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Enhancing brain tumor diagnosis: an

optimized CNN hyperparameter model for


improved accuracy and reliability
Abdullah A. Asiri1, Ahmad Shaf2, Tariq Ali2, Muhammad Aamir2,
Muhammad Irfan3 and Saeed Alqahtani1
1
Radiological Sciences Department, College of Applied Medical Sciences, Najran University,
Najran, Najran, Saudi Arabia
2
Department of Computer Science, COMSATS University Islamabad, Sahiwal, Punjan, Pakistan
3
Electrical Engineering Department, College of Engineering, Najran University, Najran, Najran,
Saudi Arabia

ABSTRACT
Hyperparameter tuning plays a pivotal role in the accuracy and reliability of
convolutional neural network (CNN) models used in brain tumor diagnosis. These
hyperparameters exert control over various aspects of the neural network,
encompassing feature extraction, spatial resolution, non-linear mapping,
convergence speed, and model complexity. We propose a meticulously refined CNN
hyperparameter model designed to optimize critical parameters, including filter
number and size, stride padding, pooling techniques, activation functions, learning
rate, batch size, and the number of layers. Our approach leverages two publicly
available brain tumor MRI datasets for research purposes. The first dataset comprises
a total of 7,023 human brain images, categorized into four classes: glioma,
meningioma, no tumor, and pituitary. The second dataset contains 253 images
classified as “yes” and “no.” Our approach delivers exceptional results, demonstrating
an average 94.25% precision, recall, and F1-score with 96% accuracy for dataset 1,
while an average 87.5% precision, recall, and F1-score, with accuracy of 88% for
dataset 2. To affirm the robustness of our findings, we perform a comprehensive
comparison with existing techniques, revealing that our method consistently
outperforms these approaches. By systematically fine-tuning these critical
Submitted 6 November 2023 hyperparameters, our model not only enhances its performance but also bolsters its
Accepted 24 January 2024
generalization capabilities. This optimized CNN model provides medical experts
Published 14 March 2024
with a more precise and efficient tool for supporting their decision-making processes
Corresponding author
Ahmad Shaf,
in brain tumor diagnosis.
ahmadshaf@cuisahiwal.edu.pk
Academic editor Subjects Computer Vision, Neural Networks
Giovanni Angiulli Keywords Hyperparameter tuning, Brain tumor diagnosis, Feature extraction, Spatial resolution,
Additional Information and Model complexity, Decision-making processes, Optimization techniques
Declarations can be found on
page 23
DOI 10.7717/peerj-cs.1878
INTRODUCTION
Brain tumors, the leading cause of demise with the lowest survival rate among cancers,
Copyright
2024 Asiri et al. pose challenges in early detection due to their asymmetrical shapes and dispersed borders.
Distributed under Accurate analysis at the initial stage is crucial for precise medical interventions and saving
Creative Commons CC-BY 4.0 lives. Brain tumors manifest as benign (non-cancerous) or malignant (cancerous) types,

How to cite this article Asiri AA, Shaf A, Ali T, Aamir M, Irfan M, Alqahtani S. 2024. Enhancing brain tumor diagnosis: an optimized
CNN hyperparameter model for improved accuracy and reliability. PeerJ Comput. Sci. 10:e1878 DOI 10.7717/peerj-cs.1878
with primary and secondary distinctions based on origin (Siegel, Miller & Jemal, 2015;
Sauer, 2019).
Common types include meningioma, glioma, and pituitary cancer. Meningiomas
originate from the meninges, gliomas from glial cells supporting nerve function, and
pituitary tumors impact various bodily processes (Abiwinanda et al., 2019; Abir, Siraji &
Khulna, 2018). Understanding these types and their characteristics is vital for effective
diagnosis and treatment, supporting healthcare professionals in providing appropriate
care.
Identifying and estimating the duration of brain tumors presents a significant challenge
in medical diagnostics. The datasets used for this purpose comprise images obtained
through various diagnostic techniques, including biopsies, spinal taps, computed
tomography scans, and magnetic resonance imaging. These datasets undergo
segmentation, classification, and feature extraction based on specific requirements. Deep
learning techniques have emerged as highly effective tools in this domain, particularly in
brain tumor detection. Unlike traditional methods focusing on segmenting tumors for
classification and feature extraction, deep learning approaches employ classification
algorithms to identify and categorize brain tumors. Deep learning, a branch of machine
learning and artificial intelligence, mimics how humans acquire knowledge. Deep learning
algorithms handle complex and abstract tasks, surpassing the performance of traditional
linear machine learning systems that are more suited for smaller datasets. By harnessing
the power of deep learning, accurate and efficient brain tumor diagnosis becomes a reality,
potentially revolutionizing the field of medical imaging and enhancing patient care
(Naseer et al., 2020).
Accurate segmentation of brain tumors is crucial for cancer diagnosis, treatment
planning, and outcome evaluation. However, manual segmentation is a laborious, time-
consuming, and challenging task. To overcome these limitations, researchers have
extensively investigated automatic and semi-automatic brain tumor segmentation
methods (Núñez-Martín, Cervera & Pulla, 2017). A generative or discriminative model is
the foundation for automatic and semi-automatic segmentation. These methods are built
upon either generative or discriminative models. The discriminative model relies on image
features to categorize normal and malignant tissues, while the generative model utilizes
probabilistic information obtained from images for brain tumor segmentation.
Classification techniques, such as support vector mechanism (SVM) and random forest,
are commonly employed in discriminative models (Kleesiek, 2014) based on visual features
like local histograms, image textures, and structure tensor eigenvalues. These research
efforts aim to develop efficient and reliable segmentation approaches that can alleviate the
burden of manual segmentation, enabling accurate tumor delineation and facilitating
treatment planning and evaluation (Meier et al., 2014).
Deep learning algorithms are now often used for object identification, classification, and
feature extraction. Mainly, convolutional neural networks are acknowledged as an
outstanding method for semantic picture segmentation, and convolutional neural
networks-based algorithms performed and generated reliable results (Long, Shelhamer &
Darrell, 2015). The most advanced mechanism, convolutional neural network (CNN), can

Asiri et al. (2024), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.1878 2/28


learn through the representation of data and can predict and draw conclusions depending
on available data. It successfully accomplished picture categorization and feature
extraction tasks by extracting low and high-level information through self-learning.
Although a large training dataset was necessary, CNN-based approaches effectively
formulate predictions and conclusions. The implementation of CNN is problematic in this
situation since brain tumor is a clinical research topic, and the dataset is constrained.
Deep learning, including CNNs, can be used effectively with smaller datasets, it relies on
a transfer learning strategy built upon two hypotheses: (1) fine-tuning the ConvNet, and
(2) freezing the ConvNet layers. Transfer learning techniques involve using two datasets: a
large dataset known as the base dataset and a smaller dataset used for training purposes. A
pre-trained network is initially applied to the large dataset, extracting valuable
information. This extracted information is transferred and utilized as input for the smaller
dataset (Rehman et al., 2019). This process, known as fine-tuning, enables the adaptation
of the pre-trained network to the specific characteristics of the smaller dataset. By adopting
transfer learning, the information acquired from the base dataset can be effectively fine-
tuned, enhancing the performance of the CNN on the target task using the smaller dataset.
Our study focuses on the crucial aspect of hyperparameter tuning in CNN models for
brain tumor diagnosis. While our work specifically focuses on fine-tuning, its contribution
lies in the effective optimization of hyperparameters, which is a critical step in achieving
accurate and reliable results in medical image analysis. Our main contributions are as
follows:

1. Optimized hyperparameter tuning: We propose a fine-tuned CNN hyperparametric


model that systematically optimizes key hyperparameters, including the number and
size of filters, stride padding, pooling techniques, activation functions, learning rate,
batch size, and number of layers. This optimization process is designed to enhance the
model’s performance and improve its generalization capabilities.
2. Improved diagnostic precision: Our fine-tuned CNN model showcases impressive
results in terms of various performance metrics, including average precision, recall, F1
score, and accuracy. By achieving high accuracy rates (e.g., 96% accuracy for dataset 1),
we provide a more precise and efficient tool for medical experts to aid in brain tumor
diagnosis.
3. Comparative analysis: We perform a comprehensive comparison of our fine-tuned
approach with existing techniques. The comparison clearly demonstrates that our
method outperforms these existing methods, reinforcing the effectiveness of our
hyperparameter optimization strategy.

The remaining sections of the manuscript are structured as follows: related work, which
describes the current advancement and their limitations; methodology, the specifics of our
hyperparameter-based CNN model utilized with two distinct brain tumor datasets,
discussing their characteristics and preprocessing steps; results, which designates the
outcomes of the applied model; and conclusion, which provides a summary of the article
and future directions

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RELATED WORK
Deng et al. (2009) implemented CNNs using a sizable dataset called ImageNet and
successfully obtained the best result on visual recognition tests. Its limitations include
biases, label noise, class imbalance, fixed resolutions, and potential domain shift challenges
The best outcomes were obtained when CNNs were applied to image classification and
detection datasets by Everingham et al. (2015). Its limitations include limited diversity,
fixed object categories, imbalanced classes, static scenes, annotations’ limitations, static
object views, and potential lack of semantic context and temporal variation In a study
(Cheng et al., 2015), the Figshare dataset explored an alternative algorithm for enhancing
tumor regions as areas of interest, which were subsequently divided into sub-sections. The
approach involved extracting features such as intensity histogram, gray-level co-
occurrence matrix, and employing a bag of words (BoW) model. Using a ring-form
partitioning technique, the algorithm achieved impressive accuracy values of 87.54%,
89.72%, and 91.28%.
Meningioma, glioma, and pituitary tumors are all classified by Ismael & Abdel-Qader
(2018) with a 91% accuracy rate. Using a 2D Gabor filter and MRI, statistical characteristics
were retrieved on MRI brain tumor dataset. Multilayer perceptron neural networks were
trained using back-propagation for classification purposes. Shakeel et al. (2019) applied
fractional and multi-fractional dimension algorithms for a feature and essential feature
extraction on MRI brain tumor dataset. A classification approach was suggested, and
machine learning with back-propagation improved the performance of brain tumor
detection. However, the generalizability of the results to different datasets or tumor types
may be limited, and the absence of comparative analysis with other state-of-the-art
methods raises questions about the relative effectiveness of their proposed approach.
Xie et al. (2022) presented a comprehensive review of CNN techniques applied to brain
tumor classification from 2015 to 2022. It highlights the advancements, challenges, and
achievements in this domain, providing insights into state-of-the-art methodologies. The
article concludes with a discussion of future perspectives and potential directions for
further research in brain tumor classification using CNNs. By using five alternative CNN
designs, Abiwinanda’s (2018) experiment obtained 98.51% accuracy on training sets of
brain tumor datasets consisting of 3064 T-1 weighted CE-MRI images publicly available
via Figshare. Providing insights into the choice of hyperparameters, training strategies, and
data augmentation techniques would enhance the reproducibility and understanding of
the proposed classification method. In order to distinguish between benign and malignant
tissues in MRIs brain tumor dataset, Al-Ayyoub et al. (2012) used MATLAB and ImageJ.
Nearly ten different features were extracted from the MRIs to identify brain tumors.
Potential limitations of the study may include the need for a more detailed description of
the machine learning algorithms and methodologies employed, such as the specific
features extracted from the images and the choice of classifiers used. Parihar (2017)
suggested a CNN-based approach that entails intensity normalization during
pre-processing on MRIs dataset, CNN architecture for classification, and tumor

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classification during post-processing. The study might include the need for more extensive
experimentation and validation on diverse datasets to establish the robustness and
generalizability of the CNN-based segmentation approach.
In order to classify tumors into meningioma, glioma, and pituitary tumors, Sultan,
Salem & Al-Atabany (2019) used two publically accessible datasets known as T1-weighted
contrast-enhanced images and Cancer Imaging Archive (TCIA) as well as two deep-
learning models—a second model graded gliomas as Grade II, III, or IV. The need for
comprehensive evaluation on diverse datasets to establish the generalizability of the
proposed deep neural network across various types of brain tumors and imaging
conditions. Using a relatively small dataset from CE-MRI, Ismael, Mohammed & Hefny
(2020) experimented to determine the prevalence of three different types of tumors,
including meningioma, gliomas, and pituitary tumors, and they found rates of 45%, 15%,
and 15%, respectively. The study’s reliance on ResNet architecture might require careful
consideration of model complexity and potential overfitting, especially with limited data.
A frequent type of brain tumor is called a glioma, which is further divided into high-
grade and low-grade gliomas. The severity of the tumor is taken into account when
assigning these grades. Both have different classifications, benign and cancerous,
respectively. The research study in Vinoth & Venkatesh (2018) suggested a CNN technique
to identify low and high-grade tumors on the MRI brain tumor dataset. An effective SVM
classifier categorizes benign and malignant tumors based on the constraints and outcomes
collected. However, potential limitations of the study might include the need for careful
parameter tuning and validation of the CNN and SVM models to ensure optimal
performance. A work by Rehman et al. (2020) uses CNN architecture and transfer learning
to categorize brain tumors. Three deep CNN architectures AlexNet, GoogLeNet, and
VGGNet were applied to the target dataset’s MRIs to control the type of tumor. The
framework’s performance could be influenced by factors such as the availability and
quality of labeled data, and the generalizability of the approach to various tumor subtypes
and imaging modalities might require further validation. To classify images of brain
tumors, the author in Swati et al. (2019) proposed a block-wise fine-tuning technique using
transfer learning and fine-tuning on the T1-weighted contrast-enhanced magnetic
resonance images (CE-MRI) benchmark dataset. The results with traditional machine
learning and deep learning CNN approaches were compared; under five-fold cross-
validation, the applied method had an accuracy of 94.82%. It could include the potential
sensitivity of the transfer learning approach to variations in dataset characteristics,
potentially leading to suboptimal performance when applied to datasets with significantly
different imaging conditions or tumor characteristics. The latest literature comparison of
different techniques is also given in Table 1.

METHODOLOGY
This section explains the methodology’s overall structure. Here is a detailed explanation of
every parameter used in the proposed system. Graphical representation of the proposed
work has been illustrated in Fig. 1.

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Table 1 Literature comparison of existing work.
Dataset Author Methodology Accuracy Limitations
(%)
MRI Mahmud, Mamun CNN 93.3 More work can be performed to correctly identify brain cancers by using
& Abdelgawad individual patient information gathered from any source.
(2023)
MRI Alsaif et al. (2022) VGG19 93 More datasets, complex structure, and augmented techniques may be
used to enhance the model accuracy.
BraTS18 Rehman et al. CNN 92.67 More techniques can be employed to enhance the accuracy results on
(2021) BraTS dataset.
BraTS15,17 Nema et al. (2020) GAN-Net 94.01 Limited dataset diversity and size may impact generalization to different
brain tumor types. Lack of detailed explanation of data preprocessing
steps and augmentation techniques.
MRI Deng et al. (2019) FCNN 90.89 FCNN may struggle with capturing complex spatial patterns in brain
tumor images, leading to limited accuracy.
BraTS18 Sun et al. (2019b) CA-CNN 61.0 The study’s limitations include the use of a relatively small dataset and
the lack of ground truth data.
BraTS Gonella (2019) V-Net 85 The study only used a single dataset, the BraTS 2018 dataset. It is
important to evaluate the model on other datasets to ensure that it
generalizes well to new data.
BraTS18 Kuzina, Egorov & U-Net-RI, U-Net-PR 74 The study did not compare the proposed model to other methods that
Burnaev (2019) use transfer learning. The study did not evaluate the computational
complexity of the model.
BraTS17,2015 Chen, Ding & Liu U-Net, DeepMedic, MLP 89 Limited discussion of the model’s sensitivity to hyperparameters and
(2019) optimization choices.
BraTS17 Mlynarski et al. 2D-3D Model, U-NET 91.8 The study did not compare the proposed model to other methods that
(2019) use long-range context. The study did not explore the use of different
CNN architectures for tumor segmentation.
MRI Thaha et al. (2019) CNN, ECNN 92 The study did not use ground truth data to evaluate the performance of
the model. This makes it difficult to compare the results to other
studies that use ground truth data.
BraTS13,15 Havaei et al. (2017) CNN 88 It does not provide sufficient details about how this architecture is
different from traditional CNNs or how it contributes to solving the
problem of brain tumor segmentation.
BraTS13, Pereira et al. (2016) CNN 78 The relatively lower accuracy of 78% suggests potential limitations in
2015 feature extraction or model complexity.
MRI Zhai & Li (2019) VGG-16 82.2 VGG-16 may struggle with balancing model complexity and overfitting
in brain tumor classification tasks.
BraTS15 Sun et al. (2019a) 3D CNN 84 Computational complexity and memory requirements of 3D CNN may
limit its applicability on larger datasets. The study did not evaluate the
performance of the model on different imaging modalities.
MRI Pereira et al. (2018) RBM-RF 84 Limited discussion on the choice and hyperparameters of the RBM-RF
model components.
BraTS16 Hoseini, DCNN 90 Limited exploration of alternative architectures and their impact on
Shahbahrami & accuracy.
Bayat (2018)
BraTS Zhao et al. (2018) FCNNs, CRF-RNN 84 CRF-RNN may face challenges in capturing long-range dependencies
13,15,16 and spatial relationships in complex tumor images.
BraTS17 Saouli, Akil & XCNet-ELOBAk 89 Limited insight into how the proposed XCNet-ELOBAk architecture
Kachouri (2018) compares to other state-of-the-art methods.

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Table 1 (continued )
Dataset Author Methodology Accuracy Limitations
(%)
MRI Charron et al. 3D-CNN, DeepMedic 79 3D-CNN may face challenges in efficiently processing 3D volumes,
(2018) potentially impacting performance.
BraTS15 Liu (2018) DCR, ResNet-50 87 Limited discussion on the challenges and implications of using deep
residual networks (ResNet) for tumor classification.
BraTS15 Iqbal et al. (2018) SkipNet, SENet, IntNet 90 The choice of architectures may not fully exploit the unique features of
(VGG) brain tumor images.
BraTS15 Cui et al. (2018) TLN/ITCN, FCN 89 Limited analysis of the trade-offs between the proposed architectures
and their impact on accuracy.
MRI Wang et al. (2018) CNN 86.1 Possible challenges in effectively capturing subtle and intricate tumor
patterns using a traditional CNN.
MRI Wang et al. (2019) WRN, ResNet 91 Limited discussion on the potential limitations of wide residual
networks (WRN) in tumor classification tasks.
BraTS17 Zhang (2017) CNN 72 Lower accuracy of 72% suggests that the chosen CNN architecture may
not effectively capture relevant features.
IBSR2 Gottapu & Dagli DenseNet, Growth rate, 92 Limited analysis of how the growth rate and bottleneck architecture
(2018) Bottleneck impact accuracy and training dynamics.

Figure 1 Flowchart of the proposed work. Full-size  DOI: 10.7717/peerj-cs.1878/fig-1

Dataset details
This study utilized the two brain tumor MRI datasets publicly available at Kaggle. The
dataset 1 comprises a total of 7,023 images of the human brain having dimensions of 512 
512 and JPG format. It consists of four classes: glioma (1,621), meningioma (1,645), no
tumor (2,000), and pituitary (1,757). The “no tumor” class images were sourced from the
Br35H dataset. Figure 2 illustrates the different categories present in the dataset, including
no tumors, meningioma, pituitary, and glioma. The dataset 2 consists of 253 images with

Asiri et al. (2024), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.1878 7/28


Figure 2 Sample images of dataset 1. Image source credit: https://www.kaggle.com/datasets/
masoudnickparvar/brain-tumor-mri-dataset, CC0. Full-size  DOI: 10.7717/peerj-cs.1878/fig-2

yes (155) and no (98) classes. To train and evaluate the hyperparameter-tuned model for
brain tumor detection, the datasets were divided into training, validation, and testing sets
for dataset 1 and 80:20 ratio of training and testing for dataset 2. A detailed description of
the dataset can be found in Tables 2 and 3.

Pre-processing
Pre-processing a brain tumor MRI dataset involves several steps to optimize the data for
analysis and modeling. This includes addressing challenges like varying resolutions and
intensity ranges in MRI images. Rescaling the images to a standardized resolution ensures
consistency across the dataset while normalizing intensity values enhances subsequent
algorithms and models. Techniques like rescaling pixel values to a specific range (0, 1) or
using z-score normalization are commonly employed. Aligning the MRI images to a
standard reference frame is essential due to variations in position and orientation. Image

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Table 2 Dataset 1 details and distribution.
Dataset 1

Class name Num. of images Training Testing Validation


Glioma 1,621 1,021 300 300
Meningioma 1,645 1,033 306 306
No tumor 2,000 1,190 405 405
Pituitary 1,757 1,157 300 300
Total 7,023 4,401 1,311 1,311

Table 3 Dataset 2 details and distribution.


Dataset 2

Class name Num. of images Training Testing


Yes 155 124 31
No 98 78 20
Total 253 202 51

registration techniques facilitate spatial alignment, enabling improved comparison and


analysis. Additionally, addressing noise and artifacts in MRI images caused by factors like
patient motion or equipment variations is crucial. Denoising techniques like Gaussian
smoothing or non-local means filtering effectively reduce noise while preserving vital
details. These pre-processing steps optimize the brain tumor MRI dataset, enabling
accurate analysis and meaningful insights.

Hyperparameters of convolutional neural networks for training


Hyperparameters in CNNs are parameters not learned during the training process but
instead set by the user prior to training. The input layer is the parameter where the CNN
training process starts, and the classification layer is where it ends the process in a feed-
forward fashion. Nevertheless, the opposite process begins with classification and moves
through the first convo layer. Neuron J sends information in a forward fashion computed
according to Eq. (1) to the value of neurons N in layer L. The non-linear ReLU function
determines the output, as indicated in Eq. (2).
X
N
IPNL ¼ WN J L xj þ bN (1)
J¼1

OPNL ¼ maxð0; IPNL Þ (2)


where IP: input, OP: output, W: weight, and b: neuron number. All neurons use Eqs. (1)
and (2) to construct output results and form the non-linear activation function by taking
input values. The pooling layer employs a k × k window to gather the results to calculate
maximum average feature values. Equation (3) explains how to perform this calculation
using the SoftMax function for each tumor type.

Asiri et al. (2024), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.1878 9/28


L
eIPN
OPNL ¼ P OPL (3)
Ne
k

The back-propagation cost function is calculated by minimizing the new weights, as


presented in Eq. (4).

1XS
C¼ IPðXðai =bi ÞÞ (4)
S N

In the training process, the letter S represents the training set sample, while bi represents
the ith sample of the training set with its corresponding label ai . The probability of
classification, denoted as Xðai =bi Þ, is used to minimize the cost C through the stochastic
gradient function. To calculate the weights of each convolutional layer L, the weight of the
convolutional layer L at iteration t is represented by WLt , as depicted in Eq. (5).

WLtþ1 ¼ WLt þ VLtþ1 (5)

Here WLt : weight of the convolutional layer L, VLtþ1 is the updated weight value at
iteration t. The essential component of convolutional neural networks, feature extraction,
is made possible by the convolutional layer. Several filters to extract features are present in
this layer. The resultant value and layer sizes are evaluated by using Eqs. (6) and (7);
correspondingly, here niL is the resultant feature map of the images, r is the function of
activation, yL is the input width and xLi 2 f; zi 2 f is the filter ðf Þ channels.

niL ¼ rðxLi  yL þ z i Þ (6)


 
input size  filter size
Convolutional layer output size ¼ þ1 (7)
stride

A convolutional neural network often employs the pooling layer after each
convolutional layer. This layer manages the parameters, which are also in charge of
overfitting. The most widely used pooling layer is max pooling, which performs distinct
functions from other layers like min pooling and average pooling. Equations (8) and (9)
are used to determine the output and size of the pooling layer when x is the output and R is
the pooling region, respectively.
Ploi;j ¼ max (8)
r;s2R
 
convolutional layer output size  Pooling Size
Pooling layer output size ¼ þ1 (9)
stride

Fine-tuning of CNN hyperparameters


As depicted in Algorithms 1 and 2, optimizing various aspects of the network’s
architecture and the training procedure is necessary to fine-tune the hyperparameters of a
CNN for brain tumor detection, classification. The quantity and size of filters control

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convolutional layer depth and receptive field. Consider alternative numbers, such as
(16, 32, 64), and different filter sizes, like [3 × 3, 5 × 5]—altering the stride value to regulate
the output feature maps’ spatial dimensions. The spatial resolution is decreased with a
more excellent stride, whereas the spatial resolution is increased with a smaller stride. The
input volume’s spatial size is preserved during convolutional processes by choosing the
suitable padding parameters. Padding may reduce the impact of margins without retaining
crucial spatial information.
The varied pooling methods used during the tests, such as min, max, or average pooling,
aid in capturing invariant information and lower the spatial dimensions. ReLU, sigmoid,
and tanh are three appropriate activation functions for the CNN layers that introduce non-
linearity and allow the network to model complicated relationships in the input. A lower
learning rate may necessitate more repetitions but can produce better convergence. In
contrast, a more significant learning rate may result in faster convergence but runs the risk
of overshooting the ideal solution. The experiment with various batch sizes will decide how
many training examples will be processed in each iteration. Different network depths can
be achieved by changing the number of convolutional and fully connected layers.
Regularization techniques like dropout or L2 regularization improve generalization and
reduce overfitting. Various optimization techniques, which regulate how the network’s
weights are changed during training, are being tested, including stochastic gradient descent
(SGD) and Adam.

Working of hyperparameter CNN


Hyperparameteric CNN refers to a CNN model that utilizes hyperparameters to configure
its architecture and optimize its performance. The grid search hyperparameters create a
grid of possible values for each hyperparameter that we want to tune including the number
of filters (num_filters), number of units (num_units), dropout rate (dropout), and
optimizer. These hyperparameters are crucial in determining the model capacity,
regularization, and learning behavior. As shown in Figs. 3 and 4 for Dataset 1 and
Dataset 2, the given data depicts that the different combinations of hyperparameter values
are tested, and their corresponding accuracies are recorded, tested, and their
corresponding accuracies are recorded. The hyperparameter values are varied for
num_filters, num_units, dropout, and optimizer, while the accuracy represents the model’s
performance with those specific hyperparameter settings.

Comparison of hyperparameter values and accuracy


The various combinations of hyper parameters values and their corresponding accuracies
are given in Fig. 2 for dataset 1 and dataset 2. The given data show the following
comparison of various accuracies for different parameters.

 num_filters: The number of filters determines the number of feature maps extracted
by the convolutional layers. Higher values of num_filters may allow the model to
capture more complex patterns but can also increase computational requirements.

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Algorithm 1 Algorithm for hyperparameter tuning of CNN.
1: Initialize hyperparameters: a ¼ ½16; 32; 64 b ¼ ½64; 128; 256 c ¼ ½0:1; 0:2 d ¼ ½ 0adam0 ; 0sgd0 
2: Set the evaluation metric: METRIC_ACCURACY = ‘accuracy’
3: Create a file writer for logging: Create a file writer for ‘logs/hparam_tuning’
4: Configure hyperparameter tuning: Set hparams_config with hyperparameters [α, β, γ, δ] and metric [METRIC_ACCURACY]
5: Function train_test_modelhparams
6: Create a sequential model
7: Add Conv2D and MaxPool2D layers using α and activation=tf.nn.relu
8: Add another Conv2D and MaxPool2D layers using α and activation=tf.nn.relu
9: Flatten the output
10: Add a dense layer with β and activation=tf.nn.relu
11: Add a dropout layer with γ
12: Add a dense output layer with 4 classes and activation=tf.nn.softmax
13: Compile the model using δ, loss=′sparse_categorical_crossentropy′, and metrics=[′accuracy′]
14: Train the model on x train and y train for a specified number of epochs
15: Evaluate the model on x test and y test and get the accuracy
16: Return accuracy EndFunction
17: Function run run_dir, hparams
18: Create a file writer for the run directory
19: Set the hyperparameters using hparams
20: Train and evaluate the model using train_test_model function
21: Write the accuracy metric to the summary file
22: EndFunction
23: Set session_num to 0
24: for a value in α do
25: for b value in β do
26: for c value in γ do
27: for d value in δ do
28: Create a dictionary hparams with current hyperparameter values
29: Set run_name as “run-” + session_num
30: Print ‘—Starting trial:’ + run_name
31: Print the hyperparameters {h.name: hparams [h] for h in hparams}
32: Call run with run_dir as ‘logs/hparam_tuning/’ + run_name and hparams
33: Increment session_num by 1
34: end for
35: end for
36: end for
37: end for

Asiri et al. (2024), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.1878 12/28


Algorithm 1 (continued )
38: Select best hyperparameters:
39: Let best_accuracy = 0
40: Let best_hyperparameters = {}
41: for each summary file in ‘logs/hparam_tuning’ do
42: Read and store accuracy metric for each run
43: if accuracy is greater than best_accuracy then
44: Update best_accuracy to current accuracy
45: Update best_hyperparameters with hyperparameters of current run
46: end if
47: end for

Algorithm 2 Fine-tuned hyperparameter tuning of CNN.


1: Train final model with best hyperparameters:
2: Create new instance of model using best_hyperparameters
3: Train model on entire training dataset for specified number of epochs
4: Evaluate model on testing dataset and get final accuracy
5: Print best hyperparameters and final accuracy achieved

 num_units: The number of units represents the size of the fully connected layers. It
controls the model’s capacity to learn complex relationships in the data. The values
used range from 64 to 256. Higher values of num_units generally allow the model to
capture more intricate patterns, but they can also increase the risk of overfitting if not
balanced appropriately.
 Dropout: Dropout is a regularization technique that helps prevent overfitting by
randomly dropping out a fraction of the units during training. A dropout rate of 0.1
or 0.2 is used in the experiments. Higher dropout rates provide more regularization
but can potentially decrease the model’s learning capacity.
 Optimizer: The optimizer determines the algorithm used to update the model
weights during training. Two optimizers are used: Stochastic Gradient Descent (SGD)
and Adaptive Moment Estimation (Adam). Adam is an adaptive optimizer that
dynamically adjusts the learning rate, while SGD uses a fixed one. Adam generally
performs well in a wide range of scenarios, but the choice between the two can depend
on the specific problem and dataset.
 Accuracy: Accuracy represents the model’s performance on the validation or test set.
It indicates the proportion of correctly classified samples. The accuracy values range
from 0.75 to 0.96, with different hyperparameter settings achieving varying levels of
accuracy. It is important to note that accuracy alone does not provide a

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Figure 3 Working architecture of fine-tuned hyperparametric CNN model for dataset 1.
Full-size  DOI: 10.7717/peerj-cs.1878/fig-3

comprehensive evaluation of the model performance, and other evaluation metrics


should be considered, such as precision, recall, and area under the curve
(AUC)-receiver operating characteristic curve (ROC).

In Fig. 3 the x-axis has the following parameters: num_filters, num_units, dropout,
optimizer. The y-axis shows the accuracy of the neural network. The graph is a line graph
with multiple lines, each representing a different combination of the parameters. In the
evaluation of CNN architectures with varied hyperparameters, namely the number of
filters, units, dropout rate, and optimizer, the obtained accuracies of 0.96 across different
configurations highlight a remarkable consistency. The combinations tested,
encompassing variations in the number of filters (16, 64), units (64, 128, 256), and a
constant dropout rate of 0.2 with the ’Adam’ optimizer, all yield identical accuracies. In
contrast, one specific set of hyperparameters comprising 16 filters, 64 units, a dropout rate
of 0.1, and utilizing the ‘SGD’ optimizer yielded a comparatively lower accuracy of 0.75.
In Fig. 4, on the second dataset, the highest accuracies achieved were 0.9, obtained from
two distinct configurations. The first configuration utilized 16 filters, 64 units, a dropout
rate of 0.2, and employed the ‘SGD’ optimizer. Meanwhile, the second configuration
comprised 32 filters, 64 units, a dropout rate of 0.1, and utilized the Adam optimizer. Both
configurations yielded the same highest accuracy of 0.9, showcasing the effectiveness of
these particular hyperparameter settings on this dataset. The lowest accuracies observed
were both recorded at 0.39, resulting from two separate configurations. The first
configuration involved 64 filters, 128 units, a dropout rate of 0.1, and utilized the Adam
optimizer. Similarly, the second configuration consisted of 64 filters, 64 units, a dropout
rate of 0.2, also employing the Adam optimizer. Both configurations resulted in the same
lowest accuracy, indicating that these specific combinations of hyperparameters and
optimizer choices might not be effectively capturing the essential patterns or features
within this particular dataset.
By comparing the hyperparameter values and their corresponding accuracies, it is
possible to identify trends and gain insights into the effect of different configurations on

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Figure 4 Working architecture of fine-tuned hyperparametric CNN model for dataset 2.
Full-size  DOI: 10.7717/peerj-cs.1878/fig-4

the model performance. However, further analysis and experimentation may be required
to draw definitive conclusions about the optimal hyperparameter settings, such as cross-
validation and statistical significance testing. We did not use Bayesian hyperparameter
tuning in our research. Bayesian hyperparameter tuning is a powerful technique, but we
decided to use random search for a few reasons. Simplicity and ease of implementation:
Random search is a simpler and easier-to-implement technique than Bayesian
optimization. This is important because our research aims to provide a practical solution
that can be easily adopted by researchers and practitioners who might have limited
computational resources.
Baseline comparison: We wanted to establish a baseline comparison against which the
performance of our fine-tuned CNN model could be evaluated. By using random search,
we can ensure that the improvements achieved by our proposed approach can be
attributed to the fine-tuning strategy itself, rather than the specific optimization algorithm.
General applicability: Random search is a versatile method that can work effectively
across a wide range of problem domains. We wanted to demonstrate the effectiveness of
our fine-tuned CNN approach in a generalizable manner, showcasing its potential
applicability to various medical image analysis tasks beyond brain tumor diagnosis.
Efficiency and exploration: Random search provides a good balance between exploration
and exploitation of the hyperparameter space. While Bayesian optimization is highly
efficient in exploitation, random search’s exploration-centric nature allowed us to
comprehensively explore the hyperparameter configurations, potentially uncovering
valuable insights.

RESULTS
This section explains the experimental results for the hyperparameters of the fine-tuned
CNN, explained with various evaluation criteria. The proposed model and the predicted
hyperparametric fine-tuned CNN were implemented in Python on a computer system
with a GPU of 6 GB GTX 1060, an 8th generation Core i7, and 16 GB of RAM to calculate
the results of a brain tumor. The following evaluation criteria were used:

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Evaluation criterion
Several statistical equations are used to test the proposed model for classifying and
detecting brain tumors Eqs. (10)–(13). True positive images are those correctly classified
and denoted as Tp, while true negative images are those incorrectly classified as negative
and denoted as Tn. Fp stands for the number of incorrectly positive classified images, while
Fn stands for incorrectly negative classified images. The statistical metrics accuracy,
precision, recall, and F1-score were used to gauge the model output. The F1-score was used
to evaluate the outcomes when there was a conflict between accuracy and sensitivity,
informative and technical.
Tp
Precision ðPreÞ ¼ (10)
Tp þ Fp
Tp
Recall ðRÞ ¼ (11)
Tp þ Fn
2ðSe  PreÞ
F1  score ðF1Þ ¼ (12)
Se þ Pre
Tp þ Tn
Accuracy ðAccÞ ¼ (13)
Tn þ Tn þ Fp þ Fn

Model results
The confusion matrix of the test data for the four-class (dataset 1) and two-class (dataset 2)
classification is shown in Figs. 5 and 6. The test dataset 1 includes four categories:
meningioma, pituitary, no tumor, and glioma while dataset 2 contains yes and no class.
The confusion matrix is a square matrix with dimensions equal to the number of classes. In
this scenario, with four classes, the confusion matrix is a n  n matrix; where n is the
number of classes. Each cell in the matrix represents a combination of predicted and actual
class labels. The numbers within the matrix represent the total number of images utilized
for classification. Each entry in the matrix corresponds to the count of images that belong
to a specific actual class (represented by rows) and were predicted to belong to a specific
predicted class (represented by columns).
The model’s ability to generalize new data is measured by the validation and training
accuracy, as shown in Figs. 7 and 8, which is determined using a different dataset not used
during training. The x-axis represents the number of epochs, and the y-axis represents the
accuracy. The graph has two lines, one for training accuracy and one for validation
accuracy. The training accuracy line is a dashed blue line, and the validation accuracy line
is a dotted orange line. The training accuracy starts at around 0.75 and increases steadily to
around 0.98. The validation accuracy starts at around 0.8 and increases steadily to around
0.95. It helps identify overfitting and evaluates the model performance on real-world data.
A model may have overfitted to the training data and not generalized well if training
accuracy is high, but validation accuracy is noticeably lower. Validation Loss denotes the
inconsistency between the predictions of the model and the actual targets in the validation

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Figure 5 The confusion matrix generated by the proposed model on the testing data from dataset 1.
Full-size  DOI: 10.7717/peerj-cs.1878/fig-5

Figure 6 The confusion matrix generated by the proposed model on the testing data from dataset 2.
Full-size  DOI: 10.7717/peerj-cs.1878/fig-6

dataset, as shown in Figs. 9 and 10 for dataset 1 and dataset 2. It acts as a gauge of the
model’s effectiveness using previously unobserved data. It is estimated using a loss
function, like training loss, and the objective is to minimize it to improve the model’s
accuracy on the novel, untried samples.
The ROC curve explains the concession among the true positive (sensitivity) and the
false favorable rates (specificity minus sensitivity) for various categorization thresholds, as
shown in Figs. 11 and 12 for dataset 1 and dataset 2. A point on the curve shows the
model’s performance at each threshold, which represents a different threshold setting. As
the threshold changes, the actual positive rate is drawn against the false positive rate to
form the curve. The AUC value calculates the total effectiveness of the model. The

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Figure 7 Accuracy graph for dataset 1. Full-size  DOI: 10.7717/peerj-cs.1878/fig-7

Figure 8 Accuracy graph for dataset 2. Full-size  DOI: 10.7717/peerj-cs.1878/fig-8

likelihood that a casually designated positive sample will be graded higher than a negative
sample is represented by this parameter. The range of AUC values is 0 and 1, with higher
values representing improved performance and discrimination capacity.
The statistical information in Tables 4 and 5 summarizes brain tumor classification, and
detection performance. Impressive results are displayed in the table, including an average
precision, recall, and F1-score of 0.94, showing remarkable accuracy in detecting brain
tumors. The accuracy of 0.96 shows the model’s overall performance in accurately
classifying cases of brain tumors. At the same time, the AUC value of 0.99 indicates
outstanding discrimination abilities due to the fine-tuning of hyperparameters of CNN for
dataset 1.

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Figure 9 Loss graph for dataset 1. Full-size  DOI: 10.7717/peerj-cs.1878/fig-9

Figure 10 Loss graph for dataset 2. Full-size  DOI: 10.7717/peerj-cs.1878/fig-10

In dataset 2, for the ‘Yes’ class, the precision, recall, and F1 score are all 0.90, indicating a
consistent performance in predicting this class. The Support for ‘Yes’ is 31, implying that
this class appeared 31 times in the dataset. The AUC for ‘Yes’ is also 0.90, indicating good
discrimination ability for this class.
The ‘No’ class shows slightly lower precision, recall, and F1 score at 0.85 but has an
AUC of 0.10, which seems unusually low. Typically, AUC values are between 0.5 and 1.
This is a point of interest, possibly indicating issues with the model’s ability to distinguish
the ‘No’ class correctly. The ‘Average’ row displays the mean values of precision, recall, and

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Figure 11 ROC graph for dataset 1. Full-size  DOI: 10.7717/peerj-cs.1878/fig-11

Figure 12 ROC graph for dataset 2. Full-size  DOI: 10.7717/peerj-cs.1878/fig-12

F1 score for both classes, which are all 87.5. The average AUC is 0.5, suggesting good
overall discrimination ability across both classes.
Figure 13 show the accuracy values comparison for different hyperparameters of the
CNN model. The accuracy values occurred against several filters (num_filters), number of
units (num_units), dropout rate (dropout), and optimizer. Two optimizers are used:
Stochastic Gradient Descent (SGD) and Adaptive Moment Estimation (Adam). Adam is
an adaptive optimizer that dynamically adjusts the learning rate, while SGD uses a fixed
one. The highest accuracy value of 96% shows an occurrence rate of 11.1%, and the lowest
accuracy value is 75, with an occurrence rate of 2.8%. Generally, the accuracy occurrence
range a maximum value of 19.4% for both 92% and 95%.

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Table 4 Statistical results of the model on dataset 1.
Class name Pre R F1 Support AUC Accuracy
Glioma 0.95 0.90 0.93 300 0.99 0.96
Meningioma 0.92 0.87 0.89 306 0.98
No tumor 0.97 1.00 0.99 405 1.00
Pituitary 0.93 1.00 0.96 300 1.00
Average 0.94 0.94 0.94 – 0.99

Table 5 Statistical results of the model on dataset 2.


Class name Pre R F1 Support AUC Accuracy
Yes 0.90 0.90 0.90 31 0.90 0.88
No 0.85 0.85 0.85 20 0.10
Average 87.5 87.5 87.5 – 0.5

Figure 13 Comparing the accuracy percentage proportions across various hyperparameter


configurations of the CNN model on dataset 1. Full-size  DOI: 10.7717/peerj-cs.1878/fig-13

For dataset 2, the accuracy values range from 0.39 to 0.90, indicating the correctness of
our proposed model as shown in Fig. 14. The associated percentages vary, showcasing the
distribution of how frequently each accuracy level occurs within the dataset. For instance,
an accuracy of 0.61 is associated with a high percentage of 27.6%, suggesting a relatively
low precision in that specific case. Conversely, some values, like 0.81, 0.82, 0.85, and 0.86,
exhibit consistent accuracy percentages of 3.4%, implying more stable performance.
Intriguingly, accuracies of 0.39, 0.73, 0.76, 0.84 and 0.90 have percentages of 6.9%,
potentially indicating areas of interest or significance within the context of the data.

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Figure 14 Comparing the accuracy percentage proportions across various hyperparameter
configurations of the CNN model on dataset 2. Full-size  DOI: 10.7717/peerj-cs.1878/fig-14

Table 6 Statistical results compared with state-of-the-art techniques.


Reference Method Accuracy
Srinivas et al. (2022) Fine-tuned ResNet-50 with CNN 0.95
Ayadi et al. (2022) Hybrid approach 0.90
Asiri et al. (2023) U-Net with fine-tuned ResNet-50 0.94
Bhatele & Bhadauria (2022) Hybrid Ensemble 0.95
Murthy, Koteswararao & Babu (2022) CNN Ensemble 0.95
Proposed model (dataset 1) HPCNN 0.96
Proposed model (dataset 2) HPCNN 0.88

Moreover, there are instances where relatively high accuracy levels, such as 0.88, are
accompanied by a 10.3% percentage, possibly suggesting that precision is balanced with
occurrences.
Table 6 presents a comprehensive comparison of various brain tumor classification
methods, revealing their respective accuracy scores. Each method’s accuracy value
indicates the percentage of correctly classified brain tumor images in the dataset. Notably,
the “Fine-tuned ResNet-50 with CNN” achieves an accuracy of 0.95, leveraging the
combined strengths of the fine-tuned ResNet-50 model and a CNN architecture. Similarly,
the “Hybrid approach” attains an accuracy of 0.90 by employing a combination of
traditional machine learning algorithms and deep learning models, enhancing
classification robustness. The “U-Net with fine-tuned ResNet50” method achieves an
accuracy of 0.94, benefiting from U-Net’s segmentation capabilities in conjunction with a
fine-tuned ResNet-50 model. The “Hybrid Ensemble” and “CNN Ensemble” methods both
achieve an accuracy of 0.95 through the ensemble of diverse models and techniques,

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resulting in enhanced accuracy. The “Proposed model” stands out with the highest
accuracy of 0.96, outperforming all other methods, potentially advancing brain tumor
diagnosis in medical imaging applications. In one of our experiments, we conducted tests
on a smaller dataset comprising 253 images from two distinct classes. Despite the reduced
data size, our system demonstrated remarkable performance, achieving an accuracy of
88%. This outcome underscores the robustness and versatility of our hyperparameter
tuning approach in scenarios where data availability is constrained.

CONCLUSION
In this study, we developed a new CNN model for brain tumor diagnosis. We carefully
tuned the hyperparameters of the model, including the number of filters, filter size, stride
padding, pooling techniques, activation functions, learning rate, batch size, and layer
configuration. This resulted in a significant improvement in diagnostic accuracy. We tested
our model on two publicly available brain tumor MRI datasets. For the first dataset, which
contains 7,023 brain images across four classes, our model achieved an accuracy of 96%,
along with an average precision, recall, and F1-score of 94.25%. For the second dataset,
which contains 253 images, our model achieved an accuracy of 88%, along with precision,
recall, and F1-score values of 87.5%. These results demonstrate the effectiveness of our
CNN model for brain tumor detection and classification. Our model outperforms existing
methods in terms of accuracy and efficacy, and it offers the potential to improve the
precision and efficiency of brain tumor diagnosis. This could lead to earlier detection and
treatment of brain tumors, which could save lives. In addition, our study demonstrates the
importance of hyperparameter optimization in CNN models for medical diagnostics. By
carefully tuning the hyperparameters of our model, we were able to achieve significant
improvements in accuracy. This suggests that hyperparameter optimization could be used
to improve the performance of CNN models for other medical applications, such as cancer
detection and diagnosis.

ADDITIONAL INFORMATION AND DECLARATIONS

Funding
This work is supported by the Deanship of Scientific Research, Najran University,
Kingdom of Saudi Arabia under the Distinguished Research funding program grant code
number (NU/DRP/MRC/12/28). The funders had no role in study design, data collection
and analysis, decision to publish, or preparation of the manuscript.

Grant Disclosures
The following grant information was disclosed by the authors:
Deanship of Scientific Research, Najran University. Kingdom of Saudi Arabia,
Distinguished Research funding program: NU/DRP/MRC/12/28.

Competing Interests
The authors declare that they have no competing interests.

Asiri et al. (2024), PeerJ Comput. Sci., DOI 10.7717/peerj-cs.1878 23/28


Author Contributions
 Abdullah A. Asiri conceived and designed the experiments, analyzed the data, prepared
figures and/or tables, and approved the final draft.
 Ahmad Shaf conceived and designed the experiments, performed the computation work,
prepared figures and/or tables, and approved the final draft.
 Tariq Ali conceived and designed the experiments, analyzed the data, authored or
reviewed drafts of the article, and approved the final draft.
 Muhammad Aamir conceived and designed the experiments, performed the
experiments, performed the computation work, authored or reviewed drafts of the
article, and approved the final draft.
 Muhammad Irfan performed the experiments, analyzed the data, performed the
computation work, authored or reviewed drafts of the article, and approved the final
draft.
 Saeed Alqahtani performed the experiments, prepared figures and/or tables, and
approved the final draft.

Data Availability
The following information was supplied regarding data availability:
The code is available at GitHub and Zenodo:
- https://github.com/iamshaf/CNN-HyperParameter.
- iamshaf. (2024). iamshaf/CNN-HyperParameter: HPCNN (HPCNN). Zenodo.
https://doi.org/10.5281/zenodo.10476557.
Dataset 1 is available at Kaggle: https://www.kaggle.com/datasets/masoudnickparvar/
brain-tumor-mri-dataset.
Dataset 2 is available at Kaggle:
https://www.kaggle.com/datasets/navoneel/brain-mri-images-for-brain-tumor-
detection.

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