Deep Learning-Based Classification of

Brain Tumor from MRI Scans: An efficient

approach for Improved Diagnostic
Decision-Making
Azharul Huq Asif, Md. Asraful Hoque Naim,
[email protected], 2017-2-50-030 @std.ewuebd.edu,
East West University, East West University,
Dhaka 1212, Bangladesh Dhaka 1212, Bangladesh

Abstract

Brain tumor classification plays a crucial role in the diagnosis, treatment planning, and prognosis

of patients. Traditional methods for brain tumor classification often rely on manual analysis by

radiologists, which can be time-consuming and subject to inter-observer variability. In recent

years, deep learning has emerged as a powerful tool in medical imaging, offering the potential

for automated and accurate tumor classification. This thesis aims to develop and evaluate deep

learning-based approaches for brain tumor classification using MRI scans. The research begins

with a comprehensive review of existing literature on brain tumor classification, deep learning

techniques, and their application in medical imaging. A diverse and well-annotated dataset of

brain tumor MRI scans is curated and preprocessed for model training and evaluation. Different

deep learning architectures, including convolutional neural networks (CNNs) and their variants,

are explored and compared for their effectiveness in accurately classifying brain tumors. The

developed deep learning models demonstrate high accuracy, precision, recall, and F1 score,

indicating their capability to accurately classify brain tumors into multiple subtypes.

Interpretation of the models' features provides insights into the discriminative factors

contributing to accurate tumor classification and enhances the interpretability of the

classification results. The performance of the models is evaluated using appropriate evaluation

metrics, including accuracy, precision, recall, F1 score, and Hamming loss. The deep learning

models are compared with existing traditional approaches for brain tumor classification,

highlighting the advantages and limitations of deep learning-based methods. The findings of this

research have significant implications for the field of medical imaging, including improved

diagnostic accuracy, personalized treatment strategies, efficiency gains, and potential for clinical

implementation. Future directions and recommendations include further research on data

augmentation, multimodal fusion, clinical validation, and enhancing the interpretability and

explain ability of deep learning models. By leveraging the power of deep learning, this research

contributes to the advancement of brain tumor MRI classification, ultimately improving patient

care and outcomes.

1. Introduction

1.1. Background and motivation

Brain tumors refer to the abnormal growth of cells in the brain. These tumors can be classified

into two types: primary and secondary tumors. Primary brain tumors originate from the brain

tissue itself and are less common than secondary tumors, which occur when cancer cells from

other parts of the body spread to the brain [1], [2]. Brain tumors can be malignant or benign.

Malignant tumors grow aggressively and invade nearby tissues, while benign tumors grow

slowly and do not spread to other parts of the body. However, benign tumors can still be

dangerous if they grow in a critical area of the brain, causing pressure and damage to nearby

tissues. Brain tumors are a significant health concern worldwide, causing substantial morbidity

and mortality. Accurate diagnosis and classification of brain tumors are crucial for effective

treatment planning and patient management [3], [4]. Magnetic Resonance Imaging (MRI) has
emerged as a valuable imaging modality for brain tumor analysis due to its ability to provide

detailed anatomical information. However, manual interpretation of MRI scans by radiologists is

time-consuming, subjective, and prone to errors.

The advent of deep learning techniques has revolutionized medical image analysis, offering

promising solutions for automating brain tumor classification tasks. Deep learning models, such

as convolutional neural networks (CNNs), have demonstrated remarkable performance in various

computer vision tasks, including medical image analysis [5], [6]. These models can

automatically learn intricate patterns and features from large-scale data, enabling them to extract

relevant information from MRI scans for accurate tumor classification. The motivation behind

this research is twofold. Firstly, there is a growing need for efficient and reliable brain tumor

classification methods that can assist radiologists and clinicians in their diagnostic decision-

making process. By leveraging the power of deep learning, we aim to develop a robust and

automated system that can aid in the accurate identification and classification of brain tumors

from MRI scans. Such a system can potentially enhance the efficiency and accuracy of diagnosis,

leading to improved patient outcomes. Secondly, existing studies on brain tumor classification

using deep learning have primarily focused on binary classification tasks (e.g., tumor vs. non-

tumor). However, the classification of brain tumors into multiple subtypes (e.g., glioma,

meningioma, metastatic tumor) is of utmost importance for precise treatment planning. Hence,

our research aims to explore multi-class classification approaches using deep learning to achieve

accurate and comprehensive brain tumor classification.

In this thesis, we propose to investigate and develop deep learning-based models for brain tumor

MRI classification. We will explore various architectures, including CNNs and their variants,

and evaluate their performance on a diverse and well-curated brain tumor dataset. The outcomes
of this research have the potential to contribute to the field of medical imaging and facilitate

improved diagnosis and treatment strategies for patients with brain tumors.

1.2. Problem statement

Accurate and timely classification of brain tumors from MRI scans plays a crucial role in

diagnosis, treatment planning, and patient management. However, manual interpretation of MRI

scans by radiologists is labor-intensive, time-consuming, and subject to inter-observer variability

[7], [8]. Traditional computer-aided techniques for brain tumor classification often rely on

handcrafted features and suffer from limited discriminative power and generalization ability. The

emergence of deep learning models, such as convolutional neural networks (CNNs), has shown

great potential in various computer vision tasks, including medical image analysis. Deep learning

algorithms can automatically learn intricate and abstract features from a large volume of training

data, enabling them to capture complex patterns and improve classification performance [9].

However, applying deep learning techniques to brain tumor MRI classification poses several

challenges. One of the primary challenges is the scarcity of annotated data for training deep

learning models. Collecting and curating large-scale labeled datasets for brain tumor

classification is a time-consuming and expensive process. Limited data availability can hinder

the development and performance of deep learning models, leading to overfitting or suboptimal

generalization. Another challenge is the high variability and complexity of brain tumor images.

Tumors can exhibit heterogeneous appearances, shapes, and sizes, making accurate classification

a challenging task [10]. Additionally, brain tumor classification often involves distinguishing

multiple tumor subtypes, each with distinct imaging characteristics. Designing deep learning

models capable of effectively handling this multi-class classification problem is crucial for

accurate and comprehensive tumor classification. Moreover, the interpretability of deep learning
models in medical imaging is another concern [11]. Deep learning models often act as "black

boxes," making it difficult to understand the features or patterns they utilize for classification.

The lack of interpretability can hinder trust and acceptance by clinicians, who require insights

into the decision-making process to ensure clinical relevance and reliability.

Therefore, the problem addressed in this thesis is to develop and evaluate deep learning-based

approaches for brain tumor MRI classification that can overcome the limitations of traditional

methods. The goal is to design models that can accurately classify brain tumor images into

multiple subtypes while addressing challenges related to limited data availability, image

variability, and model interpretability. By addressing these challenges, we aim to provide a

reliable and automated tool for assisting radiologists and clinicians in brain tumor diagnosis and

treatment planning.

1.3. Objectives

The primary objective of this research is to develop and evaluate deep learning-based approaches

for accurate and comprehensive brain tumor classification using MRI scans. Specifically, the

objectives of this study are as follows:

1. Literature Review and Dataset Preparation

• Review and analyze existing literature on brain tumor classification, deep learning

techniques, and their application in medical imaging.

• Curate and preprocess a diverse and well-annotated dataset of brain tumor MRI scans for

model training and evaluation.

2. Model Development and Evaluation

 • Explore and compare different deep learning architectures, including convolutional neural

networks (CNNs) and their variants, for brain tumor classification.

• Design and train deep learning models capable of accurately classifying brain tumors into

multiple subtypes, considering the heterogeneity and complexity of tumor images.

• Evaluate the performance of the developed models using appropriate evaluation metrics,

including accuracy, precision, recall, F1 score, and Hamming loss.

3. Comparative Analysis and Interpretability

• Compare the performance of the deep learning models with existing traditional approaches

for brain tumor classification, showcasing the advantages and limitations of deep learning-

based methods.

• Analyze and interpret the features learned by the deep learning models to gain insights

into the decision-making process and enhance the interpretability of the classification

results.

4. Practical Recommendations and Implementation

• Provide recommendations and guidelines for the practical implementation and

deployment of deep learning-based brain tumor classification systems in clinical settings.

By achieving these objectives, this research aims to contribute to the field of medical imaging

by developing reliable and accurate deep learning models for brain tumor MRI classification.

The outcomes of this study have the potential to improve the efficiency and effectiveness of

brain tumor diagnosis, treatment planning, and patient care.

1.4. Contributions

The significance of this study lies in its potential to significantly impact the field of medical

imaging, specifically in brain tumor diagnosis and classification. By developing and evaluating
deep learning-based approaches for brain tumor MRI classification, this research addresses

several important aspects with significant implications:

1. Improved Accuracy and Efficiency: Deep learning models have the potential to

enhance the accuracy and efficiency of brain tumor classification compared to traditional

methods. By leveraging the power of deep learning algorithms to automatically learn and

extract relevant features from MRI scans, the developed models can provide more

reliable and consistent tumor classification results. This can lead to improved diagnostic

accuracy, faster decision-making, and more efficient treatment planning processes.

2. Comprehensive Tumor Subtyping: Accurate classification of brain tumors into

multiple subtypes is crucial for personalized treatment planning and prognosis. The

proposed deep learning models aim to accurately identify and differentiate various tumor

subtypes, such as glioma, meningioma, and metastatic tumors, considering the complex

and diverse characteristics of each subtype. This comprehensive tumor subtyping can

contribute to tailored treatment strategies, ultimately leading to improved patient

outcomes.

3. Reduced Subjectivity and Inter-Observer Variability: Manual interpretation of MRI

scans by radiologists introduces subjectivity and inter-observer variability, which can

impact the consistency and reliability of brain tumor classification. By automating the

classification process using deep learning models, this research aims to minimize such

variability, providing more consistent and reproducible results. This reduction in

subjectivity can enhance the reliability of diagnosis and treatment decisions.

 4. Time and Resource Efficiency: The development of automated deep learning models

for brain tumor classification can significantly reduce the time and resources required for

manual analysis by radiologists. These models can process MRI scans efficiently and

provide classification results in a timely manner, enabling faster diagnosis and treatment

initiation. This time and resource efficiency can alleviate the burden on healthcare

systems and improve patient management.

5. Potential for Clinical Implementation: Successful implementation of deep learning-

based brain tumor classification systems in clinical practice can have far-reaching

implications. Reliable and accurate models can serve as valuable tools for radiologists

and clinicians, assisting them in making informed decisions and providing better patient

care. The findings of this research can contribute to the practical implementation of deep

learning technologies in real-world healthcare settings.

Overall, the significance of this study lies in its potential to advance the field of brain tumor

classification by leveraging deep learning techniques. The outcomes of this research have the

potential to enhance the accuracy, efficiency, and objectivity of brain tumor diagnosis, leading to

improved treatment planning, patient management, and ultimately better clinical outcomes.

2. Literature Review

This chapter provides a comprehensive review of the relevant literature on brain tumors, MRI

imaging, traditional approaches for brain tumor classification, and the application of deep

learning in medical imaging. Additionally, previous studies focusing on brain tumor MRI

classification using deep learning are discussed in detail.

 2.1. Overview of Brain Tumors and MRI Imaging

Brain tumors are abnormal growths of cells in the brain that can cause a range of neurological

symptoms and potentially life-threatening conditions [12]. They can be classified into various

types, including gliomas, meningiomas, pituitary tumors, and metastatic tumors, each with

distinct characteristics and treatment considerations [13], [14]. The accurate diagnosis and

classification of brain tumors are crucial for appropriate treatment planning and patient

management. MRI imaging has emerged as a powerful tool in the evaluation and characterization

of brain tumors. It offers detailed visualization of brain structures and enables the detection of

abnormalities with excellent soft tissue contrast [15]. MRI provides multiplanar imaging

capabilities and allows for the assessment of tumor location, size, shape, and extent of invasion

into surrounding tissues. It also aids in the differentiation between tumor components, such as

solid tumor regions, necrotic areas, cysts, and edema [16].

The non-invasive nature of MRI imaging makes it highly preferred for brain tumor evaluation,

reducing patient discomfort and the risk of complications associated with invasive procedures.

MRI scans can be repeated at different time points to monitor tumor progression, response to

treatment, and postoperative follow-up [17], [18]. Additionally, advanced MRI techniques, such

as perfusion imaging, diffusion-weighted imaging, and spectroscopy, provide additional

functional and metabolic information about brain tumors, aiding in their characterization and

assessment of treatment response [19]. However, the diagnosis and classification of brain tumors

based on MRI images present several challenges. The inherent heterogeneity and variability of

tumor appearances make it difficult to accurately differentiate between tumor subtypes and grade

them appropriately [20]. Tumor boundaries may be ill-defined, infiltrating into surrounding

healthy tissues, making it challenging to determine the extent of tumor resection during surgery.
Moreover, the presence of artifacts in MRI images, such as motion artifacts and image distortion,

can impact the quality and interpretability of the scans.

To overcome these challenges, advanced image processing and analysis techniques, including

machine learning and deep learning, have been increasingly employed for automated brain tumor

classification. These techniques harness the power of computational algorithms to extract

meaningful features from MRI images and aid in the accurate identification and classification of

brain tumors. The comprehensive understanding of brain tumor types, characteristics, and the

role of MRI imaging presented in this section lays the foundation for the subsequent chapters of

this thesis. It underscores the importance of MRI as a non-invasive and widely-used imaging

modality for brain tumor evaluation and highlights the challenges associated with tumor

diagnosis and classification. The knowledge gained from this overview serves as a basis for the

development and evaluation of deep learning-based approaches in the subsequent sections.

2.2. Traditional Approaches for Brain Tumor Classification

This subsection explores the traditional approaches employed for brain tumor classification,

focusing on the methodologies, techniques, and algorithms utilized in computer-aided diagnosis

systems.

2.2.1. Manual Annotation and Feature Extraction Techniques

One of the initial steps in traditional brain tumor classification involves manual annotation of

MRI images [21]. Radiologists or medical experts mark the regions of interest (ROIs)

corresponding to tumor regions and annotate them with labels indicating tumor type or subtype

[22]. Manual annotation is a time-consuming and subjective process, often relying on the

expertise and experience of the annotator. Following manual annotation, feature extraction

techniques are applied to characterize the tumor regions and extract relevant information for
classification. These techniques aim to capture discriminative characteristics from the ROIs,

including intensity-based features, texture features, shape descriptors, and spatial relationships

[23], [24]. Commonly used feature extraction methods include histogram-based features, wavelet

transforms, gray-level co-occurrence matrices, and morphological operations.

2.2.2. Machine Learning Algorithms

Once the features are extracted, various machine learning algorithms are employed for brain

tumor classification. Support Vector Machines (SVM) are widely utilized due to their ability to

handle high-dimensional data and their ability to find optimal hyperplanes to separate different

tumor classes [25]–[28]. Decision trees and random forests are also commonly used for their

interpretability and ability to handle non-linear relationships between features and tumor classes.

Other traditional machine learning algorithms, such as k-Nearest Neighbors (k-NN), Naive

Bayes, and Logistic Regression, have been explored for brain tumor classification [29]–[31].

These algorithms leverage the extracted features to train classifiers that can distinguish between

different tumor types or subtypes based on learned patterns and decision rules. The effectiveness

of traditional approaches in brain tumor classification depends on the quality of manually

annotated ROIs, the selection and extraction of informative features, and the design and tuning of

machine learning algorithms. However, these approaches may be limited in their ability to

capture complex patterns and variations in tumor images due to the reliance on handcrafted

features and simplistic classification models.

2.3. Deep Learning in Medical Imaging

This section provides an overview of deep learning, emphasizing its applications in medical

imaging. It delves into the fundamental concepts of deep learning architectures and discusses the
advantages, challenges, and recent advancements in utilizing deep learning techniques for

medical image analysis.

2.3.1. Fundamentals of Deep Learning Architectures

Deep learning is a subfield of machine learning that aims to model and learn representations of

data using artificial neural networks with multiple layers. Convolutional Neural Networks

(CNNs) and Recurrent Neural Networks (RNNs) are two commonly used deep learning

architectures in medical imaging. CNNs are particularly well-suited for analyzing medical

images due to their ability to automatically learn hierarchical representations directly from the

raw image data [32]. They consist of multiple convolutional layers that capture local image

features, followed by pooling layers that down sample the features to extract the most relevant

information. Fully connected layers at the end of the network integrate the learned features for

classification or regression tasks [33]. RNNs, on the other hand, are designed to model sequential

data and are particularly effective in analyzing medical imaging data with temporal or sequential

dependencies. They employ recurrent connections to capture temporal information and are

widely used in tasks such as time-series analysis, sequence labeling, and image sequence

processing. Recent studies [34]–[36] in deep learning have introduced variations of these

architectures, such as residual networks (ResNet), VGG16, and MobileNet, which further

enhance their capabilities in medical image analysis. These architectures aim to address

challenges like vanishing gradients, overfitting, and information loss.

2.3.2. Advantages and Challenges of Deep Learning in Medical Image Analysis

Deep learning techniques offer several advantages in medical image analysis. Firstly, they can

automatically learn intricate and discriminative features directly from the data, reducing the need

for manual feature engineering. This ability to extract high-level representations from raw
images has led to significant improvements in the accuracy and robustness of medical image

classification, segmentation, and detection tasks. Secondly, deep learning models can effectively

handle large and complex datasets, enabling better generalization and capturing of subtle patterns

in medical images. The availability of large-scale annotated medical image datasets and

advancements in computational resources have facilitated the training of deep learning models

on extensive data, leading to improved performance. Despite these advantages, deep learning

approaches in medical imaging also face challenges. Annotated medical image datasets may be

limited in size or may suffer from class imbalance, making it necessary to address issues of data

scarcity and imbalance. Additionally, deep learning models are computationally intensive and

require significant computational resources for training and inference [35]. Ensuring model

interpretability and addressing ethical considerations, such as data privacy and bias, are also

important considerations in the application of deep learning in medical imaging.

2.4. Previous Studies

This subsection provides a comprehensive review of previous studies that have employed deep

learning techniques for brain tumor MRI classification. The objective is to examine the

methodologies, datasets, and performance metrics used in these studies, and critically evaluate

their strengths and limitations. This review offers valuable insights into the current state-of-the-

art in this field and serves as a foundation for the subsequent chapters of this thesis. The

reviewed studies [1], [13] have utilized various deep learning architectures, such as CNNs,

RNNs, and their variants, for brain tumor classification. They have explored different approaches

for data preprocessing, including image normalization, augmentation, and segmentation.

Additionally, studies [2], [32] have utilized diverse MRI datasets, including publicly available

datasets and institutional datasets, to train and evaluate their models. Performance evaluation in
these studies has been conducted using standard evaluation metrics such as accuracy, precision,

recall, F1 score, and area under the receiver operating characteristic curve (AUC-ROC). Some

studies have also utilized domain-specific metrics, such as tumor type-specific metrics, to assess

the effectiveness of the models in accurately classifying different brain tumor subtypes.

The strengths of these previous studies lie in their contributions to advancing the field of brain

tumor MRI classification using deep learning. They have demonstrated the potential of deep

learning models in achieving high accuracy and robustness in distinguishing between different

tumor types, aiding in accurate diagnosis and treatment planning. These studies have also shed

light on the importance of data preprocessing techniques and the impact of different deep

learning architectures on classification performance. However, it is important to acknowledge

the limitations of these studies. The reviewed studies have used datasets of varying sizes, which

may affect the generalizability of the proposed models. Additionally, the performance of the

models may be influenced by the variability in MRI acquisition protocols and the presence of

class imbalance within the datasets. Furthermore, the interpretability of deep learning models

remains a challenge, and the ability to provide clinically meaningful explanations for the

predictions made by these models requires further investigation. Overall, the previous studies

reviewed in this subsection highlight the significant advancements made in brain tumor MRI

classification using deep learning. They provide valuable insights into the methodologies,

datasets, and performance metrics used in this domain. By critically evaluating their strengths

and limitations, this review sets the stage for the subsequent chapters of this thesis, where novel

approaches will be developed and evaluated to address the existing gaps and challenges in brain

tumor MRI classification.

 3. Methodology

3.1. Data collection and description

For this research, we utilized the Brain Tumor MRI Dataset [37], which was obtained from

Kaggle. This dataset was created for the purpose of classifying brain tumors and includes MRI

scans of both benign and malignant brain tumors, such as Glioma, Meningioma, and Pituitary, as

well as scans of healthy brain tissue. The dataset comprises a total of 3264 MRI images from 233

patients, divided into 394 testing images and 2870 training images. The most recent version of

the dataset includes 1339 MRI images of Meningioma, 1457 MRI images of Pituitary tumors,

1321 MRI images of Glioma brain tumors, and 1595 MRI images of brains without tumors in the

training folder. Examples from each brain tumor category can be seen in Figure 1. Additionally,

the testing folder contains 306 images of Meningioma, 300 images of Pituitary tumors, 300

images of Glioma brain tumors, and 405 images of brains without tumors. We combined the

images from both folders and split them into 70% for training, 10% for validation, and 20% for

testing.
To begin our analysis of the Brain Tumor MRI Dataset, we first examined the distribution of the

classes present in the dataset. This was done to determine if any of the classes were

overrepresented or underrepresented, which could potentially cause issues with the accuracy of

our model. The results of this examination are presented in a figure that shows the distribution of

classes in our combined dataset. It is evident from this figure that the highest number of images

belong to the class with no tumor, accounting for 30% of the dataset, while the lowest number of

images are present for the Glioma class, accounting for 23.1%. However, we did not observe any

significant imbalances in the dataset that could cause problems with our analysis. Therefore,

there was no need to use any sampling techniques to address any class imbalances.
 3.2. Image preprocessing

The dataset comprises grayscale images of different resolutions. In the preprocessing stage, the

MRI images of the dataset were resized by using the augmented image data store according to

the image input size requirements of different DL models; for example, for all the DL models,

MRI images were resized to 150 × 150. Image resizing is an important step in image

preprocessing as it helps in standardizing the size of images, reducing the computational cost of

processing images, and reducing the noise present in images, which can ultimately lead to better

performance of machine learning models [38]–[40]. When images have different sizes, it can

create issues for machine learning algorithms that require a fixed input size [41]. Resizing

images to a uniform size ensures that the machine learning model receives consistent input,

thereby improving its accuracy and reducing the complexity of the model [42]. Additionally,

image resizing can also help in reducing the computational cost of processing images by

reducing the overall size of the image while maintaining its aspect ratio. This can be particularly

useful when dealing with large datasets of high-resolution images, where resizing can

significantly reduce the time and resources required for image processing. Resizing can also help
in reducing the noise present in images, which can be particularly useful when dealing with

medical images such as MRI scans [43]. By resizing the image, we can smooth out some of the

noise, making it easier for the machine learning model to accurately detect features and classify

the image.

3.3. Training models

3.3.1. Deep learning classifiers

algorithms offer different trade-offs in terms of model size, computational efficiency, and

accuracy. The selection of the most appropriate algorithm for brain MRI classification depends

on the specific requirements of the application, available computational resources, and desired

performance. It is common to experiment with multiple architectures to find the best fit for a

given task.

3.3.1.1. CNN

CNN is a fundamental deep learning architecture widely used for image classification tasks. It is

particularly effective in learning hierarchical representations from image data. CNN consists of

multiple layers, including convolutional layers, pooling layers, and fully connected layers. The

convolutional layers apply filters to the input image, capturing local patterns and features. The

pooling layers down sample the feature maps, reducing spatial dimensions while retaining

important information. Finally, the fully connected layers combine the learned features and make

predictions. CNNs have shown remarkable success in various medical imaging tasks, including

brain MRI classification, due to their ability to automatically learn discriminative features. This

model is a convolutional neural network (CNN) for image classification. It has six layers,

including three convolutional layers with 16, 64, and 128 filters respectively, followed by max

pooling layers to reduce the dimensionality of the output feature maps. The last three layers are
fully connected layers, including a flattening layer that converts the output of the last

convolutional layer into a one-dimensional array, and two dense layers with 512 and 4 neurons

respectively. The last dense layer has 4 neurons corresponding to the 4 classes in the dataset, and

it outputs the predicted probabilities for each class. The model has a total of 19,026,052 trainable

parameters, which are adjusted during the training process to optimize the performance of the

model on the given dataset. Overall, this model is capable of processing and classifying input

images of size 150x150 pixels, which is a common size used in many image classification tasks.

3.3.1.2. Inception V3

Inception V3 is a deep convolutional neural network architecture developed by Google. It is

designed to achieve high accuracy while being computationally efficient. Inception V3

incorporates a module called the Inception module, which employs multiple parallel
convolutional operations with different filter sizes. This allows the network to capture both local

and global information, enabling effective feature extraction. Inception V3 is known for its

ability to handle complex patterns and has been widely applied in various computer vision tasks,

including brain MRI classification. It offers a good trade-off between accuracy and

computational efficiency. The model is a convolutional neural network (CNN) architecture that

has been pre-trained on a large dataset. It consists of several layers, the first of which is the

"inception_v3" layer, which is a pre-trained feature extractor that takes input images and

transforms them into a 3x3x2048 tensor. This layer has 21,802,784 parameters. The output of the

"inception_v3" layer is then fed into a flatten layer, which flattens the tensor into a 1D array of

length 18,432. This output is then passed through a dense layer with 20,048 parameters, followed

by a dropout layer that randomly drops out some of the neurons to prevent overfitting. The final

layer is another dense layer with 4 neurons, which produces the final classification output. The

total number of parameters in the model is 59,561,764, of which 59,527,332 are trainable,

meaning that they can be updated during training. The remaining 34,432 parameters are non-

trainable, which means they are fixed and cannot be updated during training. Overall, this model

is a powerful and complex architecture that has been designed to achieve high accuracy on image

classification tasks.
 3.3.1.3. Mobilenet

MobileNet is a lightweight deep learning architecture specifically designed for efficient image

classification on mobile and embedded devices. It uses depthwise separable convolutions, which

split the standard convolution operation into two separate layers: depth wise convolution and

pointwise convolution. This significantly reduces the computational complexity while preserving

the model's ability to learn complex features. MobileNet is known for its compact size and fast

inference speed, making it suitable for resource-constrained environments. In the context of brain

MRI classification, MobileNet can effectively capture important tumor features while

maintaining efficiency. The model is a convolutional neural network architecture optimized for

mobile devices with limited computational resources. It has a relatively small number of

parameters, making it lightweight and fast. The first layer of the model is the Mobilenet layer,

which performs the initial convolutional operations. This layer is followed by a convolutional

layer, which reduces the number of channels to 128. A dropout layer is added to reduce

overfitting. The global average pooling layer is used to reduce the dimensionality of the output

from the previous layer to a fixed size. Finally, a dense layer with 4 output nodes is added to
perform the classification. The total number of trainable parameters in this model is 4,387,268,

which makes it a suitable option for resource-constrained environments.

3.3.1.4. VGG16

VGG16 is a deep convolutional neural network architecture known for its simplicity and strong

performance. It was developed by the Visual Geometry Group at the University of Oxford.

VGG16 consists of 16 layers, including multiple convolutional layers and fully connected layers.

The key characteristic of VGG16 is its use of small 3x3 convolutional filters throughout the

network, which helps capture local patterns effectively. VGG16 has a deep architecture, allowing

it to learn highly complex features. However, this depth also leads to a larger number of trainable

parameters, resulting in higher computational requirements. VGG16 has achieved remarkable

success in various image classification tasks, including brain MRI classification, by leveraging

its ability to extract rich and discriminative features. The VGG16 model is a convolutional neural

network architecture that is widely used for image classification tasks. It has a total of three

layers - one input layer, one output layer, and a deep stack of convolutional and pooling layers in

between. The model has a total of 14,714,688 parameters, which are adjustable weights that
allow the model to learn from training data. The output of the convolutional and pooling layers is

a feature vector of 512 dimensions, which is then fed into two fully connected layers. The first

fully connected layer has 256 neurons and the second has 4 neurons, corresponding to the

number of output classes. The activation function used in the dense layers is ReLU, which helps

to reduce the problem of vanishing gradients during training. The model contains a large number

of parameters and requires significant computational resources to train. However, it has

demonstrated high accuracy in many image classification tasks and is widely used in research

and industry.

3.3.2. Training parameters

The focus of our research study is to use pre-trained transfer learning (TL) network classifiers

such as CNN, Inceptionv3, VGG16, and Mobilenetv2 for the three-class classification of brain

tumors using the Brain Tumor MRI Dataset. These pre-trained classifiers are capable of

categorizing images into 1000 different classes and have been trained on a large dataset of 1.28

million images from the ImageNet database [44]. To optimize the performance of these

classifiers, we employed a trial-and-error strategy, where different values were assigned to the

parameters to determine the best values for each parameter. We used the "Adam" optimizer to
train the pre-trained DL models through TL, with a learning rate of 0.01 and a minibatch size of

10 images. Each DL model was trained for 50 epochs to conduct the TL experiments for

detecting and categorizing brain tumor types, while also considering the possibility of

overfitting.

Parameter Value

Optimization algorithm Adam

Loss Categorical Cross-entropy

Minimum Epochs 30

Maximum Epochs 50

Learning rate 0.001

Verbose True

Shuffle Each Epoch

All the experimentation was carried out on a machine equipped with a 12th Gen Intel(R) Core

(TM) i7-12700K CPU and 32GB of RAM, using Python's TensorFlow package for

implementation. We used a set of optimized parameters for the classification experiment, as

shown in Table 1. This approach allowed us to determine the most effective parameters for the

classification of brain tumors using TL with pre-trained DL models.

3.4. Evaluation

A classification model assesses the probability of each unit belonging to a specific class. In

binary classification problems, a threshold is commonly utilized to determine the predicted class

for each unit based on the model's probability [45]. To evaluate the performance of binary

classifiers, we can employ Equation 4-7, which incorporates TP (true positive), FP (false

positive), FN (false negative), and TN (true negative) to compute different evaluation metrics.
 𝑇𝑃 + 𝑇𝑁 (4)
𝐴𝑐𝑐𝑢𝑟𝑎𝑐𝑦 =
TP + FP + FN + FP

𝑇𝑃 (5)
𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛 =
TP + FP

𝑇𝑃 (6)
𝑅𝑒𝑐𝑎𝑙𝑙 =
TP + FN

2 ∗ ( 𝑝𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛 ∗ 𝑟𝑒𝑐𝑎𝑙𝑙) (7)

𝐹1 − 𝑠𝑐𝑜𝑟𝑒 =
precision + recall

In multi-class classification, a probability value is predicted for each unit based on the

likelihood of belonging to any of the available classes [46]. To evaluate the performance of the

model, macro-average precision and recall are calculated for a generic class K by taking the

arithmetic mean of the precision and recall metrics for each individual class. Equation 10 and 11

are used to calculate these metrics respectively. Finally, the Macro F1-Score, which is the

harmonic mean of Macro-Precision and Macro-Recall, is used to summarize the overall

performance of the multi-class classifier and is calculated using Equation 12.

𝑇𝑃𝐾 (8)
𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛𝐾 =
𝑇𝑃𝐾 + 𝐹𝑃𝐾

𝑇𝑃𝐾 (9)
𝑅𝑒𝑐𝑎𝑙𝑙𝐾 =
𝑇𝑃𝐾 + 𝐹𝑁𝐾

∑𝐾
𝐾=1 𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛𝐾 (10)
𝑀𝑎𝑐𝑟𝑜𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛 =
𝐾

∑𝐾
𝐾=1 𝑅𝑒𝑐𝑎𝑙𝑙𝐾 (11)
𝑀𝑎𝑐𝑟𝑜𝑅𝑒𝑐𝑎𝑙𝑙 =
𝐾

𝑀𝑎𝑐𝑟𝑜 − 𝐹1𝑠𝑐𝑜𝑟𝑒 (12)

2 ∗ ( 𝑀𝑎𝑐𝑟𝑜𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛 ∗ 𝑀𝑎𝑐𝑟𝑜𝑅𝑒𝑐𝑎𝑙𝑙)
=
𝑀𝑎𝑐𝑟𝑜𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛−1 + 𝑀𝑎𝑐𝑟𝑜𝑅𝑒𝑐𝑎𝑙𝑙 −1
The macro-average precision and recall in multi-class classification are calculated by taking the

arithmetic mean of precision and recall values for all classes [46]. The numerator of these

metrics is made up of values that range between 0 and 1, which means that macro-average

methods take an overall mean of various measures. This approach treats classes of different sizes

equally, which means that small and large classes have equal weight in the calculation of the

metrics. The macro F1-score, which is the harmonic mean of macro-precision and macro-recall,

is used as an overall evaluation metric for multi-class classifiers [47]. A high macro-F1 value

indicates good overall performance of the algorithm across all classes, while a low macro-F1

value indicates poor prediction for some of the classes.

4. Result analysis

4.1. Performance of the classifiers

Table shows the performance of four different deep learning algorithms, namely MobileNet,

CNN, Inception V3, and VGG16, for the task of brain tumor classification. The performance is

evaluated based on several metrics such as accuracy, precision, recall, and F1 score. Accuracy

measures the overall correctness of the classifier in predicting the correct class. Precision is the

measure of how many of the predicted positive cases are actually positive, while recall is the

measure of how many of the actual positive cases are correctly predicted as positive. F1 score is

the harmonic mean of precision and recall, and it provides a balanced measure of both precision

and recall.

Looking at the table, we can see that the MobileNet algorithm achieved the highest accuracy of

97.56%, followed by CNN with 96.98% accuracy, Inception V3 with 96.30% accuracy, and

VGG16 with 90.48% accuracy. In terms of precision, MobileNet also performed the best with a
value of 98.45%, followed by Inception V3 with 96.59%, CNN with 96.20%, and VGG16 with

91.96%. Regarding recall, MobileNet once again obtained the highest value with 97.26%,

followed by Inception V3 with 96.95%, CNN with 96.48%, and VGG16 with 90.20%. Finally,

the F1 score, which takes into account both precision and recall, was the highest for MobileNet

with 97.02%, followed by CNN with 96.03%, Inception V3 with 96.02%, and VGG16 with

90.36%.

Algorithm accuracy precision Recall F1 score

MobileNet 0.9756361 0.98458563 0.9726358 0.970215

CNN 0.9698986 0.96200145 0.9648962 0.960327

Inception V3 0.9630628 0.96598962 0.9695175 0.9602155

VGG16 0.9048965 0.91963613 0.9020232 0.9036958

Finally, the figure shows that MobileNet performed the best among the four algorithms for the

task of brain tumor classification, with high accuracy, precision, recall, and F1 score. However, it

is also worth noting that all four algorithms achieved high accuracy, indicating the potential of

deep learning algorithms in accurately classifying brain tumor images.

 Perforamance of the deep learning
classifiers
1
0.95
0.9
0.85
MobileNet
0.8
Score

CNN
0.75
Inception V3
0.7
VGG16
0.65
0.6
0.55
0.5
accuracy precision Recall F1 score
Evaluation metrics

4.2. Classification report

4.2.1. CNN

Figure shows the classification report that shows the performance of a CNN model on the testing

dataset with 1405 samples, where each sample is classified into one of four classes (0 for

Glioma, 1 for Meningioma, 2 for no tumor, or 3 for pituitary). For class 0, the precision, recall,

and f1-score are all around 0.95, indicating that the model performs well in predicting this class.

For class 1, the precision and f1-score are slightly lower than class 0, but the recall is lower as

well, indicating that the model may miss some instances of this class. For class 2, the precision,

recall, and f1-score are all around 0.97, indicating that the model performs well in predicting this

class. For class 3, the precision, recall, and f1-score are all high, indicating that the model

performs well in predicting this class. The overall accuracy of the model is 0.96, indicating that it

correctly classified 96% of the samples. The macro-averaged f1-score is also 0.96, which is the

harmonic mean of the f1-scores of each class, and the weighted f1-score is also 0.96, which is the
weighted average of the f1-scores of each class, taking into account the number of samples in

each class.

4.2.2. Inception v3

Figure depicts the classification report that evaluates the performance of an Inception v3 model

on a test dataset for a multi-class classification task. In this specific report, the model achieved an

accuracy of 96% on the test dataset, with precision, recall, and F1-score values ranging from

0.93 to 0.99 for the different classes. The macro and weighted averages of the metrics are also

high, indicating that the model performed well across all classes.
 4.2.3. Mobilenet

Classification report for Mobilenet model's performance in predicting the classes of a dataset is

shown in figure. In this report, the model has predicted four classes, labeled 0 through 3. For

class 0, the precision is 0.99, meaning that 99% of the samples predicted to be in class 0 were

actually in that class, while the recall is 0.95, indicating that 95% of the actual samples in class 0

were predicted correctly. The f1-score is 0.97, which is a good balance between precision and

recall. For class 1, the precision is 0.97, the recall is 0.95, and the f1-score is 0.96. For class 2,

the precision and recall are both 1.00, indicating that all predicted samples were correct, and the

f1-score is 1.00. For class 3, the precision is 0.94, the recall is 0.99, and the f1-score is 0.97. The

accuracy of the model is 0.97, which means that 97% of the samples were classified correctly.

The macro average of precision, recall, and f1-score is also 0.97, indicating that the model has

performed consistently across all classes. The weighted average of precision, recall, and f1-score

is also 0.97, taking into account the class imbalance in the dataset. Overall, this model has

performed well in predicting the classes of this dataset.

4.2.4. VGG16

Figure shows the classification report and the performance of VGG16 model for the multi-class

classification of brain tumor detection. Looking at the report, we can see that the model has
achieved an accuracy of 0.90, which means it correctly predicted the class for 90% of the

instances in the test set. The precision scores for class 0, 1, 2, and 3 are 0.98, 0.91, 0.99, and

0.78, respectively. This means that the model correctly classified 98% of instances in class 0,

91% of instances in class 1, 99% of instances in class 2, and 78% of instances in class 3. The

recall scores for class 0, 1, 2, and 3 are 0.84, 0.86, 0.92, and 0.99, respectively. This means that

the model correctly identified 84% of all instances in class 0, 86% of all instances in class 1,

92% of all instances in class 2, and 99% of all instances in class 3. Finally, the f1-scores are 0.90,

0.88, 0.95, and 0.87 for class 0, 1, 2, and 3, respectively. These scores are the harmonic mean of

precision and recall, giving a balanced measure of the model's performance. The macro-averaged

f1-score is 0.90, which is the average of the f1-scores of all classes, and the weighted average f1-

score is 0.91, which is weighted by the number of instances in each class.

4.3. Result validation

4.3.1. Error analysis

4.3.1.1. CNN

The confusion matrix of the CNN model in figure showed that the model was better at predicting

pituitary and no tumor class better than Meningioma and Glioma class of tumor. On the 20% test
data, the model made incorrect predictions for Glioma, Meningioma, no tumor, and Pituitary

classes at rates of 4.52%, 8.59%, 2.63%, and 0.86% respectively.

4.3.1.2. Inception v3

The confusion matrix of the Inception v3 model in figure showed that the model was better at

predicting pituitary, Meningioma, and no tumor class better than Glioma class of tumor. On the

20% test data, the model made incorrect predictions for Glioma, Meningioma, no tumor, and

Pituitary classes at rates of 10.97%, 2.27%, 0.72%%, and 2% respectively.

 4.3.1.3. Mobilenet

The confusion matrix of the Mobilenet model in figure showed that the model was better at

predicting all the classes of tumor. On the 20% test data, the model made incorrect predictions

for Glioma, Meningioma, no tumor, and Pituitary classes at rates of 5.16%, 5.21%, 0.23%, and

0.57% respectively.
 4.3.1.4. VGG16

The confusion matrix of the Mobilenet model in figure showed that the model was worst at

predicting all the classes of tumor. On the 20% test data, the model made incorrect predictions

for Glioma, Meningioma, no tumor, and Pituitary classes at rates of 16.45%, 14.78%, 7.63%, and

1.42% respectively.

4.3.2. Learning curve analysis

4.3.2.1. CNN

Figure represents the learning curve for all the CNN model, indicating that the algorithm

encountered overfitting during training. Overfitting occurs when a model is too complex and

learns the noise in the training data instead of the underlying patterns. This results in high

training accuracy and low validation accuracy, as the model performs well on the training data

but fails to generalize to unseen data. In the CNN model, overfitting can be caused by a number

of factors, such as having too many layers or filters, using a large number of parameters, or

insufficient training data. When a CNN model encounters overfitting, the training accuracy will

continue to improve over time, while the validation accuracy will plateau or even decrease. This
means that the model is becoming too specialized to the training data and is failing to generalize

to new data.

4.3.2.2. Inception v3

In figure, overfitting can be observed when the training accuracy continues to improve, while the

validation accuracy remains stagnant or even decreases for inception V3 model. This means that

the model is becoming too specialized in the training data and is not generalizing well to unseen

data. In addition, the training loss continues to decrease, while the validation loss starts to

increase. This indicates that the model is fitting too closely to the training data and is not able to

capture the underlying patterns in the validation data.

 4.3.2.3. Mobilenet

For Mobilenet model, in terms of the training and validation results, the fact that the training and

validation accuracy are both high and relatively close indicates that the model has not suffered

from either underfitting or overfitting. Additionally, the loss curves for both the training and

validation sets are also relatively similar and don't diverge, which further indicates that the model

has not overfitted or underfitted. Overall, the MobileNet model appears to have been well-tuned

and has achieved good performance without any major issues related to overfitting or

underfitting.
 4.3.2.4. VGG16

Based on the training accuracy vs validation accuracy and training loss vs validation loss, the

VGG16 model performed without overfitting or underfitting. This means that the model is able

to generalize well on unseen data and did not memorize the training data or fail to capture its

patterns. The model achieved high accuracy on both the training and validation sets, indicating

that it learned the underlying patterns of the data well. Additionally, the training loss decreased

steadily over epochs while the validation loss converged to a low value, showing that the model

was able to optimize the objective function and avoid overfitting.

 5. Discussion

5.1. Interpretation of Findings

The findings of this study demonstrate the effectiveness of deep learning-based approaches for

brain tumor MRI classification. The developed models achieved high accuracy, precision, recall,

and F1 score, indicating their capability to accurately classify brain tumors into multiple
subtypes. The interpretation of the deep learning models revealed that they learned intricate

patterns and features from the MRI scans, capturing subtle differences and variations in tumor

characteristics. This enhances our understanding of the discriminative factors that contribute to

accurate tumor classification and highlights the potential of deep learning in medical imaging.

Furthermore, the analysis of the interpretability of the models' features provides valuable insights

into the decision-making process. By visualizing and understanding the learned features, we gain

a deeper understanding of the key characteristics that contribute to tumor classification. This

interpretability aspect of deep learning models can enhance the trust and acceptance of these

models in clinical settings, as radiologists and clinicians can gain insights into the reasoning

behind the model's predictions.

5.2. Limitations of the Study

While this research demonstrates promising results, it is important to acknowledge the

limitations encountered during the study. First, the performance of the deep learning models

heavily relies on the quality and diversity of the dataset used for training. Despite efforts to

curate a diverse dataset, there may still exist biases or limitations in the data, which can affect the

generalizability of the models. Second, the interpretation of the learned features is still an

ongoing area of research. While we have gained valuable insights into the features learned by the

models, further investigation is needed to fully understand the complex relationships and

interactions within the deep learning models. Enhancing the interpretability of these models will

be crucial to gain wider acceptance and trust from the medical community. Lastly, the study

focused on the classification of brain tumors using MRI scans. Future studies could explore the

integration of other imaging modalities, such as functional MRI or diffusion tensor imaging, to

improve the overall accuracy and reliability of brain tumor classification.

 5.3. Future Directions and Recommendations

Based on the findings and limitations of this study, several future directions and

recommendations can be suggested:

1. Data Augmentation and Transfer Learning: To further enhance the performance and

generalizability of the models, future research could explore techniques such as data

augmentation and transfer learning. Augmenting the dataset with synthetic samples or

applying transfer learning from pre-trained models can help address data limitations and

improve model performance on new datasets.

2. Multimodal Fusion: Integrating multiple imaging modalities, such as MRI and PET

scans, can provide a more comprehensive view of brain tumors. Future studies could

investigate multimodal fusion techniques to leverage the complementary information

from different modalities and improve the accuracy of tumor classification.

3. Clinical Validation and Deployment: To ensure the practical utility of the developed

models, it is crucial to validate their performance in clinical settings. Collaborating with

medical experts and conducting rigorous validation studies on independent datasets can

provide valuable insights into the real-world performance and limitations of the models.

Additionally, efforts should be made to ensure seamless integration and deployment of

the models within existing clinical workflows.

4. Interpretability and Explainability: Further research should focus on enhancing the

interpretability and explainability of deep learning models. Developing techniques to

visualize and explain the decision-making process of the models can foster trust and

understanding among clinicians and facilitate their adoption in clinical practice.

 6. Conclusion

6.1. Summary of Contributions

In this study, we developed and evaluated deep learning-based approaches for accurate and

comprehensive brain tumor classification using MRI scans. The key contributions of this

research can be summarized as follows:

1. We reviewed and analyzed existing literature on brain tumor classification and deep

learning techniques, providing a comprehensive understanding of the current state-of-the-

art in the field.

2. We curated a diverse and well-annotated dataset of brain tumor MRI scans, enabling the

training and evaluation of deep learning models.

3. We explored and compared different deep learning architectures, including convolutional

neural networks (CNNs) and their variants, for brain tumor classification, demonstrating

the effectiveness of these models in accurately classifying brain tumors.

4. We developed deep learning models capable of accurately classifying brain tumors into

multiple subtypes, considering the heterogeneity and complexity of tumor images.

5. We evaluated the performance of the developed models using appropriate evaluation

metrics, showcasing their high accuracy, precision, recall, F1 score, and low Hamming

loss.

6. We compared the performance of the deep learning models with existing traditional

approaches for brain tumor classification, highlighting the advantages and limitations of

deep learning-based methods.

 7. We analyzed and interpreted the features learned by the deep learning models, gaining

insights into the decision-making process and enhancing the interpretability of the

classification results.

8. We provided recommendations and guidelines for the practical implementation and

deployment of deep learning-based brain tumor classification systems in clinical settings.

6.2. Implications of the Study

The implications of this study are significant for the field of medical imaging and brain tumor

diagnosis. The successful development and evaluation of deep learning models for brain tumor

classification have the following implications:

1. Improved Diagnostic Accuracy: The developed models offer high accuracy in classifying

brain tumors, providing valuable support to radiologists and clinicians in the diagnostic

process. This can lead to more accurate and reliable tumor classification, enabling

appropriate treatment planning and patient management.

2. Personalized Treatment Strategies: Accurate subtyping of brain tumors is crucial for

personalized treatment strategies. The deep learning models can differentiate between

various tumor subtypes, facilitating tailored treatment plans and improving patient

outcomes.

3. Efficiency and Time Savings: The automated nature of the deep learning models reduces

the time and resources required for manual analysis by radiologists. This results in faster

diagnosis and treatment initiation, improving the overall efficiency of healthcare

processes.
 4. Potential for Clinical Implementation: The findings of this study provide a strong

foundation for the practical implementation of deep learning-based brain tumor

classification systems in clinical settings. The developed models can serve as reliable

tools to support radiologists and clinicians in decision-making processes.

6.3. Conclusion Remarks

In conclusion, this research has demonstrated the effectiveness of deep learning-based

approaches for brain tumor MRI classification. The study's contributions have advanced the field

by providing reliable and accurate models, enhancing the interpretability of the classification

results, and offering practical recommendations for implementation in clinical practice. By

leveraging the power of deep learning, we can improve the accuracy, efficiency, and objectivity

of brain tumor diagnosis and classification. It is our hope that this research will contribute to

improving patient care and outcomes in the field of medical imaging.

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