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ResNet-50 vs VGG-19 vs Training from Scratch: A comparative

analysis of the segmentation and classification of Pneumonia from
chest x-ray images

Victor Ikechukwu A Research Scholar , Murali S dProfessor ,

Deepu R dProfessor , Shivamurthy RC Professor

PII: S2666-285X(21)00055-8
DOI: https://doi.org/10.1016/j.gltp.2021.08.027
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To appear in: Global Transitions Proceedings

Please cite this article as: Victor Ikechukwu A Research Scholar , Murali S dProfessor ,
Deepu R dProfessor , Shivamurthy RC Professor , ResNet-50 vs VGG-19 vs Training from Scratch:
A comparative analysis of the segmentation and classification of Pneumonia from chest x-ray images,
Global Transitions Proceedings (2021), doi: https://doi.org/10.1016/j.gltp.2021.08.027

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ResNet-50 vs VGG-19 vs Training from Scratch: A comparative analysis of the segmentation and
classification of Pneumonia from chest x-ray images

Victor Ikechukwu Aa*., Murali Sb., Deepu Rc., Shivamurthy R.C.d

a
Research Scholar, Department of CSE, Maharaja Institute of Technology Mysore-571477, India
b,c,d
Professor, Department of CSE, Maharaja Institute of Technology Mysore-571477, India
* Corresponding author. Tel.: +91-78928 19690; E-mail address: victor.agughasi@gmail.com

Abstract

In medical imaging, segmentation plays a vital role towards the interpretation of X-ray images where salient features are
extracted with the help of image segmentation. Without undergoing surgery, clinicians employ various modalities ranging from
X-Rays and CT-Scans to ultrasonography, and other imaging techniques to visualise and examine interior human body organ and
structures. To ensure appropriate convergence, training a deep convolutional neural network (CNN) from scratch is tough since it
requires more computational time, a big amount of labelled training data and a considerable degree of experience. Fine-tuning a
CNN that has been pre-trained using, for instance, a huge set of labelled medical datasets, is a viable alternative. In this paper, a
comparative study was done using pre-trained models such as VGG-19 and ResNet-50 as against training from scratch. To
reduce overfitting, data augmentation and dropout regularization was used. With a recall of 92.03%, our analysis showed that the
pre-trained models with proper finetuning was comparable with Iyke-Net, a CNN trained from scratch.

Keywords: Chest x-rays; CNNs; Deep Learning; Medical imaging; Pneumonia detection; ResNet-50; Segmentation; VGG-19

1. Introduction Fine-tuning a CNN that has been trained using large,

In many clinical applications, medical image segmentation
has a significant impact on all subsequent research and
diagnosis. Manual annotation, on the other hand, is reliant on
domain expertise and expert skills. It is boring and
time-consuming, and prone to intra and inter-observer
inconsistencies. As a result, creating automated segmentation
algorithms for exact annotation of medical images is both
clinically useful and necessary. Convolutional neural networks
(CNNs), which found useful application in computer vision
for several decades [1][2] has become a standard deep
learning algorithm amongst researchers in various application
areas such as natural language processing, medical image
segmentation and analysis [3][4][5] because of its ability to
discriminate features from differing abstraction levels.
However, it is often difficult to train deep neural networks
(without the use of pre-trained models) because of various
limitations such as – data imbalance, where there are more
samples of normal as against malignant datasets. Second, the
availability of large unlabeled dataset which requires
annotation by experts. Third, the problem of poor
generalization, where the model performs below average on
an unseen dataset (validation dataset) and the dependence on
the enormous amount of computational resources[6][7][8].
labelled dataset from a separate application is a viable
alternative to building a CNN from scratch. The pre-trained
models have been used successfully as a baseline for transfer
learning in a variety of computer vision tasks[9][10]. In this
paper, we seek to provide an answer to the central question:
Will the accuracy of training deep neural networks from
scratch for pneumonia detection supersede that of pre-trained
models such VGG19 and ResNet-50?. This is an obvious
question to answer because of limited computational resources
that we employed. To address this, we conducted experiments
on three (3) publicly available chest X-ray datasets namely
CheXpert from Stanford university [11], NIH and Chest X-ray
images of pneumonia obtained from Kaggle repository. We
compared the performance of VGG-19 and ResNet-50 with
our fine-tuned CNN models trained from scratch on the chest
x-ray images.
In the next section, related works on chest-x-ray image
segmentation and pneumonia classification using deep
learning are introduced as well as highlights the major
contributions of our work. Section 3 describes the methods
used in detail. In Section 4, the experimental results obtained
through a performance comparison of the proposed method
with an existing state-of-the-arts (SOTA) medical image
classification techniques were discussed.
The conclusion of the work, limitations and future directions
were highlighted in the last section.
2. Related Works
The early application of CNNs in medical imaging dates
back to 1990s when a computer-aided diagnostic (CAD) tool
was used in mammography[12][13]. The evolution of
powerful computing (GPU and TPU) fueled more research in
medical imaging which translates into more literatures and the
proposal on new detection systems with better performance.
The application of CNNs is not limited to the development of
clinical decision support systems (CDSS) but to the
segmentation and classifications of disease subtypes.
2.1. Deep Learning in Lung Segmentation
Conventionally, medical image processing involves the
following steps – Image formation (acquisition and
digitization), Image enhancement (calibration, registration,
and transformation) and Image analysis (feature extraction,
segmentation, and classification). The very step towards
building a robust CDSS lies in efficient lung segmentation
and localization. Standard image processing technique such as
clustering, edge detection, threshold and vector quantization
have been studied for lung segmentation in chest x-ray images
(CXR)[14][15][16]. The image processing approaches, on the
other hand, use relatively basic algorithms and perform poorly
when the input image contains noise and some other artefacts.
Lung segmentation using convolutional neural networks is
being intensively investigated with the emergence of deep
learning. Researchers are currently striving to improve lung
segmentation performance by employing a variety of
approaches, including attention modules, in addition to
proposing more advanced image segmentation network
techniques.
Current research revolves using the state-of-the-arts
algorithms as a benchmark. A robust segmentation algorithm
called Total Variation-based Active Contour (TVAC) was
proposed by Narathip et al.[17] which proved successful when
compared the U-Net architecture. Faizan et al.[18] used
Generative Adversarial Networks (GANs) to train different
discriminators for lung segmentation from CXR. The
proposed approach, with a dice-score of 97% and IOU of
94%, outperformed existing state-of-the-arts techniques. Deep
learning based method called “Self-Attention Deep Neural
Network” was proposed by Kim et al.[19] for the automatic
segmentation of CXR. Experimental results show the
performance was comparable to most of the existing
techniques based on the dice score.
A common trend across existing literature is the absence of
a well annotated training dataset which yields low
performance in situations where the lungs are either deformed
or occluded.
2.2. Deep Learning in Pneumonia Classification
The correct detection of lung borders is one of the most
crucial steps in automatic CXR analysis where boundary
regions are extracted, which hence helps in diagnosing
pneumonia, pneumothorax, emphysema, and cardiomegaly; a
family of lung diseases commonly known as Chronic
Obstructive Pulmonary Diseases (COPDs)[20][21]. The work
of [22] involves using various CNNs architectures for the
classification of viral pneumonia diseases from
non-COVID-19. The overall accuracy of 99.51% and an AUC
of 99.4% was reported, which showed that ResNet-101 could
distinguish COVID-19 from non-COVID-19 cases. Wang et
al.[23] trained a CNN for the discrimination of viral
pneumonia from COVID-19 cases based on clinical changes
from CT images collected from 453 unique patients.
Similarly, Zhang et al.[24] proposed an automated intelligent
assistive system for the detection and quantification of
COVID-19 pneumonia using CT images of 2215 patients with
multiple lesions. A detailed study on deep learning
approaches for automatic detection and prediction of
pneumonia in the era of COVID-19 was presented by Shoebi
et al.[25]. The study also highlighted the challenges faced by
clinicians and future research directions. The use of transfer
learning with the help of data augmentation was proposed by
Chowdhury et al[26] for the screening of COVID-19
pneumonia from digital CXR images with 97% accuracy. A
deep neural network called Deep-COVID was proposed by
Minaee et al[27] was proposed for forecasting the spread of
COVID-19 pneumonia from chest x-ray images. A
comprehensive dataset of CXR and CT scan images from
variety of sources presented for the diagnoses of COVID-19
pneumonia[28]. Experimental results showed that transfer
learning via pre-trained models was better to training a model
from scratch.
In summary, the “transferability” of knowledge
incorporated in pre-trained CNNs is one of the most crucial
aspects of deep neural networks. However, few research was
done in the performance evaluation of CNNs trained from
scratch against pre-trained networks.
2.3. Contributions
Our primary contributions are:
 We present a fine-tuned CNN based model for
classification of pneumonia in chest x-ray images.
 We demonstrated that although it is computationally
intensive, training a deep neural network from
scratch using limited resources is possible.
 We analyzed the effects of hyperparameter
optimizations to identify the effects of dropout
variations tailored towards achieving better accuracy
than most traditional approaches.
We presented overall accuracy of 87%, and a recall of 98%
using pre-trained models with appropriate fine-tuning which
is comparable with the state-of-the-art techniques on medical
image analysis.
3. Methods

Deep convolutional neural networks have proven to yield

better accuracy when dealing with large volumes of dataset,
and many researchers tend to use them as de-facto standards.
This was made possible because of transfer learning, where
models trained from large datasets like the ImageNet with
modified optimizers were used.
We present the experiments and procedures undertaken to
verify the effectiveness of our proposed model based on the
publicly available chest x-ray (CXR) datasets from the NIH
and Kaggle repositories. Keras and TensorFlow, both
open-source Python libraries were used to train the CNNs to Fig. 3: The distribution of chest x-ray images
discriminate features for the classification of pneumonia from
chest x-ray images. The dataset is highly imbalance with more of pneumonia
cases versus normal cases, hence data augmentation was used
to balance the dataset, thereby eliminated the possibility of
3.1. Dataset Description overfitting the model.
To evaluate the performance on other COPD diseases, 4999
A more reliable database other than GitHubs‟ is the very CXR images were randomly chosen from the NIH dataset;
popular chest X-ray database on “Kaggle” with the with 2999 used for training and 1000 each for testing and
anterior-to-posterior (AP) and posterior-to-anterior (PA) CXR validation.
images consisting of 5856 images of normal, bacterial, and
viral pneumonia with varying resolution of 400p to 2000p.
However, only chest X-ray images for normal and viral 3.2. System Requirement
pneumonia were used in this study as shown in figure (1).
The hardware used for all experiments were on an 8th
generation Core i7 laptop PC with a 16GB RAM, an NVIDIA
GeForce 1060Ti GPU of 6GB and 256GB of SSD with the
usual Windows OS.

(a) (b) 3.3. Baseline for preprocessing

Fig. 1: The chest x-ray images of (a) a patient with highly enhanced edges,
There was no need for image quality enhancement as the
and (b) normal patient. dataset images has already been denoised and in high
resolution. However, to make the model more robust,
It was further subdivided into training, testing and
rescaling and normalization was used. Furthermore, images
validation set with each containing both normal and
were randomly rotated at 30 degrees during training and
pneumonia annotated images. For pneumonia cases, 3875
flipped both vertically and horizontally by 25 degrees each as
images were used for training, 390 for testing and 8 for
illustrated in table (1).
validation as illustrated in figure (2).
Table 1: Parameters for image augmentation.
Method Default Adjusted
Horizontal flip None True
Horizontal shift 0 0.25
Vertical shift 0 0.25
(a) (b) Shear range 0 0.3
Fig. 2: The chest x-ray images (a), (b) of Pneumonia patients. Rescale - 1./255

The remaining normal images were 1341, 234 and 8 Zoom range - 0.3
respectively as shown in the figure (3). Fixed image size 1024 x 1024 224 x 224

3.4. ResNet-50

The ResNet-50 (residual neural network) is a variation of

ResNet architecture with 50 deep layers that has been trained
on at least one million images from the ImageNet database.
  1 * 1, 6 4 
 
Double or triple-layer skips with nonlinearities (ReLU) and 3 * 3 , 6 4at  the
applied x 3 fully connected layer, followed by
 
batch normalisation are used in most ResNet models.  1 * 1, 2 5for
softmax 6 classification.
HighwayNet, a model that employ an additional weight  (1)
matrix to learn the skip weights are often incorporated.
ResNet-50 architecture consists of sequences of convolutional Table 2: ResNet-50 architecture summary

Layer Output size 18-layer 34-layer 50-layer 101-layer 152-layer

name
conv1 112 x 112 7 x 7, 64, stride 2
conv2_x 56 x 56 3 x 3 max pool, stride 2

[ ] [ ]
[ ] [ ] [ ]

conv3_x 28 x 28
[ ] [ ]
[ ] [ ] [ ]

conv4_x 14 x 14
[ ] [ ]
[ ] [ ] [ ]

conv5_x 7x7
[ ] [ ]
[ ] [ ] [ ]

1x1 average pool, 1000-d fc, softmax

FLOPs 1.8 x 109 3.6 x 109 3.8 x 109 7.6 x 109 11.3 x 109

blocks with average pooling. Softmax is used as at the last

layer for classification. The basic idea of ResNet50 was better Table 2: ResNet-50 architecture summary
explained by Quingge et al[29], in their study for
identification of macular diseases from optical coherency
tomography images as shown
in figure (4).

3.5. VGG-19

The VGG network is a tradename for the pre-trained CNN

Fig. 4: The basic architecture of ResNet-50 (only 34 layers are
shown for simplicity)
The ResNet-50 consists of five convolutional layers namely;
conv1, conv2_x, conv3_x, conv4_x and conv5_x. Once the
input image is loaded, it is passed through a convolutional
layer with and kernel size of (conv1 layer)
followed by a max pooling layer of stride length of 2 in both
cases. Next, in the layers are grouped in pairs
because of how residual networks are connected. The matrix
shown in equation (1) means there are two layers of
respectively,
and another layer of
repeated thrice corresponding to the layers between
. Similarly, the process continued until the fifth
convolutional layer after which average pooling is
model proposed by Simonyan and Zisserman [30] in early
2014 at the University of Oxford, UK. VGG (Visual
Geometry Group) was trained on ImageNet ILSVRC dataset
of 1.3million images consisting of 1000 classes for which
100, 000 images were used for training and 50,000 for
validation. VGG-19, a variant of VGG architectures has 19
deeply connected layers which has consistently achieved
better performance as compared to other state-of-the-arts
model. The model consists of highly connected convolutional
and fully-connected layers which enables better feature
extraction and, the use of Maxpooling (in the place of average
pooling) for downsampling prior classification using SoftMax
activation function. The architecture of VGG-19 is as in
figure (5).
 Fig. 5: VGG-19 architecture (CREDIT: [30])
3.6. Iyke-Net: A CNN trained from Scratch
There was no need for image quality enhancement as the
dataset images has already been denoised and in high
resolution. However, to make the model more robust,
rescaling and normalization was used. The block diagram for
our Iyke-Net can be summarized as in figure (6). This section
illustrates the design of the proposed CNN approaches for
identifying pneumonia cases from chest x-ray images, as well
as the implementation details for the proposed CNN models.
A simple CNN architecture built from the ground up is
included in the proposal. CNN algorithms extract meaningful
features using a series of convolutional layers and fully
connected neural layers.
Fig. 6: Block diagram of the training process
The default step was to load the input images from the
directory followed by data augmentation. In this study, two
different pretrained model were trained and tested and their
performance compared against a tunned convolutional neural
network.
Fig. 7: Block diagram of Iyke-Net
Proposed CNN model (Iyke-Net): The architecture of
Iyke-Net depicted in figure (7) mirrors that of VGG-11, 10
filters were used followed by batch normalization and dropout
regularizations added in between the convolutional layers of
each block. The rectified linear unit (ReLU), used as an
activation function, with a fully connected (FC) layer and
Softmax for classification.
Input Layer: Since the architecture is like that of VGG
Networks, the input image must be resized to the standard 224
x 224 pixels, this was needful because medical images like an
x-ray, when taken from different devices come in various
sizes. For efficient preprocessing, the images must be resized
to 224 x 224 x 3 depicting the width, height, and channel
numbers (3 for RGB) respectively.
Convolutional Layer: This is the most important layer in
our proposed CNN model, as it is where majority of the
computations would be done. This layer's main job is to
retrieve features from the image while keeping the spatial
relationship between image pixels intact. This is
accomplished by utilising a series of filters to learn the
retrieved features. In this study, a two-dimensional
convolution was performed using 10 filters, each of which
was built using a 7 * 7 filter size. In addition, the filters move
along the input images, calculating the dot product function,
also known as convolved features.
Batch Normal Layer: Batch normalisation is a technique
for training very deep neural networks that standardises each
mini-inputs batches to a layer. This stabilises the learning
process and significantly reduces the number of training
epochs needed to create deep networks. It is a transformation
that keeps the mean output close to 0 and the standard
deviation of the output close to 1 the following
hyperparameters (epsilon = 0.001 & momentum = 0.99) was
used for training our model.
ReLU Layer: This layer is responsible for replacing all
negative values to zero while allowing positive numbers to
assume their respective values from the convolved features,
thereby introduces non-linearity in the feature map.
Fully Connected (FC) Layer: All the activation functions
from the preceding layer are related to the neurons in this
layer. This layer's primary function in this study is to classify
the returned convolved features from dataset images into their
respective classes.
SoftMax Layer: After the fully connected layers, a proper
interpretation of the probabilities is needed, and that is the
function of the SoftMax layer. It simply classifies the values
between „0‟ and „1‟ or 0% and 100%.
 Output Layer: The final layer, consisting of the two
classes (Normal and Pneumonia) is presented at this layer.
ResNet-50 vs VGG-19: We conducted two (2)
experiments using pre-trained models as it is easier to
fine-tune the parameters unlike a network trained from scratch
as the results presented in table (3).
Iyke-Net (Trained from Scratch): Subsequently, we
trained a deep neural network called Iyke-Net whose
architecture is illustrated in figure (7) from scratch to check
computational intensity and accuracy. As a standard approach,
the input images were first resized to 224 x 224 with a three
(3) colour channel and used a learning rate of 0.001. To
improve on the accuracy of our model, further experiments
were performed and detailed in figures (8), (9) and (10).
3.7. Performance Evaluation Metrics
To compare the performance of various deep learning
algorithms for classifying the prevalence of pneumonia from
chest x-ray images, the standard metrics were used. It is worth
highlighting that the experiment‟s performance measures are
based on an average of 3 simulated runs, with each consisting
of 100, 200 and 400 epochs with mini-batch size of 64. The
accuracy, precision (NPV), recall(sensitivity), and F1-scores
employed in this investigation will be described next.
(2)
(3)
(4)
(5)
(6)
Where pneu = the pneumonia class
4. Results and Discussion
The results were based on two different approaches; first
we conducted experiments using VGG-19 and ResNet-50,
pretrained models to discriminate pneumonia images from
normal chest x-ray images taken from the anterior to posterior
(AP/PA) at high resolution. The choice of ResNet-50 over
ResNet-101 was to compensate for limited resources at our
disposal. As a standard technique, the image was reduced into
smaller sizes which is then passed into the convolutional
neural network for classification. The validation accuracy of
our model was slightly higher when compared to other
conventional approaches due to the efficiency of using
pretrained models.
Second, we created a model to detect and categorise
pneumonia from frontal chest images. The technique starts by
reducing the input size of chest X-ray images. The
convolutional neural network framework, which collects
features from the images and classifies them, is then used for
identification in the next stage. We experimented on training
from scratch by starting with an epoch of 20 and increased the
epochs to 100 using a fixed batch size of 64.
The table (3) shows that our proposed CNN approach
works effectively on both the normal and pneumonia X-ray
images utilised in our study. It is quite interesting to achieve
93.6& accuracy and 92.03% recall using our approach. On the
other hand, pretrained VGG-19 and ResNet-50 performs
admirably on X-ray images, correctly identifying all
pneumonia images with 97.3% accuracy and 99.2% recall of
typical X-ray images.
Table 2: Model accuracy under various epochs
Epochs Training Validation
Accuracy (%) Accuracy (%)
10 65.02 45.34
100 81.24 79.02
200 83.97 83.91
300 93.6 93.55
400 88.60 88.68
It can be seen from table (2) that the accuracy was below
average, and that led us to conduct more experiments. Data
augmentation was done, and the epochs increased to 100
while keeping all the hyperparameters constant. We observe
improvements in the performance of the baseline model
highlighting the possibility of more accuracy as we finetune
our model. The model shown in figure (8) trained in
02Hours:31Mins:05Secs with an accuracy(validation) of
79.02%. Furthermore, the model was fine-tuned by adding
dropout layers in between convolutional layers.
We started by dropping out 20% of the dataset at random
during training. Variations of dropout (30%, 45%, and 55%)
were used alongside increasing the epochs to 200 while
keeping other parameters constant and obtained an
accuracy(validation) of 83.91% as shown in figure (9) and the
model trained in 05Hours:06Mins:11Secs. Although slight
improvement was recorded in accuracy, but that came at the
cost of resources. Finally, we tried tunning the
hyperparameters, in this case, the learning rate was changed
from 0.001 to 0.0001 and the epochs increased to 400 which
took 16Hours:43Mins:11Secs to train with an accuracy of
88.68% as depicted in figure (10).
 Fig. 10: Cross entropy loss and classification accuracy curves for 400 epochs

It can be observed that the model did not improve beyond

300 epochs, suggesting that we may have overtrained our
model. Further, we retrained our model by decreasing both the
number of epochs and learning rates to 300 and 0.00001
respectively. The model trained in 13Hours:05Mins:33Secs
yielded an accuracy of 93.6%, better than using 400 epochs.
In summary, the performance accuracy of each model is
presented in Table (3).

Table 3: Accuracy of VGG-19, ResNet-50 and Iyke-Net.

Metrics VGG-19 ResNet-50 IykeNet
Accuracy (%) 97.3 96.2 93.60
Fig. 8: Cross entropy loss and classification accuracy curves for 100 epochs
Specificity (NPV) (%) 97.2 96.4 91.66
Precision (%) 96.7 95.3 91.30
Recall (%) 99.2 98.4 92.03

Training Results: Our findings on using pretrained

models such as VGG-19 and ResNet-50 trained on same
datasets, gave better results as compared to training from
scratch. Further, to validate the performance of our approach,
a comparative analysis was done using state-of-the arts
models.

Validation Results: The performance of our model when

compared against existing state-of-the arts (SoTA)
approaches, which in most cases serves as the “ground truth”
highlighted the fact that Iyke-Net (our network trained from
scratch) outperforms most robust pre-trained models as shown
table (4).

Table 4: Comparison with state-of-the-arts model.

Fig. 9: Cross entropy loss and classification accuracy curves for 200 epochs Method Models Accuracy F1-Score Precision Recall
(%) (%) (%) (%)

Rajpukar et ChexNet 85 95 - -
al(2017)[31]
Loey et ResNet-50 84.5 - - 0.10
al(2020)[32]
Apostolopoulos VGG-19 93.5 - - 86.0
et al(2020)[33]
Proposed Proposed 93.60 91.66 91.30 92.03
method (Iyke-Net)

Note: Bold numbers indicate best performance metrics

It was observed that CheXpert[31] gave an accuracy of

85% for positive pneumonia case with an F1-score of 95%, a
very robust approach considering the size of the dataset used
(112, 120 frontal-view chest X-ray images) and the authors
did not report the precision and recall. The works of Loey et
al[32] yielded an accuracy lesser than our model despite using
only 158 images of pneumonia patients. A similar approach
was investigated by Apostolopoulos et al[33] with an
accuracy of 93.50, and no performance metrics in terms of
F1-Score and precision were reported. Their works on the
classification of covid-19, pneumonia and lung cancer from
chest x-ray images using pre-trained networks validates our
findings that pre-trained model with adequate fine-tuning
yields similar performance with a CNN trained from scratch.
5. Conclusion
The advances in transfer learning notwithstanding, we
demonstrated the possibility of training a deep neural network
on “not-so-powerful” laptop PC with a commensurable
accuracy. Our approach was able to discriminate salient
features which helped in the classification of pneumonia from
chest x-ray images. We compared the performance of two
pre-trained against a deep neural network trained from scratch
by fine-tuning appropriate hyper-parameters. Our
examinations showed that our model is able generalize to
unseen dataset, a positive step in building a robust computer
aided diagnostic tool. However, our experiments proved that
it is computationally intensive to achieve state-of-the arts
accuracy by training a deep neural network from scratch as
shown in Table (4). Our findings highlighted that it is
expensive to guarantee an efficient generalization by training
a deep neural network from scratch.
More so, we used only chest x-ray images as a benchmark
where CT scan images should have been used. Only binary
classification (pneumonia vs normal) was studied. This work
will be extended to detect and classify all the families of
COPDs from both chest X-ray and CT images suggesting that
deep learning could be useful in diagnosis of chronic
obstructive pulmonary diseases.
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