biocybernetics and biomedical engineering 39 (2019) 63–74

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Original Research Article

Magnetic resonance imaging-based brain tumor

grades classification and grading via convolutional
neural networks and genetic algorithms

Amin Kabir Anaraki a, Moosa Ayati b,*, Foad Kazemi c

a
Advanced Instrumentation Lab, School of Mechanical Engineering, College of Engineering, University of Tehran,
Tehran, Iran
b
School of Mechanical Engineering, College of Engineering, University of Tehran, Tehran, Iran
c
Iran University of Medical Sciences, Tehran, Iran

article info abstract

Article history:
Received 2 February 2018
Received in revised form
16 June 2018
Accepted 10 October 2018
Available online 18 October 2018
Keywords:
Brain tumor
Magnetic resonance imaging
Medical image classification
Convolutional neural networks
Genetic algorithms
Bagging ensemble algorithm
Gliomas are the most common type of primary brain tumors in adults and their early
detection is of great importance. In this paper, a method based on convolutional neural
networks (CNNs) and genetic algorithm (GA) is proposed in order to noninvasively classify
different grades of Glioma using magnetic resonance imaging (MRI). In the proposed
method, the architecture (structure) of the CNN is evolved using GA, unlike existing methods
of selecting a deep neural network architecture which are usually based on trial and error or
by adopting predefined common structures. Furthermore, to decrease the variance of
prediction error, bagging as an ensemble algorithm is utilized on the best model evolved
by the GA. To briefly mention the results, in one case study, 90.9 percent accuracy for
classifying three Glioma grades was obtained. In another case study, Glioma, Meningioma,
and Pituitary tumor types were classified with 94.2 percent accuracy. The results reveal the
effectiveness of the proposed method in classifying brain tumor via MRI images. Due to the
flexible nature of the method, it can be readily used in practice for assisting the doctor to
diagnose brain tumors in an early stage.
© 2018 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish
Academy of Sciences. Published by Elsevier B.V. All rights reserved.

brain, while metastatic brain tumors originate from other body

1. Introduction
Brain tumor referred to the aggregation of abnormal cells in
some tissues of the brain. According to the brain tumors origin,
they are divided into two categories, primary and metastatic
brain tumors. The origin of primary brain tumors is in the
parts. Tumors can be cancerous (or malignant) or noncancer-
ous (or benign). Malignant brain tumors grow fast and spread
to other areas of the brain and spine and compared to benign
tumors, they are more life-threatening. A more detailed
categorization classifies tumors into four grades where, the
higher the grade, the tumor is more malignant. Due to the

* Corresponding author at: School of Mechanical Engineering, College of Engineering, University of Tehran, P.O.B. 11155-4563, Tehran, Iran.
E-mail addresses: amin.kabir@ut.ac.ir (A. Kabir Anaraki), m.ayati@ut.ac.ir (M. Ayati), foadkazemi@gmail.com (F. Kazemi).
https://doi.org/10.1016/j.bbe.2018.10.004
0208-5216/© 2018 Nalecz Institute of Biocybernetics and Biomedical Engineering of the Polish Academy of Sciences. Published by Elsevier
B.V. All rights reserved.
64 biocybernetics and biomedical engineering 39 (2019) 63–74
presence of brain tumors in the center of the nervous system
of human body, even benign tumors may incapacitate the
brain and cause irrecoverable effects.
Gliomas are considered as the most common type of
primary brain tumor in adults [1]. According to the World
Health Organization grading system [2], gliomas are diagnosed
in grades of severity from I to IV. Grade I tumors have cells that
are benign and are approximately normal in appearance.
Grade II tumors have cells that appear to be slightly abnormal.
Grade III tumors have cells that are malignant and clearly
abnormal. The most severe type of brain tumors that contain
fast-spreading and abnormal cells are considered as Grade IV.
Glioblastoma multiforme (GBM) are quintessential tumors of
this type. Meningioma tumors, arise from a layer of tissue
called the meninges. Meninges cover the brain and spinal cord
and act as protector. They are mostly considered as benign
tumors, because they grow at a slow pace and are also less
likely to spread. Pituitary tumors develop in the pituitary gland
and account for 14% of all primary intracerebral tumors, with
most of them are due to spontaneous mutation and some are
due to inherited genetic defects [3]. These tumors are also
benign and they are much less likely to spread. Although these
tumors are considered benign, they can cause serious
health problems due to their presence in sensitive areas of
the brain [4].
Early detection plays a major role in treatment and recovery
of the patient [5]. Diagnosing a brain tumor and its grade
usually undergoes a complicated and time-consuming pro-
cess. Usually, the patient refers to MRI when the brain tumor
has grown sufficiently and several harassing symptoms have
appeared. After examining the brain images, if tumor exis-
tence is suspected, the patient's brain biopsy comes to action.
Unlike MR, biopsy has an invasive procedure and in some
cases, it may even take up to a month for a definite answer.
MRI specialists perform techniques such as perfusion to grade
tumor and biopsy to confirm. It should be noted that in recent
years some novel methods have been introduced in order to
grade brain tumors other than biopsy. In particular, distin-
guishing high-grade and low-grade glioma using perfusion MR
imaging has been able to resolve some biopsy drawbacks. For
these reasons, utilization of a computer-aided system for
detection is helpful. An automatic efficient system for brain
tumor classification assists doctors in interpretation of
medical images and supports decision of specialists in an
early stages of tumor growth. In this study, brain tumor
grading is done by spending much less time and as is
confirmed in this paper with high accuracy. Furthermore,
the whole process of classification is non-invasive.
Considerable attention has been paid to medical image
analysis for diagnosis purposes. Recently, the emergence of
modern machine learning algorithms and their proven
efficiency in solving various problems in the field of artificial
intelligence, have also doubled the interest to the field of
health-related topics and algorithms [6]. Many researches on
classifying various tumors using MRI, especially MR brain
images, artificial neural networks and evolutionary algorithms
have been done [7–9] and various methods have been
implemented as well. Previous studies indicate that normal
and abnormal classes in brain MR images are easily distin-
guished using shallow machine learning algorithms such as
support vector machine, neural network, Hybrid intelligent
techniques and probabilistic neural network [10–14].
In [15] classification schemes and their performance in
order to classify several types of brain tumors and grades of
Gliomas are investigated. In their proposed method, the region
of interest is first defined and then some features such as the
shape of the tumor are extracted from the MR images. In order
to select the appropriate features, support vector machines
(SVM) with recursive feature elimination has been used. By
observing their results, it is seen that their proposed method in
binary classifications has obtained high accuracies, but the
accuracy of the multi-class classification according to the
confusion matrix provided in this paper, is low. In a recent
article, [16], the classification performance of three tumor
types using fully connected and convolutional neural net-
works (CNNs) is compared. As described in this article, the
performance of various structures of the convolutional net-
works has been tested and, eventually, a relatively shallow
network with two convolutional layers, two max-pooling
layers, and two fully connected layers is used for classification.
It has also been mentioned that the use of Vanilla preproces-
sing has been effective in classification accuracy. In another
recent study [17], CNN is used to classify healthy and
unhealthy brain images as well as high-grade and low-grade
Glioma tumors. A modified version of the famous AlexNet was
used as their network architecture. Despite the valuable works
being done in this area, developing a robust and practical
method to classify brain MR images still requires more effort.
Convolutional neural networks have had many remarkable
successes in solving complex problems of machine learning
and currently are considered as the most successful method
for image processing [18]. Instead of matrix multiplication,
convolution operators are used in most layers of these
networks. This contributes to the superiority of convolutional
networks in solving problems with high computational costs.
This is very important since the MRI datasets in MRI-based
diagnosis include thousands of images with different qualities
and types. Another advantage of this method compared to
shallow machine learning methods, is automatic feature
extraction. In conventional methods, a method was usually
proposed for extracting features, and to further reduce the
dimensions, a method was used to select the dominant
features. Recently, CNN has also been widely used in the
processing of medical images using deep neural networks
such as grade classification [19], segmentation [20,21] and skull
stripping of brain tumor images [22].
In this article, a method based on CNN is proposed to
classify three grades of Gliomas with MR images. Selecting an
appropriate deep neural network architecture for a specific
purpose, consists of a challenging procedure which is usually
done by trial and error or employing a common architecture.
Unlike conventional schemes, in the proposed method the
architecture of the convolutional neural network is evolved
using GA. Networks with different number of layers and
parameters are investigated by GA and the network with the
best performance on the dataset was selected for further
processing. Afterwards, a model averaging method called
bagging is utilized on the best model evolved by the GA.
Bagging is an ensemble method and is employed in order to
decrease the variance of final diagnosis. The proposed method
 biocybernetics and biomedical engineering 39 (2019) 63–74
is used in two case studies. In first case, three Glioma grades
are classified with 90.9% accuracy. In second case, for
demonstrating the strength of the proposed method, three
different types of tumors from another MRI database were
used as the input to CNN, and the final performance of
diagnosis was 94.2%. Results confirm that proposed method is
applicable on different brain MRI datasets in order to assist the
specialist in early detection.
The remainder of the paper is organized as follows. In
Section 2, a brief explanation about the datasets utilized as
input of the networks is given. CNNs are discussed in details in
Section 3. In Section 4, the proposed method for selecting an
appropriate architecture based on GA is presented. Experi-
mental results are presented and discussed in Sections 5 and 6,
respectively. Finally, Section 7 is dedicated to conclusions.
2. Data preparation
In this section, datasets of this paper are introduced and the
type of the input data and pre-processing steps are discussed.
2.1. Datasets
Most of the datasets used in this research are obtained from
four databases that are available online for research purposes.
Normal brain MR images were obtained from the brain
development website (IXI dataset) [23]. IXI dataset is a
collection of nearly 600 MR images from normal subjects
(without any lesion). MR images of Glioma tumors were
collected from the cancer imaging archive datasets [24].
REMBRANDT dataset [25] contains the pre-surgical magnetic
resonance multi-sequence images from 130 patients which
suffer from low or high grade Gliomas. TCGA-GBM data
collection [26], contains glioblastoma multiform brain MR
images of 199 patients and TCGA-LGG dataset [27] includes low
grade Gliomas data, collected from 299 patients. In addition,
brain MR of 60 patients were obtained from the neurosurgery
section of Hazrat-e Rasool General Hospital at Tehran. It
should be noted that except for the normal brain MRs, only the
T1 axial images with injection of contrast agent are used in this
study. Data from the mentioned databases are considered as
the Case Study I.
In addition, to evaluate the proposed method, the axial
brain tumor images of Cheng et al. [28] are also employed. They
have provided a MR brain tumor dataset containing T1-
weighted images from 233 patients with Meningioma, Glioma,
and Pituitary brain tumor types. In this paper, this dataset is
utilized in the Case Study II. Data of both case studies have
annotations (or labels) assigned by a specialist.
Fig. 1 – An example of the six selected sections from the axial MR of a normal person.
65
In the case of normal MRIs, in average six middle MR slices
are selected at identical intervals for each subject. These
images are used to distinguish between healthy and tumorous
brains. Images of brain tumors that have been identified with
infusion of contrast material are also used. Due to differences
in the size and location of tumors, the number of slices varies
from case to case.
After training the classifier network's parameters, healthy
and tumor slices can be classified. In other words, by
examining all brain-MR slices, the classifier recognizes
between normal and abnormal slices. This not only helps to
identify the tumor existence but also determines the approxi-
mate location of the tumor in the brain. Also, the number of
slides that contain a trace of tumor informs about the
approximate size and grade of the tumor.
2.2. Pre-processing and normalization
In magnetic resonance imaging (MRI), specific image appear-
ances are obtained by setting some parameters such as
radiofrequency pulses and gradients. T1 and T2 are the most
common MRI sequences and each provides particular details
about tissues. For normal cases, T1 images are employed in
this study. In order to reduce the number of normal brain
images, six sections with approximately equal intervals have
been selected from MR images of each normal subject (person).
These six selected sections belong to a normal person are
shown in Fig. 1.
In the gadolinium-enhanced T1 MR images, due to the
injection of a contrast agent called Gadolinium, tumor
boundary can be better identified. The aforementioned images
are used to classify tumor grades in this study. For instance,
Fig. 2 depicts axial MR images of 3 different grades of Glioma
tumor with gadolinium injection. In addition, Fig. 3 gives
examples of three brain tumors images belong to Case Study II.
In this study, gadolinium-enhanced T1 images are
employed. All images that are used as the proposed network's
inputs are normalized using data rescaling which projects the
data into the [0,1] range and they are dimensioned 128
128
pixels.
In addition, in the proposed method one or several slices of
an MRI image are used and it is not necessary to use all slices or
3D images.
2.3. Data augmentation
Training a machine learning model on larger dataset is the
best way to generalize it and to reduce overfitting probability
[29]. Creating fake data and adding to dataset is simple and
straightforward and is done in the data augmentation step.
66 biocybernetics and biomedical engineering 39 (2019) 63–74
Fig. 2 – Examples of three different grades of Gliomas axial brain images: (a) Glioma Grade IV; (b) Glioma Grade III; (c) Glioma
Grade II.
Fig. 3 – Examples of axial brain images from the public dataset provided by Cheng et al.: (a) Glioma; (b) Meningioma;
(c) Pituitary tumors.
In the proposed method, some manipulated images were
added to the training set by applying random changes to the
original data. Rotation of 108, 208 or 308 clockwise or
counterclockwise, translating 15 pixel to right or left, scaling
to 0.75 of the original size, mirroring tumor MR images and a
combination of these changes were performed and resulted
images were added to the original datasets. The train and test
datasets are randomly selected from this new dataset.
After selecting images and increasing the number of data,
8000 normal MR images and 8000 glioma MR images were
provided for train and test. More specifically, there are 4000
GBM (grade IV) images, 2000 grade III and 2000 grade II tumor
images in the Glioma class. Note that 500 images are randomly
excluded from the dataset of each class and they are used for
test purposes.
Cheng et al. dataset consists of 989 axial images and same
data augmentation process is applied on it. 1521 images are
used for train and 115 images from each class are employed for
test.
3. Convolutional neural networks
Structure, layers, and parameters of convolutional neural
networks are described in this section. Deep learning
algorithms are subsets of machine learning algorithms in
the world of artificial intelligence. Using simple concepts, deep
learning enables the computer to create, characterize, and
recognize complex concepts. In other words, it enables the
multilayer models to learn representations of data with
multiple levels of abstraction [18].
Convolutional neural networks (CNNs) are one of the most
efficient supervised methods of deep learning which have
made remarkable improvements in image processing field.
Generally, convolutional, pooling, and fully connected are
three main layers of a convolutional network. In convolutional
layers, the network uses different kernels to convolve the
input image to create various feature maps. Applying this layer
will significantly reduce the number of parameters (weight
sharing) of the network and the network learns the correlation
between the neighbor pixels (local connectivity) [30].
There are two stages of training in every convolutional
neural network. In feedforward step input images are fed to
the network. In other words, dot product of the input vector
and parameters vector of each neuron is performed and look at
convolution operator in each layer is applied. Afterwards, the video
output is computed. By using a loss function, the network (3brow
output is compared with the desired output (correct answers) n1blue)
and the error rate is computed then, based on the error, back
propagation stage begins. Calculation of the gradient of each
parameter is done in this step using the chain rule and finally
all the parameters are updated. This is repeated for an
adequate number of iterations. More detailed explanations are
given below.
It should be noted that in order to keep the size of the
output unchanged, the input volume is padded with zeros
 biocybernetics and biomedical engineering 39 (2019) 63–74
Fig. 4 – An example of applying a convolution layer with
zero-padding method.
around the border (zero-padding). There are two padding
methods valid padding and same padding. In this paper same
padding is used for all the convolutional layers. Fig. 4 gives an
example of applying (or convolving) a 3
3 filter on a 4
4
input matrix. As it is seen, by adding zeros to the input matrix,
the size of the output matrix remains same as the input matrix
i.e. 4
4.
3.1. Weight initialization
Proper initial weights can speed up network convergence.
Various approaches for weight initialization have been
introduced in literature. In this study, after investigating the
impact of using different initializers, it was observed that the
best performance is obtained by employing 'He' initializer with
normal distribution [31].
3.2. Activation function
Generally, a nonlinear operator or activation function is used
in deep networks after convolutions. The presence of this
function riches the model in comparison with a linear model.
It is well-known that applying the rectified linear unit (ReLU)
activation function in deep networks increases the training
speed. ReLU simply projects negative values to zero and
is defined in (1).

Categorical cross-entropy function (H) is usually a good
x if x  0
reluðxÞ ¼ (1)
0 if x < 0
In many cases Leaky ReLU, defined in (2), has performed
better than ReLU. It allows a small, non-zero gradient when the
function is not active (or for negative values).

where q(x) is the estimate for true distribution p(x).
x if x  0
leakyreluðxÞ ¼ (2)
ax if x < 0
Usually, a = 0.3. Recently using exponential linear units
(ELUs) has led to an increase in training speed and classifica-
tion accuracy [32]. ELU accept negative values allowing it to
push mean unit activations closer to zero like batch normali-
zation but with less computational cost.


x if x  0
eluðxÞ ¼ (3)
aðex 1Þ if x < 0
67
a = 1. Performance of the evolving networks is also
examined in the presence of the scaled exponential linear
unit (SELU) activation function [33], see (4). By adding a little
twist to ELU the SELU comes into existence. The corresponding
equations of these functions are given below where, a = 1.6732
and l = 1.0507.


x if x  0
seluðxÞ ¼ l (4)
aex a if x < 0
3.3. Pooling
A pooling layer usually comes after a convolutional layer and
reduces the size of the feature maps and number of
parameters of the network which cause a decrease in
computational costs. Due to the consideration of neighboring
pixels in calculations, pooling layers are also invariant to small
changes. One of the most widely used pooling methods is
called max-pooling. In this paper, a max-pooling layer always
comes after each convolutional layer with filters of size 2
2
applied with a stride of 2 and take the maximum over four
numbers (Fig. 5).
3.4. Regularization
The main issue in machine learning is to generate an
algorithm that performs well not only on the training data,
but also on the new entries. Several regularization methods for
deep learning have been proposed. This paper uses dropout
which provides a computationally inexpensive, yet powerful
method for regularization. It randomly removes some nodes of
the fully connected layer in the training phase, to prevent
overfitting. On the other hand, dropout is considered as an
ensemble method, since it provides different networks during
training.
3.5. Loss function
One of the important aspects of designing a deep neural
network is the selection of the loss function to be minimized.
candidate and has been used here. It is defined for two
distributions ( p and q) over discrete variable x and is given by:
X
Hðp; qÞ ¼  pðxÞlnðqðxÞÞ (5)
x
Fig. 5 – An example of a max-pooling layer.
68 biocybernetics and biomedical engineering 39 (2019) 63–74
3.6. Training
In order to train a deep network, the loss function must be
minimized by a gradient-based optimization algorithm.
Stochastic gradient descent (SGD) is widely used as an
optimizer in deep learning [18]. Recently a method for
stochastic optimization called Adaptive moment estimation
(Adam) is presented in [34]. It is demonstrated that Adam
works better than customary optimization algorithms.
Furthermore, its computational efficiency in the presence
of large dataset is a privilege of this method. Learning rate for
updating the weights will remain constant in SGD algorithm,
however Adam algorithm computes adaptive learning rates
by estimating the first moment (the mean) and the second
moment (the uncentered variance) of the gradients. Other
optimizers like Adagrad, Adadelta, Adamax and Nadam were
also examined in this study. In Adagrad optimizer, the
learning rate adapts to the parameters. This happens by
doing larger updates for infrequent parameters compared to
frequent parameters [35]. Unlike Adagrad which accumulates
all past squared gradients, Adadelta limits the size of the
window of the accumulated previous gradients [36]. Adamax
is a variant of Adam optimizer based on the infinity norm.
Nadam combines Adam and Nesterov Accelerated Gradient
optimizers [37]. In Nadam, before computing the gradient,
parameters with the momentum step are updated and this
makes it possible to take more precise steps in the gradient
direction.
The values of all these optimizers' parameters, other than
the learning rate, are selected based on the author's
recommendation.
4. Designing the network architecture
Typically, a desirable network architecture is found by
testing various common network structures. This process
requires a lot of trial and error and, of course high
computational cost. In this study, various CNN architectures
for the task of MRI image classification are evolved using
genetic algorithm (GA) [38]. Instead of training and compar-
ing more than one million different architectures, by
employing GA and comparing less than 500 architectures a
suitable architecture was discovered. Thus, the computa-
tional costs are decreased.
More details on selecting the network architecture
are given below.
Table 1 – The parameters employed to evolve the best CNN structure and their associated values.
Number of convolutional + max pooling layers
Number of fully connected + dropout layers
Number of filters
Kernel sizes
Number of fully connected neurons
Activation functions
Feedforward optimizers
Learning rate
Dropout rate
4.1. Genetic algorithms
The mechanism of natural selection is simulated in GAs. After
each generation the fittest individual of the population will
survive and produce more offspring in the next generation.
Sometimes a mutation occurs and an offspring with a new
characteristic is created. After several generations superior
individuals appear to be more likely to survive [38].
In this study, GA is implemented to evolve the best
structure of the CNN by choosing proper parameters for the
network. These parameters are number of convolutional and
max-pooling layers, number of filters and size of them,
number of fully connected layers, activation function, dropout
probability, optimization method and learning rate. The
values associated with these parameters are specified in
Table 1.
Considering the parameters of Table 1, over one million
different architectures are possible for the CNN. Directly
searching these possible architecture to find the best is not
possible however, GA will ease this search. The flowchart of the
genetic algorithm used in this research is illustrated in Fig. 6.
Initially, 50 networks with random parameters are created as
initial populations. Each network will be trained by 80 percent
of data and 20 percent of data are used as validation dataset.
Validation accuracy is considered as a criterion for retaining or
rejecting the network in the next generation. In the proposed
method, GA is stopped if early stopping criterion is satisfied or
the number of generations exceeds the pre-specified maximum
number of generations. Early stopping criterion is when no
improvement happens in the validation accuracy (loss func-
tion) of three sequent epochs. The early stopping criterion is
implemented in order to reduce computational costs. In this
paper, maximum number of generations is 15.
According to the validation accuracy, 40 percent of best
networks or elites will retain and move to the next generation.
With 10 percent probability rejected networks also have a
chance to be transferred to the next generation. In other
words, top 20 networks are directly entering the next
generation, and 30 other rejected networks might retain and
enter next generation by 0.1 probability. The other members of
the next generation are created through applying selection
and crossover operators. In addition, there is 20 percent
chance that a network structure is randomly mutated. This
process is repeated until stopped based on the flowchart, and
finally the network architecture that has the best performance
is selected as the main network architecture for the
classification.
2, 3, 4, 5, 6
1, 2, 3
16, 24, 32, 48, 64, 96, 128
2, 3, 4, 5, 6, 7
128, 192, 256, 384, 512
ReLU, Leaky ReLU, ELU, SELU
SGD, ADAM, ADAMAX, NADAM, ADAGRAD, ADADELTA
1e4, 1e3, 1e2
0.1, 0.2, 0.3, 0.4, 0.5
 biocybernetics and biomedical engineering 39 (2019) 63–74 69

Fig. 6 – Genetic Algorithm Flowchart.

4.2. Bagging
Bagging (or Bootstrap Aggregating) is an ensemble method
that reduce the generalization error by combining multiple
models or classifiers [39]. Bagging is a subset of a general
method for machine learning called the model averaging.
Different models do not usually create similar errors on the
test set, for this reason the model averaging works. The idea is
to train separate classifiers and then evaluate the output for
test samples by each classifier. A compound classifier is then
created as the aggregation of each particular classifiers.
In order to decrease the variance of classification error, bagging
is used on the best model evolved by the GA. First, all training and
validation images are concatenated to form a combined set. This
combined set then permuted and new training set and validation
set are randomly selected. 75 percent of the combined set is used
as training set and the remaining images are placed in the
validation set. Using the new training set all the variables are
optimized. Here, the optimization is performed with 10,000
iterations and this process is repeated 5 times. It was observed
that implementing this method improve the results.
5. Results
In this section, evaluation criteria are described and the results of
the proposed method for two case studies are presented, refer to
Section 2.1. As previously mentioned, convolutional networks
were created with random architectures, and in every iteration
of 15 GA generations better networks were evolved. Classifica-
tion accuracy of validation dataset is considered as genetic
algorithm criteria for improving networks' architecture. Accord-
70 biocybernetics and biomedical engineering 39 (2019) 63–74
Fig. 7 – Average validation accuracy of consecutive
generations of GA.
ing to Fig. 7, the average validation accuracy of 15 consecutive GA
generations had an overall increasing rate. Network that resulted
in the highest accuracy on validation dataset has been selected
and used as the classifier. In addition, applying bagging
ensemble method on the best model evolved by the GA,
increases the classification accuracy by almost 2%.
Case Study I
For classifying Glioma grades, it has been found that the
superior networks proposed by the genetic algorithm, all consist
of five convolutional and max-pooling layers as well as one fully
connected layer. Furthermore, rectified linear unit is used in
these superior networks as the activation function. The number
of neurons and dropout rate are the only difference between
these networks. On the other hand, Adam optimization method
is performed better than others, and the cost functions of the best
networks are optimized using this algorithm. Fig. 8(a) illustrates
the architecture of the proposed CNN for this case study.
Case Study II
In this case study, the network that has achieved the best
performance for classifying three types of tumors, has six
convolutional and max-pooling layers and one fully connected
layer with 384 neurons. ELU has been used in the structure of
Fig. 8 – Best CNN architectures provided by GA: (a) Case Study I; (b) Case Study II.
superior network as the activation function. Like Case Study I,
Adam is preferred to the rest of the optimization methods.
In Fig. 8(b), the structure of this network is presented in more
details.
In order to observe the performance of the models obtained
by GA, for each case study 100 epochs were trained. 20 percent
of training set is used for validation. From Fig. 9 it is seen that
the training process is done properly. The loss function almost
steadily reduced and accuracy is increased with a suitable
slope. In addition, validation has followed training to a
satisfactory level. Therefore, it is concluded that the archi-
tectures proposed by GA are sufficiently efficient.
5.1. Evaluation
The performance of a classification algorithm is evaluated in
variety of ways. Here, the confusion matrix is used to check the
performance (Fig. 10). This matrix gives valuable information
about the actual and predicted labels provided by the proposed
classification method. Using this information, the perfor-
mance is assessed from different aspects.
The diagonal values represent true positives (TP). Simply
put, the number of samples that classifier detects the condition
when the condition is present. True negatives (TN) are those
that do not detect the condition when the condition is absent.
False positives (FP) count the cases which classifier detects the
condition when the condition is absent. False negatives (FN) are
those that do not detect the condition when the condition is
present. Values corresponding to the mentioned definitions are
derived from the confusion matrices and are given in Table 2.
By calculating various quantities and ratios, the performance of
the proposed method for classifying MR brain tumor images are
characterized and compared in this table, as well.
6. Discussion
From Table 2 it is seen that the proposed method in almost all
cases has detected tumors with high precision. Also, in order to
 biocybernetics and biomedical engineering 39 (2019) 63–74 71

Fig. 9 – Loss and accuracy variations during 100 epochs for: (a, b) Case Study I; (c, d) Case Study II. Solid lines and dash dot
lines are related to the training dataset and validation dataset, respectively.

evaluate more precisely, various criteria have been investigated.
In Case Study I, Normal images were classified exceptional.
Glioblastoma multiform tumors that are the most common and
most malignant brain tumors were classified with an excellent
sensitivity of 97.4% and a total accuracy of 96.1%. In addition,
about 95% of grade II and grade III tumors were correctly
classified. By dividing correct predictions by all test data, multi-
class classification accuracy is calculated. Thus, in 4 classes, the
classification accuracy is 93.1% and if only classification of
Glioma grades is considered, 90.9% accuracy is obtained.
72 biocybernetics and biomedical engineering 39 (2019) 63–74

Fig. 10 – Confusion matrices for (a) Case Study I and (b) Case Study II.

Table 2 – Evaluation of the proposed method.

TP FP TN FN
Case Study I
Normal 499 6 1494 1
Grade II 442 32 1468 58
Grade III 434 34 1466 66
Grade IV 487 66 1434 13

Case Study II
Glioma 113 10 220 2
Meningioma 101 5 225 14
Pituitary 111 5 225 4

TPR TNR PPV NPV FPR FNR FDR ACC

Case Study I
Normal 0.998 0.996 0.988 0.999 0.004 0.002 0.012 0.997
Grade II 0.884 0.979 0.932 0.962 0.021 0.116 0.068 0.955
Grade III 0.868 0.977 0.927 0.957 0.023 0.132 0.073 0.950
Grade IV 0.974 0.956 0.881 0.991 0.044 0.026 0.119 0.961

Case Study II
Glioma 0.983 0.957 0.919 0.991 0.043 0.017 0.081 0.965
Meningioma 0.878 0.978 0.953 0.941 0.022 0.122 0.047 0.945
Pituitary 0.965 0.978 0.957 0.983 0.022 0.035 0.043 0.974

TP = True positive (hits).

TN = True negative (correct rejections).
FP = False positive (false alarms or type I error).
FN = False negative (miss or type II error).
TPR = True positive rate (hit rate or sensitivity) = TP/(TP + FN).
TNR = True negative rate or specificity = TN/(TN + FP).
PPV = Positive predictive value or precision = TP/(TP + FP).
NPV = Negative predictive value = TN/(TN + FN).
FPR = False positive rate (fall-out) = FP/(FP + TN).
FNR = False negative rate (miss rate) = FN/(TP + FN).
FDR = False discovery rate = FP/(TP + FP).
ACC = Overall accuracy = (TP + TN)/(P + N) = (TP + TN)/(TP + FP + FN + TN).

According to the results obtained for Case Study II, overall
accuracies for classifying Glioma, Meningioma and Pituitary
tumors were 96.5, 94.5 and 97.4 percent respectively. In this
case, 94.2% of the network predictions were correct. By
reviewing the results of the classifications, the great ability
of the proposed classification method to classify different MR
brain images is confirmed.
The ability of CNNs and on a larger scale deep learning
algorithms to process and classify images has been proved in
many researches. As it is clear from the results of this study,
it has also had a great performance here. An important aspect
for providing an efficient neural network for specific problems,
is to determine the proper architecture. In [40] it is demon-
strated that using convolutional neural networks with
complex structures do not guarantee a better result compared
to simpler structures. In this article, a fully automated
procedure for selecting the network structure and its param-
eters has been used. As previously stated, the genetic
algorithm has had an acceptable performance in finding a
suitable network for our particular application and the usage
 biocybernetics and biomedical engineering 39 (2019) 63–74
Table 3 – Comparison of the proposed method
with related works.
Approach Classification
accuracya
Case Study I – Glioma Grade II/Grade III/Grade IV
SVM + RFE 62.5%
(Zacharaki et al.
[14])
Proposed method 90.9%
Case Study II – Glioma/Meningioma/Pituitary
Vanilla 91.43%
preprocessing
+ shallow CNN
(Paul et al. [15])
Proposed method 94.2%
a
Classification accuracy = (correct predictions/number of all data),
using test dataset.
of bagging method was also beneficial. Table 3 compares the
performance of the proposed method with similar tasks. As is
seen, the proposed method is superior to existing methods for
classifying similar MR brain tumor classes.
The binary classification of the tumor grades proposed by
Zacharaki et al. [15] had achieved 62.5% accuracy for
classifying three glioma grades. As specified in Table 3, the
present method of this paper is about 30 percent more
accurate. Paul et al. [16] have proposed a CNN classifier using a
dataset provided by Cheng et al. [28]. Using the same dataset,
as is shown in Table 3, the proposed method also has
performed better accuracy.
7. Conclusions
In summary, in this study a CNN-based method for classifying
Glioma brain tumor MR images is proposed. Genetic algorithm
was utilized to search for a CNN structure that produces better
results. The proposed method not only has been grading
Glioma tumors with high precision, but also has been very
successful in classifying images of various types of brain
tumors.
In the proposed algorithm, classification of various grades
of Glioma and two other widespread tumor types are carried
out with high precision. There is no requirement to perform
time-consuming processes such as skull stripping or segmen-
tation and the decision is just made by the raw data of MR
images. Proposed method can be manipulated as a secondary
option for early detection in a non-invasive procedure. In
addition, the time required for the classification is very short in
comparison to the time required for analyzing biopsy.
Consequently, the proper action can be taken on proper time
with respect to the severity of the tumor.
Most of the proposed schemes in this area comprise of the
region-of-interest definition, manual feature extraction, fea-
ture selection and finally classification. In contrast, the
proposed deep learning method extracts useful features
automatically, and thus providing a feature extracting method
is not required. Using a network architecture that performs
well on some data may lead to poor results for another set of
73
data. Therefore, it is necessary to compare different network
architectures to reach the desired objective. Because it is
impossible to evaluate all possible cases, in this research GA is
performed to specify an appropriate network architecture with
far less computations. Applying Bagging algorithm on the best
network suggested by GA was also effective and has improved
the accuracy of the classification according to Table 2. This
table reflects the success of the proposed method to classify
brain tumors type via MR images.
Although it has been shown in this paper that the proposed
method yields better performance compared to similar
literature, larger datasets with several tumor types and other
CNN structures and deep learning algorithms in future works
may lead to better performances.
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