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Classification using Deep Learning Neural Networks for Brain Tumors

Article · December 2017

DOI: 10.1016/j.fcij.2017.12.001

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Future Computing and Informatics Journal xx (2017) 1e4
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Classification using deep learning neural networks for brain tumors

Heba Mohsen a,*, El-Sayed A. El-Dahshan b,c, El-Sayed M. El-Horbaty d, Abdel-Badeeh M. Salem d
a
Faculty of Computers and Information Technology, Future University, Cairo, Egypt
b
Egyptian E-Learning University, Giza, Egypt
c
Faculty of Science, Ain Shams University, Cairo, Egypt
d
Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt
Received 26 October 2017; accepted 5 December 2017
Available online ▪ ▪ ▪

Abstract

Deep Learning is a new machine learning field that gained a lot of interest over the past few years. It was widely applied to several ap-
plications and proven to be a powerful machine learning tool for many of the complex problems. In this paper we used Deep Neural Network
classifier which is one of the DL architectures for classifying a dataset of 66 brain MRIs into 4 classes e.g. normal, glioblastoma, sarcoma and
metastatic bronchogenic carcinoma tumors. The classifier was combined with the discrete wavelet transform (DWT) the powerful feature
extraction tool and principal components analysis (PCA) and the evaluation of the performance was quite good over all the performance
measures.
Copyright © 2017 Faculty of Computers and Information Technology, Future University in Egypt. Production and hosting by Elsevier B.V. This
is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Keywords: Machine learning; Deep learning; Deep neural network; Discrete wavelet transform; Principle component analysis; Fuzzy c-means; Magnetic resonance
images

1. Introduction called primary malignant tumor or to be originated elsewhere

in the body and spread to the brain which called secondary
Brain is one of the most complex organs in the human body malignant tumor [3e5].
that works with billions of cells. A brain tumor arise when Brain magnetic resonance imaging (MRI) is one of the best
there is uncontrolled division of cells forming an abnormal imaging techniques that researchers relied on for detecting the
group of cells around or inside the brain. That group of cells brain tumors and modeling of the tumor progression in both
can affect the normal functionality of the brain activity and the detection and the treatment phases. MRI images have a big
destroy the healthy cells [1,2]. Brain tumors classified to impact in the automatic medical image analysis field for its
benign or low-grade (grade I and II) and malignant tumors or ability to provide a lot of information about the brain structure
high-grade (grade III and IV). Benign tumors are non- and abnormalities within the brain tissues due to the high
progressive (non-cancerous) so considered to be less aggres- resolution of the images [3,6e8]. In fact, Researchers pre-
sive, they originated in the brain and grows slowly; also it sented different automated approaches for brain tumors
cannot spread to anywhere else in the body. However, ma- detection and type classification using brain MRI images since
lignant tumors are cancerous and grow rapidly with undefined it became possible to scan and load medical images to the
boundaries. They can be originated in the brain itself which computer. However, Support Vector Machine (SVM) and
Neural Networks (NN) are the widely used approaches for
* Corresponding author. their good performance over the last few decades [9]. But
E-mail address: [email protected] (H. Mohsen).
Peer review under responsibility of Faculty of Computers and Information
recently, deep learning (DL) models set an exciting trend in
Technology, Future University in Egypt. machine learning as the deep architecture can efficiently

https://doi.org/10.1016/j.fcij.2017.12.001
2314-7288/Copyright © 2017 Faculty of Computers and Information Technology, Future University in Egypt. Production and hosting by Elsevier B.V. This is an
open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Please cite this article in press as: Mohsen H, et al., Classification using deep learning neural networks for brain tumors, Future Computing and Informatics
Journal (2017), https://doi.org/10.1016/j.fcij.2017.12.001
 + MODEL

2 H. Mohsen et al. / Future Computing and Informatics Journal xx (2017) 1e4

represent complex relationships without requiring a huge

number of nodes like in the shallow architectures e.g. SVM
and K-nearest neighbor (KNN). For that reason, they grew
rapidly to become the state of the art in different health
informatics areas such as bioinformatics, medical informatics
and medical image analysis [7,9,10].
The contribution of this paper is applying the deep learning
concept to perform an automated brain tumors classification
using brain MRI images and measure its performance. The
proposed methodology aims to differentiate between normal
brain and some types of brain tumors such as glioblastoma,
sarcoma and metastatic bronchogenic carcinoma tumors using
brain MRI images. The proposed methodology uses a set of
features extracted by the discrete wavelet transform (DWT) Fig. 1. DNNs architecture.
feature extraction technique from the segmented brain MRI im-
ages, to train the DNN classifier for brain tumors classification.
The structure of this paper is organized as follows: in input flows from the input layer to the output layer through
Section 2 there's an overview on the deep learning concept and number of hidden layers which are more than two layers [13].
architecture, section 3 described the steps of the proposed Fig. 1 illustrates the typical architecture for DNNs where Ni is
methodology, section 4 presents the experimental results and the input layer contains of neurons for the input features, No is
discussion and the conclusion and future work is given in the output layer contains neurons for the output classes and
section 5. Nh,l are the hidden layers.

2. Overview on deep learning 3. Methodology

Deep learning (DL) is a subfield of machine learning based Our proposed methodology based on the DNN learning
on learning multiple levels of representations by making a architecture for classification where the classifier is identifying
hierarchy of features where the higher levels are defined from the brain tumors in brain MRIs.
the lower levels and the same lower level features can help in The proposed methodology for classifying the brain tumors
defining many higher level features [11]. DL structure extends in brain MRIs is as follows:
the traditional neural networks (NN) by adding more hidden
layers to the network architecture between the input and Step 1: Brain MRIs Dataset acquisition
output layers to model more complex and nonlinear relation- Step 2: Image segmentation using Fuzzy C-means
ships. This concept gained the researchers interest in the recent Step 3: Feature extraction using discrete wavelet transform
years for its good performance to become the best solution in (DWT) and reduction using Principle component
many problems in medical image analysis applications such as analysis (PCA) technique
image denoising, segmentation, registration and classification Step 4: Classification using DNN
[7,10e13].
There are various DL architectures, convolutional neural
networks (CNN) is a common used architecture in recent years 3.1. Data acquisition
that can perform complex operations using convolution filters
[7,9,10]. A typical CNN architecture is a sequence of feed- According to the World Health Organization (WHO) clas-
forward layers implementing convolutional filters and pooling sification system to identify brain tumors, there are more than
layers, after the last pooling layer CNN adopts several fully- 120 types of brain tumors which differ in origin, location, size,
connected layers that work on converting the 2D feature characteristics of the tumor tissues [15,16]. In this paper we were
maps of the previous layers into 1D vector for classification concerning with three types of malignant tumors which are:
[10]. Even though the CNN architecture has an advantage of
doesn't require a feature extraction process before being  Glioblastoma: primary malignant brain tumors that are
applied but training a CNN from scratch is a time consuming classified as Grade IV and developed from star-shaped
and difficult as it needs a very large labeled dataset for cells, called astrocytes that support nerve cells. It usually
building and training before the model is ready for classifi- starts in the cerebrum.
cation which is not always available. Moreover the hardware  Sarcoma: has different grades that vary from grade I to
requirements for processing the large number of filters for the grade IV and it arises in the connective tissues like blood
large size of images e.g. 256
256 [7,10,14]. vessels.
Deep Neural Network (DNN) is another DL architecture  Metastatic bronchogenic carcinoma: secondary malignant
that is widely used for classification or regression with success brain tumors that was spread to the brain from broncho-
in many areas. It's a typical feedforward network which the genic carcinoma lung tumor.

Please cite this article in press as: Mohsen H, et al., Classification using deep learning neural networks for brain tumors, Future Computing and Informatics
Journal (2017), https://doi.org/10.1016/j.fcij.2017.12.001
 + MODEL

H. Mohsen et al. / Future Computing and Informatics Journal xx (2017) 1e4 3

3.3. Feature extraction and reduction

After segmenting the Brain MR images into 5 sections

features of the segmented tumor is extracted using discrete
wavelet transform (DWT). DWT has the advantage of
extracting the most relevant features at different directions
and scales as they provide localized time-frequency infor-
mation of a signal using cascaded filter banks of high-pass
Fig. 2. Brain MRIs dataset sample. and low-pass filters to extract features in a hierarchy
manner [18].
Fig. 4 shows a 2-levels DWT decomposition of an image
The dataset consists of 66 real human brain MRIs with 22 where the functions h(n) and g(n) represent the coefficients
normal and 44 abnormal images which are glioblastoma, of the high-pass and low-pass filters, respectively. As a
sarcoma and metastatic bronchogenic carcinoma tumors result, there are four sub-band (LL, LH, HH, HL) images at
collected from Harvard Medical School website (http://med. each level. The LL subband can be regarded as the approx-
harvard.edu/AANLIB/) [15]. All the brain MRIs was in axial imation component of the image, while the LH, HL, HH
plane, T2-weighted and 256
256 pixel. A sample of the subbands can be regarded as the detailed components of the
dataset is illustrated in Fig. 2. image [18,19].
Our methodology utilizes a 3-levels decomposition of Haar
3.2. Image segmentation wavelet which was also used in our previous work [18] to
extract 32
32 ¼ 1024 features for each brain MRI. Although
Image segmentation is the non-trivial task of separating the this number is not so big compared to the number of feature
different normal brain tissues such as gray matter (GM), white maps resulted by the convolution filters of CNNs but we used
matter (WM) and cerebrospinal fluid (CSF) and the skull from the principal components analysis (PCA) [18] to approximate
the tumor tissues in brain MR images [17] as the resulted the original extracted features with lower dimensional feature
segmented tumor part only would be used in the next steps. In vectors.
this work we used the Fuzzy C-means clustering technique to
segment the image into 5 sections as it had good results in our 3.4. Classification
previous work and also for comparison purposes [18]. Fig. 3
shows the results of segmenting a sample image using Fuzzy After the features are extracted and selected, the classifi-
C-means. cation step using DNN is performed on the resulted feature
vector. Classification is performed by using 7-fold cross vali-
dation technique for building and training the DNN of 7 hid-
den layers structure. Also for evaluating the performance of
the selected classifier, we employed other machine learning
classification algorithms from WEKA [20] using the same
criteria. The selected classification algorithms are KNN with
K ¼ 1 and 3, Linear discriminant analysis (LDA) and from our
previous work [18] SMO-SVM.

4. Experimental results and discussion

Fig. 3. A sample image segmented using FCM.

The experiment took place using two tools:

Fig. 4. 2-levels DWT decomposition of an image.

Please cite this article in press as: Mohsen H, et al., Classification using deep learning neural networks for brain tumors, Future Computing and Informatics
Journal (2017), https://doi.org/10.1016/j.fcij.2017.12.001
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4 H. Mohsen et al. / Future Computing and Informatics Journal xx (2017) 1e4

Table 1 large size images (256
256). In addition using the DNN
Performance of DNN, KNN K ¼ 1 and 3, LDA and SMO classifiers. classifier shows high accuracy compared to traditional clas-
Algorithm Classification Recall Precision F-Measure AUC (ROC) sifiers. The good results achieved using the DWT could be
rate employed with the CNN in the future and compare the
DNN 96.97% 0.97 0.97 0.97 0.984 results.
KNN K ¼ 1 95.45% 0.955 0.956 0.955 0.967
KNN K ¼ 3 86.36% 0.864 0.892 0.866 0.954
LDA 95.45% 0.955 0.957 0.955 0.983
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Please cite this article in press as: Mohsen H, et al., Classification using deep learning neural networks for brain tumors, Future Computing and Informatics
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