On The Performance of Deep Transfer Learning Networks For Brain Tumor Detection Using MR Images
On The Performance of Deep Transfer Learning Networks For Brain Tumor Detection Using MR Images
ABSTRACT A brain tumor need to be identified in its early stage, otherwise it may cause severe condition
that cannot be cured once it is progressed. A precise diagnosis of brain tumor can play an important role to
start the proper treatment, which eventually reduces the survival rate of patient. Recently, deep learning based
classification method is popularly used for brain tumor detection from 2D Magnetic Resonance (MR) images.
In this article, several transfer learning based deep learning methods are analyzed using number of traditional
classifiers to detect the brain tumor. The investigation results are based on a labeled dataset with the images of
both normal- and abnormal brain. For transfer learning, seven methods are used such as VGG-16, VGG-19,
ResNet50, InceptionResNetV2, InceptionV3, Xception, and DenseNet201. Each of them is followed by
five traditional classifiers, which are Support Vector Machine, Random Forest, Decision Tree, AdaBoost,
and Gradient Boosting. All the combinations of deep learning based feature extractor and classifier are
investigated to evaluate the relevant performance in terms of accuracy, precision, recall, F1-score, Cohen’s
kappa, AUC, Jaccard, and Specificity. Later on, learning curves for all of the combinations that achieved the
highest accuracies were presented. The presented results show that the best model achieved an accuracy of
99.39% with a 10-fold cross validation. The results presented in this article are expected to be useful for the
selection of suitable method in deep transfer learning based brain tumor detection.
INDEX TERMS Brain tumor, magnetic resonance imaging (MRI), transfer learning, deep learning, VGG-19,
support vector machine (SVM), DCNN.
This work is licensed under a Creative Commons Attribution 4.0 License. For more information, see https://creativecommons.org/licenses/by/4.0/
VOLUME 10, 2022 59099
S. Ahmad, P. K. Choudhury: On Performance of Deep Transfer Learning Networks for Brain Tumor Detection
where the knowledge learned from a task can be reused images to extract the necessary features of brain tumor and
for another similar task to achieve improved performance in finally applied to an ANN model for classification. The pro-
classification on target dataset [1], [2]. Conventionally, the posed method shows the accuracy 99% and sensitivity 97.9%.
amount of computational complexity is quite high to train However, the system increases the computational complexity
a deep convolutional neural network (DCNN) model using due to the long processing time. In [7], three multi-resolution
a massive dataset. Therefore, such learning procedure can techniques such as wavelet transform, curvelet transform and
be simplified by reusing the model weights from previously shearlet transform are used to detect the brain abnormality.
trained models. The trained model’s layers are then employed By using only fifteen shearlet features, the SVM classifier
in a new model to be trained with new dataset of interest. with the radial basis function (RBF) kernel approach achieved
As a result, the training time and generalization error is a maximum classification accuracy 97.38%. In [8], a CNN
significantly reduced. However, a detail study of using dif- model named as BrainMRNet is proposed using the combi-
ferent traditional deep transfer learning models followed by nation of residual blocks, attention module, and hypercolumn
well-known classifiers is necessary for the selection of best technique followed by dense layer and softmax to detect brain
performing model in target application. tumor. Here, the proposed study claimed to reach the accuracy
In this article, combination of several transfer learning of 96.05%. In [9], Support Vector Machine along with a
based deep learning methods with different classifiers are Fully Automatic Heterogeneous Segmentation (FAHS-SVM)
investigated to detect the brain tumor from MR images and process is utilized to locate the tumor areas, where the model
finally, compared their relative performance. An effective accuracy reached to 98.51%. A modified ResNet50 model
deep transfer learning system is identified to detect and clas- is also constructed in [10], where the 5 layers are removed
sify brain tumor with greater accuracy even in the presence of from the existing structure and new 10 layers are added at the
lower dataset. In particular, seven transfer learning methods end. Even though the modified model shows the classification
are used as feature extractors such as VGG-16, VGG-19, accuracy of 97.01%, the system complexity is increased due
ResNet50, InceptionResNetV2, InceptionV3, Xception, and to the presence of additional layers. In [11], Le-Net and U-Net
DenseNet201. Moreover, each of the CNN model is further models are combined to develop a new model LU-Net that
followed by five traditional classifiers namely SVM, Random provides less number of layers to reduce the system complex-
Forest, Decision Tree, Adaptive Boosting (AdaBoost), Gradi- ity. A detail comparative analysis is performed by considering
ent Boosting. Pre-trained deep CNNs are used for MR brain the Le-Net, VGG-16 and proposed LU-Net, where the new
images to extract the necessary features and further catego- model achieved the highest accuracy of 98.00% in compare to
rized using classifiers with 10-fold cross-validation. Finally, other models. However, there is an uncertainty of system per-
a detail comparative results are computed in the presence of formance in the presence of large dataset. In [12], authors are
different performance matrices. used superpixels and Principal Component Analysis (PCA)
The rest of the paper is organized as follows. Section II for the feature extraction, which is again followed by a filter
covers the recent works for brain tumor detection from MR to enhance the images. Moreover, TK-means clustering is
images using CNN models. Section III presents the investi- added in the model for image segmentation and brain tumor
gation framework including the detail description of brain detection. However, the study is carried out using low number
image dataset and data augmentation, image pre-processing, of image dataset. By incorporating clinical presentations and
CNN models and classifiers used for this research. The evalu- traditional MRI analysis, a deep learning based paradigm
ation matrices and the corresponding results are discussed in is proposed in [13]. Here the backward propagation for the
section IV. Finally, the conclusion of this work is presented gradients is used to increase the depth of the network, which
in section V. eventually improves the model accuracy. However, the model
suffers with long computational time as well as increase of
II. RELATED WORKS development complexity due to the presence of additional
In [3], a hybrid technique is introduced using wavelet trans- layers. In [14], a demonstration of ensemble features and
form, principal component analysis, and supervised learning ensemble classifiers was proposed. The DenseNet-169 model
algorithms, where the detection accuracy of brain tumor is achieved an average accuracy of 92.37% using small dataset,
reached to 98.6%. However, the proposed system requires to whereas the ResNeXt-101 model achieved an average accu-
train in each time if the image database is changed. racy of 96.13% using large dataset. However, the model size
Beside this, a novel combination of methods such as dis- is insufficient for a real-time medical diagnostic system based
crete wavelet packet transform (DWPT), Shannon entropy on knowledge distillation techniques. Moreover, a single clas-
(SE), Tsallis entropy (TE) and generalized eigenvalue prox- sifier shows better results for some cases compared to ensem-
imate support vector machine (GEPSVM) are also utilized ble configuration with average results. A brief summary of
to classify the brain images [4]. In [5], tenserflow is used related works using ML based brain tumor detection are
to implement a 5-layer convolutional neural network for presented in Table 1.
MRI-based brain tumor detection. However, a limited number In summary, the aforementioned ML approaches are
of training data are used for machine learning. In [6], spa- mostly used the standard CNN models for brain tumor detec-
tial gray level dependency (SGLD) matrix is used for MRI tion. On the other hand, the pre-trained model by transfer
learning technique results in less computational time, higher III. INVESTIGATION FRAMEWORK
accuracy and removes the constraint of maintaining large The investigation framework used for this study is pre-
dataset for training. Moreover, the classification performance sented in Fig. 1. The process is started with MR brain
of traditional classifiers is better than softmax or fully con- image dataset, which is further used for data augmentation.
nected layers used in previous investigations. Overall, the The dataset splits in three ways namely train set, test set,
major contributions of this study can be summarized as and validation set. Later on, the MR brain images are fur-
follows: ther processed to reduce the noise and ready for feature
extraction. In feature extraction part, several CNN models
– To provide in-depth analysis of seven pre-trained models
are tested such as VGG-16, VGG-19, ResNet50, Inception-
such as VGG-16, VGG-19, ResNet50, InceptionRes-
ResNetV2, InceptionV3, Xception, and DenseNet201. The
NetV2, InceptionV3, Xception, and DenseNet201. The
pre-processed images were fed into the transfer learning
transfer learning techniques are used to extract deep
models with a batch size of 32. Finally, classification stages
features from target dataset of MR brain images.
are prepared using different classifiers like SVM, Random
– To provide in-depth analysis of five classifiers such as
Forest, Decision Tree, AdaBoost, and Gradient Boosting.
SVM, Random Forest, Decision Tree, Adaptive Boost-
Based on these feature extractors and classifiers, the relative
ing (AdaBoost), Gradient Boosting. Different classifiers
performance of detecting the brain tumor is evaluated to
are used to classify the brain MR images into benign and
select the best performing machine learning model using
malignant.
brain MR images.
– To conduct an extensive analysis on seven pre-trained
models followed by five classifiers considering all the A. BRAIN IMAGE DATASET AND DATA AUGMENTATION
combinations and finally, compare the effectiveness of In this investigation, a publicly accessible MRI dataset
all the CNN models and ML classifiers on the target from Kaggle [https://www.kaggle.com/navoneel/brain-mri
dataset. images-for-brain-tumor-detection] is used to analyze and
– To propose the best-performing model that achieved the evaluate the developed framework. The images are in two
highest accuracy and optimal computational time among folders labeled as ‘yes’ and ‘no’ corresponding to the
all the models. Moreover, the corresponding parameter abnormal- and normal brain images as shown in Fig.2. Orig-
settings are also explored. inally, it contains 152 abnormal brain images and 98 normal
– To provide a comparison with the state-of-the-art models brain images, thus a total of 250 images of varying dimen-
that justify the use of best performing model for classi- sions. The images are grayscale in JPG format. Later on,
fying the brain tumor MR images to achieve the highest augmentation technique is applied to increase the size of the
accuracy. dataset.
Data augmentation is a process of adding slightly changed results. Several methods can be used for augmentation, how-
copies of current data or newly created synthetic data from ever, the present article used the process like width shifting,
existing data to expand the size of present dataset. By generat- height shifting, shear intensity, brightness, horizontal flip,
ing new and varied samples of dataset, data augmentation pro- and vertical flip for dataset size improvement as shown in
cess can help to improve the performance of machine learning Fig.3. After applying the augmentation process, the dataset is
models. When a machine learning model’s dataset is large converted to 1240 abnormal- and 1078 normal- brain images.
and diverse, the model performs better to get more accurate Using this dataset, the 5 images of each category are used as
Gradient Boosting [33]. The brief details of these classifiers The accuracy can be considered as a capacity to successful
are presented in Table 3. The performance results of each detection of brain tumor from the target image dataset. The
CNN model followed by classifiers will be discussed in later fraction of true positive and true negative in all the cases
section. under investigation are used to estimate the accuracy as
follows [34]:
TP + FN
IV. RESULTS ANALYSIS AND DISCUSSION Accuracy =
TP + TN + FP + FN
This section mainly highlights the performance analysis of
Precision is a true positive measure, which is calculated
several transfer learning based CNN models for the features
as [34]:
extraction from brain MR images. The extracted features are
further classified using number of classifiers. All the com- TP
Precision =
bination of feature extractors and classifiers are evaluated in TP + FP
terms of computational time and accuracy with 10-fold cross Recall (Sensitivity) is a metric that evaluates the system’s
validation as shown in Table 4. Moreover, the presented deep capacity to accurate classification of brain tumors, and it is
learning frameworks are also tested using different evaluation determined by the percent of true positives as [34]:
matrices like accuracy, precision, recall, F1-score, Cohen’s TP
kappa, AUC (Area Under ROC (Receiver Operating Charac- Recall =
TP + FN
teristic) Curve), Jaccard, and Specificity scores as shown in
Table 5. Based on the evaluation results, the best performing The F1-score takes the harmonic mean of a classi-
model is identified for effective classification of brain tumor fier’s precision and recall to create a single statistic.
into Benign and Malignant using brain MR images. The main The F1-score is given by [34]:
parameter settings of best pre-trained model and different Recall × Precision TP
F1-score = 2 × =
classifiers are also highlighted in Table 6 and Table 7 respec- Recall + Precision TP + 1 2(FP + FN)
tively. Moreover, the best performing model is compared with
Cohen’s Kappa is a statistical measure that determines how
the state-of-the-art methods as shown in Table 8.
often two raters agree on the same quantity and is measured
as [34]:
A. EVALUATION MATRICES po − pe
K=
The efficiency of the proposed deep transfer learning frame- 1 − pe
work is measured using four key outcomes: true positives where,
(TP), false positives (FP), true negatives (TN), and false po = Overall accuracy of the model
negatives (FN). The following performance matrices are used pe = Metric for the degree of agreement between model
to evaluate the proposed ML framework: predictions and actual class values.
TABLE 4. Ten-fold cross validation results for accuracy and computational time.
FIGURE 6. Graphical representation of accuracy results for different pre-trained models with classifiers.
further followed by five classifiers such as Support Vector ‘False’ to unload the fully connected layers (classification
Machine, Random Forest, Decision Tree, AdaBoost, and layers). After the last pooling layer, here an additional flatten
Gradient Boosting. The relative performance of each feature layer is added and the networks are incorporated with dif-
extractor and classifier pair is tested to identify the best ferent traditional classifiers. The flatten layer works as a
performing model. In this investigation, the transfer learning dimensionality reduction function as it reduces the number of
models are used as standalone feature extractors and later parameters. It also converts the feature map that pooled from
on, the traditional classifiers are used to classify those fea- the last pooling layer to a single dimensional array and for-
tures to detect the tumor from brain images. As a standalone wards the output to the classifiers in the next step. All the pair
feature extractor, the pre-trained network is used to process of extractor-classifier are analyzed using the performance
the images, extract features and the fully connected layers parameters of accuracy and time in 10-fold cross validation.
(classification layers) are kept inactive. Cross-validation is used to estimate the skill of a model
Conventionally, the CNN networks are used up to the based on unseen data. In 10-folds cross-validation method,
last pooling layer and ‘include_top’ argument is defined as the dataset is shuffled randomly and split into 10 groups of
TABLE 5. Ten-folds classification results for precision, recall, F1-score, Cohen’s kappa and AUC.
equal sizes. At first, it takes data from one group for the data from a different group for validation test and the data
validation test and the data from other nine groups use for from other nine groups as training set. The final result is the
training. The system evaluates the validation test based on average of all the 10 processes.
the training set and stores the result. The process continues According to the Table 4, the number of features
10 times (a total of 10 observations) and each time, it takes that extracted by VGG16, InceptionResNetV2, ResNest50,
FIGURE 7. Learning curves (a) VGG16 - SVM pair (b) InceptionResNetV2 - Gradient Boosting pair (c) ResNet50 - SVM pair (d) VGG19 - SVM pair
(e) Xception - SVM pair (f) InceptionV3 - SVM pair (g) DenseNet201 - SVM pair.
VGG19, Xception, InceptionV3 and DenseNet201 are 25088, in Table 4. Table 4 clearly illustrates that SVM classifier
38400, 100352, 25088, 100352, 51200 and 94080 respec- shows the best accuracy results compared to other classifiers
tively. The features are extracted from the final pooling layer. while working with the ML models of VGG-16, ResNet50,
Moreover, the features are used by five classifiers to classify VGG-19, Xception, InceptionV3 and DenseNet201. For
the MR brain images into benign and malignant. The high- Inception-ResNet-V2, Gradient Boosting classifier shows
est accuracy values are marked in Bold considering all the the improved performance in terms of accuracy to clas-
combinations of pre-trained models and classifiers as shown sify the MR images. In particular, the accuracy results of
TABLE 8. Results comparison with state-of-the-art methods. works of brain tumor detection using ML model. However,
the presented model was not tested for different brain MRI
modalities along with other imaging techniques. Also the
proposed technique can also be extended for the classification
of tumor types like Glioma, Meningioma, Pituitary using the
MR image dataset. Above all, the use of larger dataset and
better GPU based processing can also improve the accuracy
results as well as computational speed of presented models.
We aim to highlight those issues as a part of the future works.
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