MR Image based Brain Tumor Classification with Deep Learning
Neural Networks
SHWETHA V.
C. H. RENU MADHAVI
R. V. College of Engineering, Bengaluru,
Affiliated to VTU, Belagavi and
S.J.C.Institute of Technology,
Chickballapur, INDIA
Department of Electronics and Instrumentation
Engineering, R V College of Engineering,
Bengaluru, INDIA
Abstract: - The unique combination of Artificial Intelligence and Machine Learning, which helps the computer
to imitate the ways and behaviour of human beings can be termed as deep learning. The field of deep learning
is an emerging field that has gained a lot of interest toward past years. The Deep Learning have proven already
to solve the complex problem using the powerful machine learning tools. One of the best deep learning
algorithm is used to classify the brain tumor data set in this paper. The deep learning architecture is able to
classify the brain tumor into 4 categories of images. The first being no tumor, the second being pituitary tumor,
the third is meningioma and the last one classified as glioma. As we are well aware, the training datasets for the
medical imaging scenario are very few. This is a challenging task to apply the deep learning that is obtained
from a trained CNN model to dig up the small data set to attain the result. A pre trained CNN model is used
here to solve the problem. The obtained results are good over all Performance is measured.
Key-words: - Artificial Intelligence, Machine Learning, Brain Tumor, CNN, Kaggle database, MRI.
Received: May 15, 2021. Revised: February 23, 2022. Accepted: March 27, 2022. Published: April 29, 2022.
1 Introduction
The complete nervous system of human body is
commanded and controlled by the very sensitive and
crucial organ of human being called brain. Alone in
United States of America, according to the survey
conducted by national Brain tumor society, 7,00,000
people live with brain tumors, the chances of
increasing the cases might be beyond 7.8 lakhs by
the end of 2021[1]. Breast cancers and lung cancer
are the most widely found cancers on the planet.
Even though the brain tumors are little uncommon,
but still, it ranks as a 10th leading cause for death.
Brain is the organ that controls the activity of a
human, If the patient is suffering from brain tumor,
definitely it will impact on the patient’s life
psychological behavior. As the other cancers, even
the brain tumor, is caused by the tissue
abnormalities. These abnormalities are found in the
central spine that interrupts the proper functionality
of the brain. In current date we can have several
methods to identify the tumor, few of them are MRI
scanning, EEG, CT scanning and others[8]. The
figure:1, shows the healthy brain and the brain with
a tumor disorder when taken with MRI images.
The major improvement of the MRI based imaging
when compared with the CT scan technique is the
capturing of the all-possible information in the test
sample under consideration with minimized effect of
the radiation on the medical subject under
investigation.
While capturing the image with MRI technique a
specific dye will be utilized for the classification
among brain tumor cells and healthy brain cells
under investigation. In conventional approach of
brain image analysis which can be named as white
matter, cerebrospinal liquid and grey matter, but for
detailing analysis which are done using the three-
dimensional planar analysis such as axial, coronal
and sagittal planes respectively as depicted in Fig. 2.
Fig. 1: Healthy brain and Brain with Tumor
The axial planar based analysis of images are
captured from head to chin as shown in Fig. 2 (c),
sagittal planar images are utilized for the right to left
ear as represented in Fig. 2 (b) and with respect to
Fig. 2 (a) coronal image based analysis. Similarly,
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the few weights are considered individually for the
analysis such as T1, T2 and Proton density weights
for MRI analysis.
Fig. 2: (a) Coronal image; (b) Sagittal image; (c)
Axial image [5]
Based on the classification that has been described
by World Health Organization (WHO), there are
about 120 types of brain tumors. These brain tumors
differ in characteristics, location, size and origin.
Among these types of brain tumors, here in this
paper, only three types are considered, which are:
1. The tumor that grows in the area of spinal
cord and glia tissue, which is called as glioma.
2. The tumor that can grow in the area of
membrane called as Meningioma.
3. The tumor that grows in the pituitary gland
area, which is called as pituitary tumor.
Figure 3 shows the different MRI images of tumors
are in a different place. In all the three images the
tumors are marked with the red outline.
Fig. 3: A normalized MRI image that shows
different forms of tumor. In each image, the tumor is
marked with red outline.
2 Review of Literature
In image processing techniques, primarily for
tumour region spotting in image identification with
segmentation it is deployed with the deep learning
and AI (Artificial Intelligence). Till date an huge
amount of works are carried in the domain of
biomedical engineering.
Badza et al. [2] discuss about new architecture of
brain tumor classification based on CNN. He
proposes a simpler system rather than the existing
complicated one. The system is capable of
classifying three types of tumors. It was mainly
based on T1 weighted contrast enhancement
magnetic resonance images. The accuracy obtained
for this system was about 96.56%.
Ruba et al., proposes a model for both the CT image
and MRI image in [3]. It shows a modified segment
semantic network, that is based on the CNN. The
paper shows a good accuracy for all the three types
of tumors. For glioma being 99.78%, for pituitary
tumor being 99.56% and four million men in glioma
99.57% of accuracy.
Kalaiselvi et al., proposes and recurrent neural
network in [4]. This paper is based on the extraction
of features from the brain image. The results of the
experiment conducted in the classification of the
tumor gives an accuracy of 98%.
Cinarer et al., mentions about a deep neural network
classification [5]. With a technique called Synthetic
Minority Oversampling Techniques, considering the
data set as Rembrandt images, this technique is used
for preprocessing. This method has achieved about
95% of accuracy rate. This method provides an F1
measure of 94.9%. The Precision of 95.4%, and the
recall value as 95%.
Sajja et al.[6] proposed a hybridized algorithm on
CNN. The open database images are considered
from BRATS, These images were based on MRI
brain images. The proposed model achieved 96.15%
of accuracy.
Khan et al.[7], proposed an automated, multimodal
classification method that utilizes the deep learning
for classifying the brain tumors. The results obtained
are, 97.8%,96.9%, 92.5% for BraTs2015,
BraTs2017, and BraTs2018, respectively, was
achieved using proposed method.
Khan et al.[8], introduces a new approach using
convolutional neural network in the image
processing and data acquisition. The cancerous and
non cancerous MRI images are used. The results of
the experiment shows the model is highly efficient
by achieving 100% accuracy. The other parameters
like ResNet-50 obtained as 89%, VGG-16 is
obtained as 96% and the Inception-V3 achieved 75%
of accuracy.
Suganthe et al.[9] tells about a recurrent neural
network architecture for the classification of brain
tumors that can detect the brain tumors with an
accuracy of 90%.
3 Methodology
3.1 Image Acquisition
It is the first step in the proposed methodology, in
which this stage of operations are done using the
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suitable hardware such as mobile phone, digital
camera and many other devices for the collection of
the data source from unified surface. The image
acquisition is the initial step for every image
processing system, by the acquisition of the image
various available techniques are performed
according to the specific need. For the process of
image acquisition in particular to the MRI data an
high precision devices are deployed for the capturing
of the brain data [4].
3.2 Image Pre Processing
This step is next process after image acquisition.
MRI data is degraded by several noises like speckle,
Gaussian, and Salt and Pepper noise. Through
denoising, the corrupted images can be converted to
high quality images. The denoising technique used
to remove noise is Anisotropic diffusion filter.
3.3 Classification of Brain MRI Images
A hybridized convolution neural networks as an
healthy brain and pains with A hybridized
convolution neural network is used in this paper to
classify the brain MRI images as an healthy brain
and brains with a tumor.
3.4 Architecture of CNN
The classification capability of CNN model is very
high based on the contextual information. There are
4 major layer divisions in CNN model as in Fig 4.
The first one is convolution layer, the second is
pooling layer, then activation function and the final
is fully connected layer. Based on the features
extracted from the images classification is done
accordingly in the output layer. Based on receptive
field, the image local features from the input images
are extracted. The neurons of the currently are
interconnected with the neurons of the previous
layer. This interconnection will generate the weight
vector. Based on the neurons that share the same
weight, in the different locations of input data
image; the classification of the image can be done.
In the pooling layer, if the feature has been extracted
and detected, it becomes less significant. The
pooling layer is also called as subsampling Layer.
The number of trainable parameters will be suddenly
reduced if pulling layer is used. The pooling
function takes the input elements as input and
process the data, as a result of which output vector is
generated. There are two pooling techniques, Max
pooling and average pooling. Among which, Max-
Pooling id widely used. The Max pooling reduces
the map size. Fully connected layer is very similar to
fully connected network. The dot product of input
vector and the weight vector is calculated, In order
to develop the final output. The functionality cost is
reduced when gradient descent is used. There are
sevral architectures in CNN few of them are, LeNet
Architecture, AlexNet Architecture, GoogleNet
Architecture and others.
Fig. 4: Architecture of the convolutional neural
network
The methods proposed by convolution neural
network.
The new method proposed by the convolution neural
network is depicted in the figure 5. This complete
structure is made out of five layers. The four layers
are Max pooling layer, convolution layer, flattened
layer, fully connected layer and finally the output
layer. We can see a significant change in the
improvement of accuracy when the convolution
layer is increased. By the increase of convolution
layer, even the noise in the input images can also be
reduced, this resulting in more interpretability of the
system. The pooling layer plays a crucial role.
Again, where if the pooling layer size is increased,
the features can also be underlined in more precise
way. This also improves the training time by
reducing the image Size.
a) Input layer
This is the primary layer, which is direct interface to
fetch the MRI images from the user end for feature
extraction at the next layer.
b) Convolutional layer
The very next layer to the input layer is an bi-
dimensional layer which is convolutional in nature.
In this layer for the orientation of the required
amount of filters are employed for the feature
extraction from the input MRI image. With the
extracted features from the MRI data are utilized for
the calculation of the similarity indexes. The
convolutional operation is conventionally termed as
mutual product of j and I object functions with the
interval [0,k] given by (3).
[]()=󰇛󰇜󰇛 󰇜
(3)
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Fig. 5: Proposed convolutional neural networks
A brief explanation of each layer is mentioned
below.
The output image of the size 64 X 64 pixels with the
performance of the convolution operation with 3 X 3
filters is applied on MRI image of dimension 64 X
64 X 3 , output image is represented in (4).
[
 󰇠+1 (4)
The output image with size of 64x64 is applied to
the max-pooling layer. In the similar manner, all
convolution layers are estimated in the proposed
network.
This is an linear function, where the resultant
obtained in accordance with the applied input if and
only if it is non-negative. ReLU is a novel and
mandatory triggering feature for various types of
neural networks as a mannequin utilizes an simpler
manner for the instruction to attain improved
performance. Its operations are relatively linear for
the values non zero, which implies the training of
neural network in backward propagation. The other
interesting feature of the ReLU function is the
normalized values to zero for other intermediate
values of non-positive hence it is nonlinear function
for the rest of the values which will be given by (5).
󰇛󰇜󰇥
 (5)
d) Max pooling layer
The pooling layer is very essential in terms of
minimizing the dimension of operation. The
minimization of the numbers of neurons in the
output of the convolutional layer, the pooling
algorithm is the hybrid combination of the adjacent
members available in the output convolution matrix.
Commonly used pooling algorithms are average and
Max Pooling. In this article of research, the two
dimensional convolution layer outcome is the
feeding input to the max-pooling layer, the max-
pooling layer output images can be estimated as
shown in (6)
[ 
 󰇠+1 (6)
where, padding (pa) is 0,number of stride (st) is 2, O
is 64×64,and size of the filter (fi) is 3×3 .So, the size
of the image produced from the max pooling layer is
32×32 ([(64+0−2)/2]+ 1). For the remaining max
pooling layers, the same approach has been
employed in the proposed architecture.
e) Flatten layer
With the following from the max-pooling and
convolution operations and multi-dimensional tensor
is mandatory at the output part, an uni dimensional
tensor is required. This is attained in the flatten layer
which are fully connected to the input layer.
f) Fully connected layer
Similar to that of feedforward neural network, Each
node in the fully connected layer is interconnected
with the other nodes. The function of activation is
much needed for MRI images to be classified.
To train the classifier, the epoch in the CNN are
increased to an adequate manner. This resulting in a
better performance. The weight updating function is
used to update the weights, while moving from
epoch to epoch, as mentioned in the equation. 7.
= + Δ (7)
where Δ = () (8)
g) Transfer learning of CNN (EfficientNet)
During the process of training, as mentioned in the
above, the weights of the CNN is updated after each
iteration. In the current design, there are 4,012,672
trainable parameters and 237 layers in EfficientNet
architecture. A considerably large data set has to be
taken to train and to optimize such DN. To calculate
the appropriate local minima, cost function will be
very difficult if the data set is smaller, and also
resulting in overfitting of the model. So the
initialization of the weight will be taken from pre-
trained EfficientNet model.
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4 Result Analysis
4.1 Classification of Brain MRI Images
In this research article for the testing of the designed
architecture of classifier for the brain tumour over
the wide range of public available database it is
chosen to operate with the KAGGLE dataset, in
which 394 test images which is the association of
100 MRI images with glioma tumor,115 Images
with Meningioma tumor,74 Images with Pituitary
tumor and healthy person MRI images of 105. In the
context of the research proposed for the classifier
approach it is considered with the 104 MRI images
with disorder oriented dataset and 65 normal dataset
of MRI images. For the classifier oriented
investigation it is done with the 105 usual healthy
person MRI data along with the 100 MRI images
with glioma,115 images with meningioma and 74
images with pituitary tumor. The distribution table
of KAGGLE database is as shown in Table 1.
Table 1. KAGGLE Dataset Distribution.
Kaggle
/
Tumor
Catego
ry
meni
ngio
ma
Pitui
tary
No
tu
mo
r
Tota
l
Trainin
g
822
827
395
2870
Testing
115
74
105
394
Total
937
901
400
3264
Some of the overall performance metrics considered
is accuracy, confusion matrix, precision, recall, and
F1 Score. From the matrix of confusion, most
performance measurements are calculated.
Performance evaluation metrics of any classifier can
be calculated using four basic building blocks.
Those are TP, FP, TN and FN. Those building
blocks are explained in Table 2 in detail. Predicted
values are taken on the X-axis and actual values are
taken on the Y-axis.
Table 2.Building blocks of classifier in Confusion
matrix
CLASS
PREDICTED
Tota
l
Positiv
e
Negativ
e
Actual
Positive
TP
FN
P
Negativ
e
FP
TN
N
Total
P
N
P+N
The rate correct identification and incorrect
identifications can be categorized as two major
segmentations logically viz., True and False
respectively. As an sub set to make sure as similar to
the confusion matrix for grouping it can be broadly
fall into Positive and Negative values making it into
four various corners of the confusion matrix such as
TP,TN,FP & FN termed as True Positive, True
Negative, False Positive and False Negative
respectively.
The recall or the sensitivity are the main Para meters
to estimate the performance of a true positive values.
It analyses the presence of true positive cases
correctly and classify the actual positive cases of the
data set using (9).
 󰇛󰇜
󰇛󰇜 (9)
Precision is the parameter used for the measurement
of the exact correct prediction which can be given by
(10). it computes the percentage of positive cases
that are correctly.
Precision = 
 (10)
The classifier performance is gauged in terms of
percentage for all the cases such as positive and
negative in terms of accuracy which can be given by
(11).
 󰇛󰇜
󰇛󰇜 (11)
For the accurate measurement of the recalls and
precisions in a single attempt it is employed with
calculation of the F1 Score which can be interpreted
as shown in (12)
F1score (F) =
 (12)
The Specifity decides the performance of true
negative rate. The percentage of negative cases that
are correctly classified from the actual negative
cases using the data set is being calculated using
(13).
Specificity = 
 (13)
The complete exercise was conducted using Google
Colab notebook, The code was written using Python,
and the data set is downloaded from Kaggle. The
heatmap of the confusion matrix created by the
classifier is mentioned in the figure 6.
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Fig. 6: Contingency matrix for the pre-trained model
Obtained result interpretation is carried out with the
confusion matrix, upon the test procedure of 84
different variants of data images with the CNN
classifier utilized for training of the 394 data images,
in which 91 images were correctly classified as
glioma tumor,92 images were classified as
meningioma tumor properly,85 images were
correctly as pituitary tumor and the 51 images were
classified as healthy images. The performance
criteria of first model and second model is tabulated
in Table 3 and 4 The pre-trained model has reached
F1 score of 98%, 98% of precision, 98% of
specificity and accuracy as 98% as tabulated in
Table 5 and represented in Fig. 6.
Table 3. Performance criteria of first model
First model
Precision
Recall
F1-
score
Support
0
0.56
0.95
0.70
105
1
0.76
0.19
0.30
100
2
0.81
0.83
0.82
115
3
0.82
0.78
0.80
74
AVG
0.73
0.69
0.66
---
Accuracy
0.69
394
Table 4. Performance criteria of second model
Second model
Precision
Recall
F1-
score
Support
0
0.59
0.96
0.73
105
1
0.95
0.18
0.30
100
2
0.73
0.83
0.78
115
3
0.89
0.88
0.88
74
AVG
0.79
0.71
0.67
---
Accuracy
0.71
394
Table 5. Performance criteria of Pre-trained model
Pre-trained model
Precisio
n
Recall
F1-
score
Suppor
t
0
0.99
0.98
0.98
105
1
1.00
1.00
1.00
100
2
0.96
0.96
0.96
115
3
0.97
0.98
0.97
74
AVG
0.98
0.98
0.98
---
Accur
acy
0.98
394
4.2 Performance Analysis of Proposed Model
For the pictorial representation of the accuracy and
training data loss rate and testing data using pre-
trained model is shown in Fig. 6.With the
comparative analysis from Fig. 7 and Table 6, it can
be clearly stated that accuracy of first model is
improved with the increased number of layers and
epochs in second model but it can be greatly
increased if a pre-trained model is used for
classification. A pre-trained model Efficientnet is
used in this paper.
Fig. 6:Accuracy and Loss of Pre-trained Model.
Fig. 7: Comparative analysis of different CNN
models
0
0,2
0,4
0,6
0,8
1
1,2
First Model
Second Model
Pretrained
Model
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Table 6: Results comparison of different CNN
models.
Precisio
n
Recal
l
F1 -
scor
e
Accurac
y
First Model
0.73
0.69
0.66
0.69
Second
Model
0.79
0.71
0.67
0.71
Pre-trained
Model
0.98
0.98
0.98
0.98
5 Conclusion
In the present research context, it is considered with
KAGGLE dataset for the analysis of the classifier
performance. Initially, MRI image denoising was
done using Anisotropic diffusion filter. In the
training phase for CNN classifier it achieved with
the almost four hundred normal images, eight
hundred images with glioma, eight hundred images
with meningioma and eight hundred images with
pituitary tumor, in total around three thousand
images were considered for the data model. The
designed Convolutional Neural Networks were
aimed to identify the type of brain tumor from the
database under consideration with the classifier
approach is carried out with 100 image sets with
glioma tumor,115 images with meningioma
tumor,74 images with pituitary tumor and 105
normal images making in total of 394 image sets. A
hybrid CNN model has been presented, with feed
forward neural network as a seed, with the
incremental values of epochs, it is assured to have
higher accuracy due to higher rate of training states.
An individual Epoch is defined as the entire process
to reach the output layer from the input layer for the
calculation of the Accuracy, Precision, Specificity,
Sensitivity and F1 score. It is observed from the
results that 69% of accuracy for the first CNN
model. When the number of layers and epochs were
increased in the second model, the accuracy was
increased to 71%. Finally, by using the pre-trained
model 98% accuracy was achieved. The major gain
in the classifier proposed to the MRI images of the
brain was more accurate when a pre-trained model
was used. Other factor of improvement as a future
scope is to minimize the processing time to process
the tumor images as a design constraint.
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[10] Ali Mohammad Alqudah, Hiam Alquraan,
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DOI: 10.37394/23203.2022.17.22
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