuzzy logic or known as neuro fuzzy model has been tested and evaluated for classification and detection of MR images.

Fuzzy set theory plays an important role in dealing with uncertainty when making decisions in medical applications. Fuzzy logic enables us to use the uncertainty in the classifier design and consequently increase the credibility of the system output. The proposed technique involves training the ANFIS classifier for symptoms detection.

73 ANFIS is the fuzzy logic based paradigm that grasps the learning abilities of ANN to enhance the intelligent systems performance using a priori Knowledge. Using a given input/output data set, ANFIS constructs a fuzzy inference system (FIS) whose membership function parameters are tuned (adjusted) using either a backpropagation algorithm alone, or in combination with a least squares type of method. This allows the fuzzy systems to learn from the modeled data.

The parameters associated with the membership functions will change through the learning process. The computation of these parameters (or their adjustment) is facilitated by a gradient vector, which provides a measure of how well the fuzzy inference system is modeling the input/output data for a given set of parameters. Once the gradient vector is obtained, any of several optimization routines could be applied to adjust parameters that will reduce some error measure (usually defined by the sum of the squared differences between actual and desired response).

These techniques provide a method for the fuzzy modeling procedure to learn information about a data set, in order to compute the membership function parameters that best allow the associated fuzzy inference system to track the given input/output data. This learning method works similarly to that of neural network.

To use ANFIS in the classification problem, the following steps need to be performed: 1. Design a Sugeno FIS appropriate to the classification problem. 2. Hands optimize the FIS, given actual input classification data. 3. Set up training and testing matrices. The training and testing matrices will be composed of inputs and the desired classification corresponding to those inputs. 4. Run the ANFIS algorithm on the training data. 5. Test the results using the testing data.

The technique that has been proposed here has shown a very encouraging level of performance for the problem of tumor classification and detection in brain

74 MR images. Efforts were made to reduce the amount of a priori knowledge used, so as to keep the method as generic as possible. This makes the approach worth serious consideration for further development as an automatic tool for image classification in medicine.

Based on the result in Chapter 5, it can be concluded that this project has achieved the objectives and problem statements as set earlier in Chapter 2. There is a need to apply the classification and detection techniques in many fields especially in the medical field whereby the data is large and time consuming to sort or classify manually. Furthermore, it is very crucial to determine the accuracy and precision of the output of the analysis, especially in the medical problems or field such as lung cancer, breast cancer and etc.

Experimental result indicates that the technique is workable with an accuracy greater than 90%. This technique is fast in execution, efcient in classification and easy in implementation. As an overall conclusion, this project is successful as it met the objectives of the project and successfully developed, run and optimized the performance of the classification technique.

6.2

Future Work

To the fields of MR images classification, this thesis is like an explorer who has just landed on a big tropical island. He is only able to gather just a few items on the island to bring back with him because his ship is not big. There could be many valuable resources on the island, but the explorer is not able to find out about them because his stay on the island is constrained by time. Nevertheless, based on those resources he can see, the explorer has a strong feeling that the island has tremendous development potential.

75 This thesis has only explored a small territory in using the neuro fuzzy approach in medical image classification. There are many possible directions for future work, which include the following:

In this project the number of medical image is less. For future work the number of brain medical images should be increased and using the real ones. By increasing the number of image, more training data set can be performed.

Upgrade the system to the application for different size brain medical images slice as shown in Figure 6.1. By doing this, the same region of the tumor but in the different slice of brain medical image can be determined.

Figure 6.1: Different slice of brain medical image

Perform the segmentation process to detect a tumor and also its size. The classification would be better performed after the segmentation method and the segmentation results will be used in classification.

Get the extra information that could be very useful in detecting some patterns in developing a certain disease. In such a system, not only the images are important, but also some patient information.

Build the complete GUI to interface all the process starting from region of interest to ANFIS classification and detection.

The use of modified version of ANFIS model instead of Sugeno type ANFIS model. Modification can be done in terms of ANFIS architecture, learning and training algorithm, convergences and determination of premise or consequent parameters.

76

Design a combining multiple classifiers that use different features such as texture features, tumor shape and size features, etc in order to get an accurate classification of the normal and abnormal brain image. A combined feature is more meaningful than the one feature representation alone and can significantly improve the performance. The method can be useful in the diagnostic of diseases if the possibility of a feature is known in the Region of Interest (ROI) of an image, and the images can be classified into category of diseases. Figure 6.2 gives the block diagram of the technique.

Figure 6.2: Block Diagram of the Neuro Fuzzy Approach

77

REFERENCES

1. L.I. Kuncheva, F. Steimann, Fuzzy diagnosis, Artificial Intelligence in Medicine, vol. 16, pp. 121-128, 1999. 2. J.-S.R. Jang, ANFIS: Adaptive-network-based fuzzy inference system, IEEE Transactions on Systems, Man, and Cybernetics, vol. 23(3), pp. 665685, 1993. 3. S.Y. Belal, A.F.G. Taktak, A.J. Nevill, S.A. Spencer, D. Roden, S. Bevan, Automatic detection of distorted plethysmogram pulses in neonates and paediatric patients using an adaptive-network-based fuzzy inference system, Artificial Intelligence in Medicine, vol. 24, pp. 149-165, 2002. 4. I. Virant-Klun, J. Virant, Fuzzy logic alternative for analysis in the biomedical sciences, Computers and Biomedical Research, vol. 32, pp. 305321, 1999. 5. Joseph P. Hornak, The Basics of MRI, 1996-2008. 6. Kasabov, N.: Foundations of Neural Networks, Fuzzy Systems and Knowledge Engineering. MIT Press, Cambridge ,1996. 7. Rami J. Oweis and Muna J.Sunna, A Combined Neuro Fuzzy Approach for Classifying Image Pixels in Medical Applications. Journal of Electrical Engineering, Vol.56, No.5-6, 2005. 8. N.Benamrane, A. Aribi, L.Kraoula, Fuzzy Neural Networks and Genetic Algorithms for Medical Images Interpretation. IEEE Proceedings of the Geometric Modeling and Imaging, 2006. 9. Ramiro Castellanos and Sunanda Mitra, Segmentation of magnetic resonance images using a neuro-fuzzy algorithm. IEEE Symposium on Computer-Based Medical Systems, 2000.

78 10. Chin-Ming Hong et al, A Novel and Efficient Neuro-Fuzzy Classifier for Medical Diagnosis. IEEE International Joint Conference on Neural Networks, 2006. 11. F.M.Frattale Mascioli, G.Martinelli, A constructive approach to neurofuzzy networks, Signal Processing, 64 : 347-358, 1998. 12. J.-S.R., Jang, Input selection for ANFIS learning, Fuzzy Systems. Proceedings of the Fifth IEEE International Conference, V012: 1493 -1499, 1996. 13. Panella, M.; Rizzi, A.; Mascioli, F.M.F.; Martinelli, G., ANFIS synthesis by hyperplane clustering, IFSA World Congress and 20th NAFIPS International Conference, vol.1: 340 -345, 2001. 14. J.S. R. Jang, C.-T. Sun, and E. Mizutani , Neuro- Fuzzy and Soft

Computing, New Jersey: Prentice Hall, USA, p. 239-240, 1997. 15. S.L.Chiu, Fuzzy model identification based on cluster estimation, Journal of Intelligent and Fuzzy Systems, 2 (3): 267-278, 1994. 16. Jang JSR, Sun C T and Muzutani E, Neuro-Fuzzy and Soft Computing-A

computational approach to learning and machine intelligence. Pearson Education Inc, 2007. 17. K. I. Diamantaras and S. Y. Kung, Principal Component Neural Networks: Theory and Applications, John Wiley & Sons,Inc., 1996. 18. Myoung Soo Park; Jin Hee Na; Jin Young Choi, "PCA-based feature extraction using class information", IEEE International Conference on Systems, Man and Cybernetics, pp.341-345, 2005. 19. Han Witjes et al. Multispectral magnetic resonance image analysis using principal component and linear discriminant analysis. Journal of Magnetic Resonance Imaging, 17:261269, 2003. 20. Lukas L. et al. Brain tumor classification based on long echo proton MRS signals. Artificial Intelligence in Medicine, 31:7389, 2004. 21. Cagnoni, Coppini, Rucci, Caramella,Valli, Neural Network Segmentation of Magnetic Resonance Spin Echo Images of the Brain. Journal of Biomedical Engineering, V 15, pp.355-362. 1993. 22. Meneganti, Saviello y Tagliaferri, Fuzzy Neural Network for Classification and Detection of Anomalies. IEEE Transactions on Neural Networks,Vol.9, no 5 September 1998.

79 23. Valli, Poli, Cagnoni and Coppini, Neural Networks and Prior Knowledge Help the Segmentation of Medical Images. Journal of Computing and Information Technology, Vol.6 No. 2. 1998. 24. M. Morrison and Y. Attikiouzel, A probabilistic neural network based

image segmentation network for magnetic resonance images, Proc. Conf. Neural Nets., vol. 3, pp. 60-65, Baltimore, 1992. 25. L. 0. Hall, et al, A comparison of neural network and fuzzy clustering techniques in segmenting magnetic resonance images of the brain, IEEE Bans. Neural Nets., Vol. 3, pp. 672-682, 1992. 26. N.Benamrane and al., A Hybrid Fuzzy Neural Networks for the Detection of Tumors in Medical Images, American Journal of Applied Sciences, 2(4), p. 892-896, 2005. 27. R. P. Li, M. Mukaidono and I . B . Turksen , A fuzzy neural network for pattern classification and feature selection , Fuzzy Sets Sys., vol. 130, pp. 101-108, 2002. 28. Rafael. C. Gonzalez, Richard. E. Woods, Digital Image Processing,

Addison Wesley, Massachusetts, 1999. 29. Anil Jain., Fundamentals of Digital Image Processing, Prentice Hall.1989. 30. Nauck, D., Klawonn, F., and Kruse, R., Foundations of Neuro-Fuzzy Systems. Wiley, Chichester, England, 1997. 31. Paul Suetens, Fundamentals of Medical Imaging, Cambridge University Press, London, 2002. 32. User manual, Fuzzy toolbox, Mathworks Inc. 33. Math works worldwide, Matlab Home, Image Processing Toolbox, Image Processing, analysis and algorithm development:

http://www.mathworks.com/products/image.

80 APPENDIX A

MATLAB source code for Transformation image to Data

%Entering the image for MATLAB fprintf('\n Entering the image for MATLAB...') imagname1 = input('\n Enter the name of the prior image file (filename.ext):','s'); al = imread(imagname1); a2 = imresize(al,[64 64]); %Resize an image to 64x64 pixel a3 = rgb2gray(a2); %convert an RGB image or colormap to grayscale

imagname2 = input('\n Enter the name of the input image file (filename.ext):','s'); b1 = imread(imagname2); b2 = imresize(b1,[64 64]); %Resize an image to 64x64 pixel b3 = rgb2gray(b2); %Convert an RGB image or colormap to grayscale

%Test size of priori model and input model Igray = rgb2gray(al); Ibw = im2bw(Igray,graythresh(Igray)); %Convert an image to a binary image Ifill = imfill(Ibw,'hole'); %Fills holes in the binary image BW figure (1),imshow(Ifill),title('original')

I2gray = rgb2gray(b1); I2bw = im2bw(I2gray,graythresh(I2gray)); %Convert an image to a binary image I2fill = imfill(I2bw,'hole'); %Fills holes in the binary image BW figure (2),imshow(I2fill),title('abnormal')

X = bwarea(I2fill) - bwarea(Ifill); %substract two binary image

if X <=10 %if size of input binary image match with prior image c = a3-b3; %find differential between image a and b d = c>20; %find the point bigger than 20 fprintf('\n Location of abnormal tissues...') [i,j]=find(d); %location point bigger than 20

81 % Find the coordinate T=[ ]; for k=1:3 B=0; C=0; for A=j(k) while A~=B L(k)=i(k)+C; B=B+1; C=C+64; end end T=[T L(k)]; end

fprintf('\n Coordinate of damage tissues:'); T

%Saving the output sav = input('\n Do you like to SAVE Result? (y/n) : ','s'); if (sav == 'y') fprintf('\n You choose to SAVE the Result') name = input('\n Type the name of the new file (filename) : ','s'); fprintf('\n Saving...') save(name,'ans'); fprintf('\n The new file is called %s and it is saved in MATLAB working Directory',name)

else fprintf('\n You choose NOT to SAVE the Result') end

82 %If size of input Dot match with prior image else fprint('\n Size of input image not match with size of prior image, Please Try again!!') return end

83

APPENDIX B

PCA Algorithm code

% PCA-based brain mri recognition system

% See also: CREATEDATABASE, EIGENMRICORE, TUMORRECOGNITION

clear all clc

% Initial directory paths can be customized and fixed TrainDatabasePath = uigetdir('D:\Program Files\MATLAB\R2006a\work', 'Select training database path' ); TestDatabasePath = uigetdir('D:\Program Files\MATLAB\R2006a\work', 'Select test database path');

prompt = {'Enter test image name (a number between 1 to 10):'}; dlg_title = 'Input of PCA-Based Brain MRI Recognition System'; num_lines= 1; def = {'1'};

TestImage = inputdlg(prompt,dlg_title,num_lines,def); TestImage = strcat(TestDatabasePath,'\',char(TestImage),'.jpg'); im = imread(TestImage);

T = CreateDatabase(TrainDatabasePath); [m, A, EigenMRI] = EigenMRICore(T); OutputName = TumorRecognition(TestImage, m, A, EigenMRI);

SelectedImage = strcat(TrainDatabasePath,'\',OutputName);

84 SelectedImage = imread(SelectedImage);

imshow(im) title('Test Image'); figure,imshow(SelectedImage); title('Equivalent Image');

str = strcat('Matched image is : ',OutputName); disp(str)

85 APPENDIX C

CreateDatabase function code

function T = CreateDatabase(TrainDatabasePath)

% Description: This function reshapes all 2D images of the training database % into 1D column vectors. Then, it puts these 1D column vectors in a row to % construct 2D matrix 'T'. % % % Argument: % % Returns: % % % % T - A 2D matrix, containing all 1D image vectors. Suppose all P images in the training database have the same size of MxN. So the length of 1D column vectors is MN and 'T' will be a MNxP 2D matrix. TrainDatabasePath - Path of the training database

%File management TrainFiles = dir(TrainDatabasePath); Train_Number = 0;

for i = 1:size(TrainFiles,1) if not(strcmp(TrainFiles(i).name,'.')|strcmp(TrainFiles(i).name,'..')|strcmp (TrainFiles(i).name,'Thumbs.db')) Train_Number = Train_Number + 1; % Number of all images in the training database end end

%Construction of 2D matrix from 1D image vectors T = [ ];

86 for i = 1 : Train_Number

% Chose the name of each image in databases as a corresponding number. However, it is not mandatory! str = int2str(i); str = strcat('\',str,'.jpg'); str = strcat(TrainDatabasePath,str); img = imread(str); img = rgb2gray(img); [irow icol] = size(img); temp = reshape(img',irow*icol,1); % Reshaping 2D images into 1D image vectors T = [T temp]; % 'T' grows after each turn End

87

APPENDIX D

EigenMRICore function code

function [m, A, EigenMRI] = EigenMRICore(T)

% Description: This function gets a 2D matrix, containing all training % image vectors and returns 3 outputs which are extracted from training % database. % % Argument: % % % % % % Returns: % % % % %Calculating the mean image m = mean(T,2); % Computing the average MRI image m = (1/P)*sum(Tj's) Train_Number = size(T,2); A m - (M*Nx1) Mean of the training database T - A 2D matrix, containing all 1D image vectors. Suppose all P images in the training database have the same size of MxN. So the length of 1D column vectors is M*N and 'T' will be a MNxP 2D matrix.

EigenMRI - (M*Nx(P-1)) Eigen vectors of the covariance matrix of the training database - (M*NxP) Matrix of centered image vectors

%Calculating the deviation of each image from mean image A = [ ]; for i = 1 : Train_Number temp = double(T(:,i)) - m; A = [A temp]; % Merging all centered images end

88 %Snapshot method of EigenMRI methods L = A'*A; % L is the surrogate of covariance matrix C=A*A'. [V D] = eig(L); % Diagonal elements of D are the eigenvalues % for both L=A'*A and C=A*A'.

%Sorting and eliminating eigenvalues L_eig_vec = [ ]; for i = 1 : size(V,2) if( D(i,i)>1 ) L_eig_vec = [L_eig_vec V(:,i)]; end end

%Calculating the eigenvectors of covariance matrix 'C' EigenMRI = A * L_eig_vec; % A: centered image vectors

89 APPENDIX E

TumorRecognition function code

function OutputName = TumorRecognition(TestImage, m, A, EigenMRI)

% Description: This function compares two brain images by % projecting the images into imagespace and % measuring the Euclidean distance between them. % % Argument: % % % m - (M*Nx1) Mean of the training database, which is output of 'EigenMRICore' function. % % % % EigenMRI - (M*Nx(P-1)) Eigen vectors of the covariance matrix of the training database, which is output of 'EigenMRICore' function. % % % A - (M*NxP) Matrix of centered image vectors, which is output of 'EigenMRICore' function. % % Returns: OutputName - Name of the recognized image in the training database. TestImage - Path of the input test image

%Projecting centered image vectors into imagespace ProjectedImages = [ ]; Train_Number = size(EigenMRI,2); for i = 1 : Train_Number temp = EigenMRI'*A(:,i); % Projection of centered images into imagespace

90 ProjectedImages = [ProjectedImages temp]; end

%Extracting the PCA features from test image InputImage = imread(TestImage); temp = InputImage(:,:,1);

[irow icol] = size(temp); InImage = reshape(temp',irow*icol,1); Difference = double(InImage)-m; % Centered test image ProjectedTestImage = EigenMRI'*Difference; % Test image feature vector

%Calculating Euclidean distances Euc_dist = [ ]; for i = 1 : Train_Number q = ProjectedImages(:,i); temp = ( norm( ProjectedTestImage - q ) )^2; Euc_dist = [Euc_dist temp]; end

[Euc_dist_min,Recognized_index] = min(Euc_dist); OutputName = strcat(int2str(Recognized_index),'.jpg');

91 APPENDIX F

Neuro Fuzzy Algorithm code

% Classification using ANFIS % Input Phase clear name_trainingdata=input('\nEnter name of Training Data files (only prefix, without neither number nor extension): ','s'); name_checkingdata=input('\nEnter name of Checking Data file (only prefix, without neither number nor extension): ','s'); name_outputdata=input('\nEnter name of Output file (only prefix, without neither number nor extension): ','s'); epoch=input('\nNumber of epoch for training process: '); numMFs=input('\nNumber of membership function: '); inmftype=str2mat('gbellmf','trimf','pimf'); outmftype=('linear'); extension='.dat'; % strcat combine two strings together axus=strcat(name_trainingdata,extension); axus1=strcat(name_checkingdata,extension); axus2=strcat(name_outputdata,extension); % Loading Training data loadingtraining=load(axus); loadingchecking=load(axus1); loadingoutput=load(axus2); data=[loadingtraining loadingoutput]; figure(1); subplot(211); bar(data); title('Training data'); subplot(212); bar(loadingchecking);

92 title('Checking data'); legend('input1','input2','input3','output'); % Classification/Fuzzy Inference System Phase to get the FIS fis=genfis1(data,numMFs,inmftype,outmftype) figure(2); subplot(311); plotmf(fis,'input',1); subplot(312); plotmf(fis,'input',2); subplot(313); plotmf(fis,'input',3); % Anfis Model Training Phase % Recording time for ANFIS training tic; [fistraining,errortraining,stepssize,checkfis,errorchecking]=anfis(data,fis,epoch,[1 1 1 1],loadingchecking); figure(3) subplot(311); plotmf(fistraining,'input',1); subplot(312); plotmf(fistraining,'input',2); subplot(313); plotmf(fistraining,'input',3); time=toc; Total_time_for_ANFIS_training=time fprintf('\n<<<<<<<<<<<<<<<<<<<<WARNING!!!!>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>') fprintf('\nResults above show second column is training error') fprintf('\nand third column is checking error') fprintf('\n<<<<<<<<<<<<<<<<<<<<WARNING!!!!>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>') fprintf('\n') % Display Error for Training and Checking final_training_error=errortraining(epoch,1)

93 final_checking_error=errorchecking(epoch,1) maximum_training_error=max(errortraining); minimum_training_error=min(errortraining); average_training_error=(maximum_training_error+minimum_training_error)/2 maximum_checking_error=max(errorchecking); minimum_checking_error=min(errorchecking); average_checking_error=(maximum_checking_error+minimum_checking_error)/2 average_global_error=(average_training_error+average_checking_error)/2 % Save the trained FIS saving=input('\nSave the Trained FIS, eg: yes=1 or no=0?= '); if saving==1; writefis(fistraining); else saving==2; end; % Application Phase %Evaluate the fis based on new set of data(application data) name_applicationdata=input('\nEnter name of Application Data files (only prefix,without neither number nor extension): ','s'); expected_result=input('\nEnter name of Expected Data Result files (only prefix,without neither number nor extension): ','s'); applicationdata=strcat(name_applicationdata,extension); axus3=strcat(expected_result,extension); loading=load(applicationdata); out=evalfis(loading,fistraining); output=round(out) % Detection Phase target=load(axus3); number=0; [a,b]=size(output); [c,d]=size(target); if a~=c error('Mismatched input and output data matrices'); end for i=1:size(output)

94 if output(i,1)==target(i,1); disp('Correct') elseif output(i,1)~=target(i,1); disp('InCorrect') number=number+1; end end Total_Misclassified=number

95 APPENDIX G

Brain MR Image for Class 1

MRI1-1

MRI1-2

MRI1-3

MRI1-4

96 APPENDIX H

Brain MR Image for Class 2

MRI2-1

MRI2-2

MRI2-3

MRI2-4

97 APPENDIX I

Brain MR Image for Class 3

MRI3-1

MRI3-2

MRI3-3

MRI3-4

98 APPENDIX J

Brain MR Image for Class 4

MRI4-1

MRI4-2

MRI4-3

MRI4-4

99 APPENDIX K

Brain MR Image for Class 5

MRI5-1

MRI5-2

MRI5-3

MRI5-4