Classification of Mammograms Using Cartesian

Genetic Programming Evolved Artificial Neural

Networks

Arbab Masood Ahmad, Gul Muhammad Khan, and Sahibzada Ali Mahmud

University of Engineering and Technology, Peshawar, Pakistan

{arbabmasood, gk502, sahibzada.mahmud}@nwfpuet.edu.pk
http://www.nwfpuet.edu.pk

Abstract. We developed a system that classifies masses or microcalci-

fications observed in a mammogram as either benign or malignant. The
system assumes prior manual segmentation of the image. The image seg-
ment is then processed for its statistical parameters and applied to a
computational intelligence system for classification. We used Cartesian
Genetic Programming Evolved Artificial Neural Network (CGPANN) for
classification. To train and test our system we selected 2000 mammogram
images with equal number of benign and malignant cases from the well-
known Digital Database for Screening Mammography (DDSM). To find
the input parameters for our network we exploited the overlay files asso-
ciated with the mammograms. These files mark the boundaries of masses
or microcalcifications. A Gray Level Co-occurrence matrix (GLCM) was
developed for a rectangular region enclosing each boundary and its sta-
tistical parameters computed. Five experiments were conducted in each
fold of a 10-fold cross validation strategy. Testing accuracy of 100 % was
achieved in some experiments.

Keywords: Mammogram, Image classification, GLCM, CGPANN,

Haralick’s parameters.

1 Introduction
Breast cancer is a leading cause of death in women worldwide. The disease has
often times no symptoms till it advances to a dangerous level. It is therefore
highly recommended to carry out screening tests after a certain age. The best
screening method to date is the mammography, in which both the breasts are im-
aged with low dose x-ray radiation. Nowadays digital mammography has become
the standard screening practice.
As mammography is highly subject to the expertise of radiologist and prone to
errors, a decision support system based on machine learning is highly desirable.
There are two main indicators for breast cancer using mammography. These
are masses and microcalcifications. Often times before a suspicious mass ap-
pears in the mammogram, very fine specs appear in the image, which is caused
by micro-calcifications (MCs). The MCs that are 1 mm or smaller in diameter

L. Iliadis et al. (Eds.): AIAI 2014, IFIP AICT 436, pp. 203–213, 2014.

c IFIP International Federation for Information Processing 2014
204 A.M. Ahmad, G.M. Khan, and S.A. Mahmud

and appear in clusters are more likely to be cancerous while those that are larger
in size and scattered randomly are often benign. A mass on the other hand is
considered benign if its shape is round or oval and the margins are circumscribed,
while it is malignant if it is irregular, stellate or micro-lobulated in shape. The
density of breast is such that the mammogram shows a very low contrast between
parenchymal tissue and a mass and hence very difficult to isolate the two, visu-
ally. A number of methods have been developed for computer based classification
of the masses and microcalcifications. Before classification the mammogram im-
age is preprocessed using digital filters to enhance the different regions of the
image. The masses and microcalcifications are then outlined using segmentation
techniques. Before these segmented images could be classified using machine, a
machine learning system is trained with a large set of mammograms that are
classified by expert radiologists. There are a number of mammogram databases
available on the internet. The two most popular of them are Digital Database
for Screening Mammography (DDSM) at the University of South Florida1 and
the MIAS 2
In this paper we present our work in classifying the masses and MCs seen
in mammograms, as either benign or malignant. The system that we devel-
oped assumes that the physician segments the masses or MCs manually using
the CROP function, found in most windows based graphic software packages.
In order to train our system for classification we had to train it with sample
mammogram images from the Digital Database for Screening Mammography
(DDSM). These images are available in compressed lossless JPEG format. The
Windows versions of the uncompressed images were downloaded under a trans-
fer agreement with Dr. Thomas Deserno (nee Lehmann) Department of Medical
Informatics Aachen University of Technology D-52057 Aachen GERMANY, un-
der the IRMA (Image Retrieval in Medical Applications) project. The database
contains 2620 cases comprising of Normal, Benign and Malignant, high resolu-
tion mammograms. Each case further consists of two views of each breast, the
cranio-caudal view and the oblique medio-lateral view. Besides the images, each
case has a .ics file that contains information about the patient and the image
file. Section 4 gives the details of the work done in preparing the training and
testing data for the CGPANN. After training the CGPANN with the former the
system is then evaluated with the later.
The paper is organized as follows: The next section titled ”Literature Sur-
vey” describes the latest research done in the field of mammogram classification.
The sections ”Cartesian Genetic Programming Evolved Artificial Neural Net-
work (CGPANN)” and ”Evolution Strategy” describe the evolutionary compu-
tation system that we used for the classification task. The section ”Experimental
setup” describes the preprocessing and statistical parameters extraction steps
needed before mammogram classification. It also describes the network parame-
ters that we chose. The section ”Results and Analyses” compares the results of

1
http://marathon.csee.usf.edu/Mammography/Database.html
2
http://peipa.essex.ac.uk/info/mias.html
 Classification of Mammograms Using CGPANN 205

our experiments with those of the competitors. Finally, the section ”Conclusion
and Future work” summarizes the paper and states our intentions for future
work in this field.

2 Literature Survey
A brief review of the work done in the field of mammogram classification is
presented below. As the abnormality in mammograms can be in the form of
microcalcifications or masses, separate subsections review each of them.

2.1 Microcalcifications
In [1] Xuejun et al. presented a number of ANN architectures for detecting
microcalcifications (MC) in mammogram images. A back propagation neural
network responds to an MC lying in the middle of a region of interest. To reduce
the image size, FFT of the image was also determined. Another network with
multiple outputs had one of its outputs as 1 when its corresponding input had a
microcalcification at its position in the image. A Shift Invariant ANN (SIANN)
was also experimented with. The performance of the networks was compared
with Triple Ring Filter (TRF) which is a rule based filter [2]. A sensitivity of
95% was achieved by using SIANN and TRF together.
In [3] Issam et al. presented an SVM based microcalcification (MC) classifica-
tion technique. In [4] Rolando et al. presented a technique in which a mammo-
gram is first preprocessed with a median filter to remove noise. This is followed
by binarization. The resulting image is then applied to two Gaussian filters. The
optimized difference of Gaussian (DoG) filters is used to enhance those regions
in the image that contain bright points. A number of techniques are then applied
to this image to detect potential MCs.
In [5] Walker et al. discussed a multi-chromosome Cartesian Genetic Pro-
gramming in general and its application for classification of microcalcifications
(MCs) in mammograms, in particular. The process is termed multi-chromosome
Evolution (MCE). About 80% test images were classified correctly. In [6] Zhang
et al. presented a technique in which areas marked by radiologists in the DDSM
database were resized and fourteen features extracted from each area. These fea-
tures are represented by genes in a chromosome of a neural-Genetic Algorithm. A
subset of features is applied as input and the NN trained. A random population
of subsets is generated and each individual is evaluated. Genetic operators of
crossover and mutation are applied. The NN with the best classification rate to-
gether with the selected feature subset is chosen. It was observed that the highest
classification result using the proposed algorithm with NN classifier was 85%.

2.2 Masses
In [7]the authors preprocessed and segmented images from popular databases on
the basis of grey level distribution and texture using Otsu’s method. They ex-
tracted the intensity histogram and Gray Level Co-occurrence Matrix (GLCM)
206 A.M. Ahmad, G.M. Khan, and S.A. Mahmud

features. To improve prediction accuracy the author used a hybrid of Genetic

Algorithm (GA) and Linear Forward Selection (LFS) algorithms. For classifi-
cation they used the machine learning package WEKA and trained the system
using J48 decision tree method. The classification accuracy based on the selected
features was 86.7%. In [8] the author presents mammogram classification tech-
nique using Linear Vector Quantization (LVQ). Best classification accuracy of
99% was achieved with 100 DDSM cases.
In [9] the authors present an algorithm that is based on the principle that a
mass segment has uniform texture, its margins should coincide with the max-
imum gradient points that corresponds to the edges and that the mass profile
shape has minimum changes. In [10], [11] the authors present mammogram image
segmentation based on Iso-level contour map representation of the image.
In [12] a detailed review of the work done in segmentation and classification
of the different anatomical regions of the breast is presented. In [13] the authors
used Gray Level Co-occurrence Matrix (GLCM) to extract second order statis-
tical descriptors of the texture from the masses. These features were applied to
error back propagation ANN for classification. The best performance result that
they obtained had 91.67% sensitivity, and 84.17% specificity.
In [14] the authors made use of the chain code in the overlay files of mam-
mograms, in the DDSM database. A rectangular image is formed from the ROI
defined by the chain code. The image is preprocessed and a GLCM formed from
it. The Haralick energy descriptors are then determined from the GLCM. Adap-
tive thresholding is applied to the image so formed to detect edges. A binary
image is thus formed. The morphological operation of image filling is applied to
all closed path edges. The filled area that has the largest overlapping with the
central part of ROI is the segmented mass.
In [15] the authors present a technique for segmentation and classification of
masses. For segmentation the highest intensity point inside the ROI is taken
as center and radial lines drawn to its margins. Critical point, the point with
highest local variance on each line is detected and new ROI drawn by linearly
interpolating in between these points. Sixteen different morphological and tex-
tural features of the segmented masses are computed and applied to an ANN for
classifying the mass as benign or malignant.
In [16] the authors present a technique focusing on utilization of mass margin
descriptors called Fourier Transform of Radial Distance (FTRD). These features
are applied to an MLP ANN for classification of the mass as either benign or
malignant. The best accuracy that they achieved was 92.8%.
In [17] the authors present a mammogram classification system based on com-
putational and human features. These features include shape, size and margins
of the mass, patient age and tissue density. The density values are represented
in Breast Imaging Reporting and Data System (BI-RADS). Textural features
are found using Spatial Gray Level Dependence Method (SGLDM) and Run
Difference Method (RDM). Sequential Forward Selection technique and genetic
algorithm technique were used for classification.
 Classification of Mammograms Using CGPANN 207

In [18] the authors present a mass detection technique in which the pec-
toral muscles are segmented and removed. The mass inside the breast is then
segmented using intensity thresholding. The segmented mass is analyzed for its
textural features, proposed by Haralick, using the gray level co-occurence matrix
(GLCM). The textural indices are applied to a support vector machine (SVM)
for training and classification. An average classification rate of 95% was achieved.

3 Cartesian Genetic Programming Evolved Artificial

Neural Network (CGPANN)

In CGPANN a neural network is developed by evolving its inter-node connec-

tions, weights, output connection(s) and the activation functions. It’s an en-
hancement to the popular Cartesian genetic programming [19]. The nodes and
connections in CGPANN are arranged as a graph with rows and columns. A
CGPANN node, shown in fig.1b, consists of a summer and an activation func-
tion, similar to an ANN neuron. The summer takes its inputs from other nodes
through weighted connections. Each connection additionally has a switch that
can be turned On or Off. The number of inputs to each node, number of rows,
number of columns and levels-back are predefined.
A CGPANN genotype is a string of integers, each representing one of the
network quantities. A typical phenotype and its related genotype can be seen in
fig.1a. For each node the letters F I W C .. have the following meanings and
possible values. F: Activation function-sigmoid or Tangent Hyperbolic; I: The
node connected to an input of this node, only a node in a column on the left or a
network input are allowed; W: connection weight (-1 to +1); C: on-off switch (0
or 1); O: Network output, all nodes and network inputs are allowed to connect
to it. Nodes of the corresponding phenotype are numbered sequentially, starting
with the top node in the first column followed by the nodes down the column,
followed by all the columns to the right in the same manner. When the genotype
is decoded to phenotype, outputs of the nodes that don’t connect to any other
node are called inactive nodes. During evolution, a certain percentage of genes
are randomly picked and mutated to allowed values only. Unlike other ANN
configurations that use both crossover and mutation, CGP and its derivative
CGPANN give excellent results with mutation only. During the process many
inactive nodes become active and vice versa. CGP architectures and its derivative
CGPANN have been investigated on a number of problems in the past[20,21,22].

3.1 Evolution Strategy

We use a 1+ λ (Number of Offspring) evolution strategy in which λ = 4. The

pseudo-code for the algorithm that we use for training and testing is presented
below.

– Prepare the set of parameters to be classified and a set of corresponding target

outputs.
208 A.M. Ahmad, G.M. Khan, and S.A. Mahmud

Inputs Outputs

III1
1 4 I
O1
Node 1 Node 4 Node 7 I
7

2 8 I
III2 Node 2 Node 5 5 Node 8 O2
I

I
O3
I
I3II Node 3 3 Node 6
6
Node 9
9

F, I1, W1, C1, I2, W2, C2 F, I1, W1, C1, I3, W2, C2 ,……………………, 1, 8, 2
(b)
(a)

Fig. 1. (a) A typical CGPANN phenotype. Nodes 3, 5, and 9 are inactive and the
remaining nodes are active. (b) Internal view of a single CGPANN neuron.

– Specify the network parameters.

– Form the initial population of fifty genotypes by assigning random, yet legit-
imate values to the genes of each genotype as discussed above.
– Generate new population with the fittest genotype and its four replicas. Ac-
curacy of the result has been used as the fitness measure for this application.
– Randomly mutate 10% (Mutation Rate) of each replica, forming four off-
spring.
– Determine fitness of the parent and the offspring and select the fittest to make
the next parent. If the parent and an offspring have equal fitness, priority
is given to the offspring over the parent, [23]. The fitness improves from
generation to generation until the iterations are stopped.
– Evaluate the performance of the trained network by applying the testing data.
– The system is now ready to classify a new pattern.
– END

4 Experimental Setup
We trained our classifier system with 1000 mammogram images
of benign and malignant types each. Using the Matlab command
GET DDSM GROUNDTRUTH we extracted the image information
from the groundtruth file. The overlay file inside the groundtruth file contains
the following information: lesion type, assessment, subtlety, pathology, anno-
tations and a chain code representing the region of interest (ROI) marked by
expert radiologists. The function is normally used to get a binary image of
the ROI but we modified it to return a rectangular image that contains this
ROI (see fig.2c). The network trained with parameters from these rectangular
images, containing masses and MCs, makes it capable to accept parameters
from manually segmented images (using the CROP function) easier. A Gray
Level Co-occurrence Matrix (GLCM) of an image is then formed. The matrix
 Classification of Mammograms Using CGPANN 209

contains information about the frequency of gray level repetition between pixels
at a certain offset distance and angle and can be used to extract statistical
parameters of the image. Out of the many possible second order statistical tex-
ture descriptors, proposed by Haralick [24], we extracted only contrast, energy,
homogeneity and correlation. Each of these four parameters were determined
for four different angles and a certain distance, using the graycoprops function
in matlab. The sample parameters were divided into a training set and a testing
set for training and testing our CGPANN. See equations (1) to (4) for the four
Haralick’s parameters.
N
 −1
Contrast = Pij (i − j)2 (1)
i,j=0

N 
 N
Energy = p(i, j)2 (2)
i=1 j=1

N
 −1
Pij
Homogeneity = (3)
i,j=0
1 + (i − j)2

[ (ij)p(i, j)] − μx μy
Correlation = (4)
σx σy
Where p(i, j) is the normalized entry in row i and column j of the GLCM, i is
the intensity of one pixel while j is that of the next pixel making the pair for
GLCM [13]. We get a total of 16 parameters. A 10-fold cross validation strategy
was adapted, where ten distinct data sets are formed. Each set has nine parts
for training and one for testing. We experimented with the following six distance
offsets (D): 4, 8, 12, 16, 20 and 24, and found that for D=20 we got the best
average 10-fold accuracy result i.e. Accuracy=90.85%, Sensitivity=86.2% and
Specificity=95.5%. We performed five experiments with this offset value, each
time using a different seed for random number generator in the initial population
in CGPANN. The tenfold results for these experiments are shown in table 1.
The CGPANN network that we used has the following features: Number of
nodes= 100 (10rows × 10columns), Inputs per node= 3 and Number of out-
puts= 1(Average of ten outputs). An input-output set contains the 16 statistical
parameters as inputs and a target output that is 0 for benign and 1 for ma-
lignant. In the process of evolution, an initial population of 50 networks was
formed randomly. Each network is applied all the 2000 sample parameters and
its fitness determined using the following metrics:
True Positive (TP):A=1, T=1
False Positive (FP):A=1, T=0
True Negative (TN):A=0, T=0
False Negative (FN):A=0, T=1
Accuracy=(TP+TN)/N
Sensitivity =TP/(TP + FN)
Specificity=TN/(FP+TN)
210 A.M. Ahmad, G.M. Khan, and S.A. Mahmud

Table 1. Average values for training and testing results for five independent evolution
runs with offset:20 and 10-fold cross validation; Acc: accuracy, Sen: Sensitivity, Spec:
Specificity

Train Fold-1 Fold-2 Fold-3 Fold-4 Fold-5

Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec
91.0 86.34 95.56 90.7 84.52 96.88 90.2 85.06 95.38 89.82 84.34 95.38 93.66 91.42 95.86
Fold-6 Fold-7 Fold-8 Fold-9 Fold-10
Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec
90.28 85.1 95.44 90.08 85.02 95.16 89.75 84.4 95.14 89.78 84.58 94.96 92.82 89.54 96.36
Test Fold-1 Fold-2 Fold-3 Fold-4 Fold-5
Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec
89.1 82.2 96.0 91.5 99.0 84.0 96.1 95.0 97.2 99.0 100.0 98.0 65 30 100.0
Fold-6 Fold-7 Fold-8 Fold-9 Fold-10
Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec Acc Sen Spec
95.4 90.8 100.0 97.5 95.0 100.0 100.0 100.0 100.0 100.0 100.0 100.0 72.2 61.2 83.2

Table 2. Comparative results from other authors and the overall 10-fold average from
the proposed method; MC: Micro-calcifications, Acc: accuracy, Sen: Sensitivity, Spec:
Specificity

Results from other researchers for comparison

Acc Sen Spec
Al Mutaz et al.[13] (mass) 87.9 91.67 84.17
M Vasantha et al.[7] (mass) 86.7
Zhang et al.[6] (MC) 85
Amir Tahmasabi et al.[16] (mass) 92.8
Fatima Eddaoudi et al.[18] (mass) 95
Proposed method (overall 10-fold average ) (Both MC and mass) 90.58 85.32 95.84

Where N=Number of samples, A=Actual, T=Target. We chose accuracy as the

measure of fitness for our network. Thus in the initial population the network
that has the highest accuracy is chosen as the parent for the next generation.
The parent, together with four of its mutated replicas, form the next generation.
The fittest of these five networks form the new parent. This process repeats till
we get the required fitness. In our case the fitness became almost stable after
100,000 generations so we stopped the experiments at 200,000 generations.

5 Results and Analyses

In this project we tried to provide a user friendly mammogram classification

system using image statistical parameters and CGPANN. Table 1 shows that
although many of the accuracy, sensitivity and specificity values in the 10-fold
cross validation strategy test results are above 90%, some are infact 100%. Table
2 shows the comparative results for a few other authors in comparison to our
 Classification of Mammograms Using CGPANN 211

1 2 3 4 5 6 7 8 90°
[-1 0]
1 1 2 0 0 1 0 0 0
135° 45°
1 1 5 6 8 0 0 1 0 1 0 0 0 [-1 -1]
2 [-1 1]

2 3 5 7 1 3 0 0 0 0 1 0 0 0
0 0 0 0 1 0 0 0 0°
4
[0 1]
4 5 7 1 2
5 1 0 0 0 0 1 2 0

8 5 1 2 5 6 0 0 0 0 0 0 0 1
7 2 0 0 0 0 0 0 0
Pixel of
8 interest
0 0 0 0 1 0 0 0

(a) (b) (c)

Fig. 2. Conceptual Illustration of (a) Gray Level Co-occurence Matrix (b) GLCM off-
sets (c) A mammogram with a malignant mass, outlined by expert (Red) and generated
by software (White Rectangle). Courtesy of TM Deserno, Dept. of Medical Informatics,
RWTH Aachen, Germany for the mammogram image

proposed work. All these authors have tried to classify either masses or micro-
calcifications alone. In comparison, our method classifies a sample set containing
both masses and microcalcifications. Amongst the authors who worked in this
area, Al Mutaz et al. [13] used the same Haralick’s statistical texture descrip-
tors as we did and the same database for their system training and testing. The
main difference however is that they used an MLP ANN as the computational
intelligence system for classification while we used CGPANN.

6 Conclusions and Future Work

In this paper we have attempted to classify mammograms for both masses and
microcalcifications. The reason for this versatility lies in the fact that irrespective
of the type of abnormality the technique relies on the textural characteristics of
the abnormality on which our network is trained. Unlike this approach, most
of the other techniques that we reviewed in the literature classify only masses
or microcalcifications alone. We also developed the method to convert the chain
code for ROIs, associated with the images, into rectangular image sections and
training our network with the statistical parameters obtained from them. This
makes the system simple to use in a windows based graphical environment for
real mammogram classification. We evaluated our system with a 10-fold cross
validation strategy and got an accuracy of 100% in some experiments (see table
1). In the current work the mammogram is segmented manually. Our system
only classifies the region for benignity or malignancy. In future, we intend to
work on automatic mammogram segmentation as well. We would then be able
to segment and classify the image on a single platform.

Acknowledgments. Many thanks to TM Deserno, Dept. of Medical Infor-

matics, RWTH Aachen, Germany, for providing the windows version of DDSM
mammogram images.
212 A.M. Ahmad, G.M. Khan, and S.A. Mahmud

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