USING ARTIFICIAL NEURAL NETWORKS

ABSTRACT:
In this project we have attempted to design a software that is able classify a particular cancer into its subtype at a much faster rate and accuracy in comparison to the conventional method and also with minimum human interferance,knowledge or experience thus leading to better prognosis and higher chances of survival for cancer patients.
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WHAT IS CANCER?
CAUSES DIAGNOSES PROGNOSIS

Oncogenes : Genes which promote cell growth and reproduction. Tumour Suppressor Genes: Genes which inhibit cell division and survival. Over-expression or the Underexpression of these genes leads to cancer.
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What Is The Prognosis For Cancer?

The prognosis is directly related to both the type and stage of the cancer.

As the staging numbers increase, the prognosis worsens.

DRAWBACKS OF CONVENTIONAL METHODS OF DETECTION AND DIAGNOSIS:

Medical Tests: False Positives and Negatives subclassifiction accuracy depends largely on Doctors knowledge and experience

Time consuming and delay in subtype identification & treatment

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NEED FOR THE PROJECT

Faster sub-classification of cancer. Minimum Human Interference required for subclassification purposes. Highly Accurate compared to traditional techniques.

High Accuracy in classification leads to better prognosis, and treatment of patients. Contains Scope in the Future for building techniques for prevention of cancer by studying genetic information
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PROJECT OVERVIEW:
3.TRAINING ANN 1.DATA COLLECTIO N 2. PREPROCESSING 4.TESTING
5.CANCER SUBCLASSIFICA TION

6.ACCURA CY MET?

7.IF YES:STOP ELSE KEEP TRAINING

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1.DATA MINING / COLLECTION

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WHAT IS MGE?

DNA Microarray :A collection of microscopic DNA spots attached to a solid surface. DNA microarrays used to measure the expression levels of large numbers of genes simultaneously.

Core principle:hybridisation
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The steps required in a microarray experiment:

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MGE EXTRACTION PROCESS VIDEO:

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MGES ROLE IN CANCER DIAGNOSIS & SUBCLASSIFICATION

Microarray is a new technology to automate th diagnostic process and can improve accuracy traditional diagnostic processes.

Examine expression of Thousands of genes at once=>Test for elevated expression genes=>Predict cancer
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WHAT IS MGE?

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LUNG CANCER

SQUAMOUS CELL CARCINOMA

ADENOCARC INOMA

LARGE CELL LUNG CANCER

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BREAST CANCER

BASAL

APOCRINE

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2. DATA PREPROCESSING
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NEED FOR COMPRESSION

MGE data is huge. Large size of input data->LARGE ANN>LONG TRAINING TIME->POOR GENERALIZATION. Require large amount of memory.

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DATA COMPRESSION

DATA COMPRESSION METHODS

DCT

DWT
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DISCRETE COSINE TRANSFORM

DCT : Technique for converting a signal into elementary frequency components.

Used to separate the image into parts (or spectral sub-bands) of differing intensity.

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DISCRETE WAVELET ANALYSIS

Wavelet analysis : revealing aspects of data that other signal analysis techniques miss: aspects like trends, discontinuities and self-similarity. Can compress or de-noise a signal without appreciable degradation. Wavelet transform defined as the sum over all time of the signal multiplied by scaled, shifted versions of wavelet MOTHER function.

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COMPRESSION LEVEL
COMPRESSIO N TECHNIQUE DCT LUNG CANCER SKIN CANCER (22283 inputs) (7480 inputs) 90%(2283 inputs) 89%(778 inputs) BREAST CANCER (7480 inputs) 89%(778 inputs)

DWT

Dwt-5, Dwt-4, Dwt-3, 87%(939 96%(707 inputs) 93%(472 inputs) inputs) Dwt-4,93%(472 inputs)

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3.
NEURAL NETWORK: BUILDING,TRAINING AND TESTING

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WHAT ARE NEURAL NETWORKS?

The motivation for the development of neural network technology stemmed from the desire to mimic human brain.

A Neural Network is a powerful datamodeling tool that is able to capture and represent complex input/output relationships.

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PROPERTIES OF NEURAL NETWORKS:

Adaptive learning

Self-learning
Real Fault

time operation tolerant

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NEURAL NETWORKS VS. CONVENTIONAL COMPUTERS

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MCCULLOH & PITTS MODEL:

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TRANSFER FUNCTIONS:

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LEARNING METHODS:
I.

SUPERVISED LEARNING UNSUPERVISED LEARNING

II.

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BUILDING NEURAL NETWORK

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NEURAL NETWORK

472

230

2
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TRAINING ALGORITHMS:

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1. ERROR BACKPROPAGATION:
Choose

random weights for the

network. Feed in input and obtain the result for each neuron. Feed forward the output of each layer to the next layer. Calculate the error for each neuron,and backpropagate it.

Update the weights.

Repeat until the network converges on the target output.

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LOCATION OF LOCAL AND GLOBAL MINIMUM

0.5

LOCAL MINIMUM
0.45 0.4 0.35

Mean Squared Error

GLOBAL MINIMUM

0.3 0.25 0.2 0.15 0.1 0.05 0

20

40

60 Epoch

80

100

120

140
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Algorithms:
1.

Gradient Descent With Momentum Backpropagation Gradient Descent With Adaptive Learning Rate Backpropagation:

2.

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3.

Gradient Descent With Momentum And Adaptive Learning Rate Backpropagation:

4.

RESILIENT PROPAGATION:

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3.K-MEANS CLUSTERING

kmeans partitions the observations in your data into K mutually exclusive clusters.

returns a vector of indices indicating to which of the k clusters it has assigned each observation.
The result is a set of clusters that are as compact and well-separated as possible.

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CODE:kmeans

X=[p1;p2;p3;p15]; %input data k=3 %number of clusters [cidx, ctrs] = kmeans(X,k); %CIDX represents the cluster indice of each sample(cluster) and CTRS represents cluster centroids figure for c = 1:3 subplot(3,1,c); plot( X((cidx == c),:)'); end suptitle('K-Means Clustering of Profiles'); figure for c = 1:3 subplot(3,1,c); plot( ctrs(c,:)'); end suptitle('K-Means Clustering of Profiles showing only centroids'); figure [silh3,h] = silhouette(X,cidx,'city'); xlabel('Silhouette Value') ylabel('Cluster')

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silhouette plot:

To get an idea of how well-separated the resulting clusters are=> silhouette plot.

It is a measure of how close each point in one cluster is to points in the neighboring clusters. Silhouette plot aids in finding(discovering) new subtypes of cancer

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4. RESULTS
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BREAST CANCER:
ALGORITHM BACKPROPA GATION BP WITH MOMENTUM BP WITH VARIABLE LEARNING RATE BP WITH VARIABLE LR AND MOMENTUM RESILIENT PROPAGATIO DCT 93.61% 93.66% 97.26% DWT-4 97.58% 97.76% 97.78% DWT-3 94.65% 97.13% 97.26%

98.03%

98.70%

98.61%

99.00%

99.75%

99.70%
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SKIN CANCER:

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LUNG CANCER:
ALGORITHM 1.BP 2.BP WITH MOMENTUM DCT 89.66 86.695 DWT-5 89.77 91.04

3.BP WITH ADAPTIVE 90.57 LEARNING

4.BP WITH MOMENTUM AND ADAPTIVE LEARNING 5.RESILIENT BP 86.705

91.97

91.51

98.52

99.52

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LIMITATIONS OF THE SYSTEM

1)The method of backwards-calculating weights not biologically plausible.

2)Each time when the power switched off the network loses its training.
3)Each time you run the network, it randomly initialises weights so difference in accuracy.

4)Very difficult and expensive to obtain geneti information of every individual.

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SCOPE FOR FUTURE

To

extend the project to do comparative study of various other compression algorithms.

implement the network on a neural network processor thus saving its training. technique to other genetic diseases/disorders,with faster neural networks. of tumor- specific markers and new subtypes.

To

Extending

Discovery

Study

the effect of drugs on gene expressions.

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REFERENCES
I.

II.

III.

IV.

V.

K.V. G. Rao, P. P. Chand, M.V.R. Murthy,"A neural Network Approach in Medical Decision Systems" Journal of Theoretical and Applied Information Technology, vol. 3 No. 4, 2007 Lawrence O. Hall, Xiaomei Liu Kevin W. Bowyer2, Robert Banfield,Why are Neural Networks Sometimes MuchMore Accurate than Decision Trees: An Analysis on a Bio-Informatics Problemin IEEE International Conference on Systems, Man & Cybernetics,Washington, D.C., pp. 2851-2856, October 5-8, 2003 Charu Gupta IMPLEMENTATION OF BACK PROPAGATION ALGORITHM (of neural networks)IN VHDL, at CHITKARA INSTITUTE OF ENGG &TECH, CHANDIGARH in June 2006. V.P. Plagianakos, D.G. Sotiropoulos, and M.N. Vrahatis, An Improved Backpropagation Method with Adaptive Learning Rate, University of Patras, Department of Mathematics, TECHNICAL REPORT No.TR98-02 Gonzales, R. C., Woods, R. E., 1993. "Digital Image Processing". Addison-Wesley, Reading, Massachusetts. MATLAB,HELP SECTION.
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VI.

VII.

VIII.

IX.

X.

Liang-Tsung Huang, An integrated method for cancer classification and rule extraction from microarray data, Journal of Biomedical Science 2009. Tripti Goel ,GPMCE, Delhi ,Vijay Nehra ,BPSMV, Khanpur,Virendra P.Vishwakarma JIIT, Noida, Comparative Analysis of various Illumination Normalization Techniques for Face Recognition, International Journal of Computer Applications (0975 8887) Volume 28 No.9, August 2011 Fayez W. Zaki, Mustafa M. Abd Elnaby, lbrahim M. Elshafiey and Amira S. Ashour, DCT AND DWT FEATURE EXTRACTION AND ANN CLASSIFICATION MATERIALS BASED TECHNIQUE FOR NONDESTRUCTIVE TESTING OF MATERIALS,EIGHTEENTH NATIONAL RADLO SCIENCE CONFERENCE March 27-29 2001 Mansoura Univ, Egypt. Ahmad M. Sarhan, A Novel Gene-Based Cancer Diagnosis with Wavelets and Support Vector Machines, European Journal of Scientific Research ISSN 1450-216X 59 Vol.46 No.4 (2010), pp.488-502 EuroJournals

THANK YOU.

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