New Trends and Future Challenges in Computational Imaging and Wireless

Communication

IBDNet- Computer Aided Detection and Diagnosis of

Inflammatory Bowel Disease using Optimized CNN
model

Himanshu Jain1, Aayush Kumar1, Sameena Pathan2, Tanweer Ali1, Jagadeesh Chandra
R B1*, Vikas Kumar Jhunjhunwala3
1
Department of Electronics and Communication Engineering, Manipal Institute of Technology,
Manipal Academy of Higher Education, Manipal 576104, India.
2
Department of Information and Communication Technology, Manipal Institute of Technol-
ogy, Manipal Academy of Higher Education, Manipal 576104, India.
3
Department of Electrical and Electronics Engineering, Manipal Institute of Technology, Mani-
pal Academy of Higher Education, Manipal 576104, India.

Abstract. This paper proposes a method for the classification of inflammatory

bowel disease (IBD) using deep learning and evaluates the performance of
different transfer learning models. IBD is a chronic condition affecting millions
of people worldwide, and accurate diagnosis is essential for effective treatment.
The two main types of IBD are Crohn’s disease and ulcerative colitis, symp-
toms include weight loss, abdominal pain and diarrhea. The exact causes of
IBD are not yet fully understood, but it is believed to be a combination of ge-
netic, environmental, and immune system factors. The potential benefits of
using CAD in the detection of diseases are increased accuracy, efficiency, CAD
systems can help standardize the diagnostic process thereby reducing the likeli-
hood of errors, reduction in overall cost and by early detection improve patient
outcomes. The proposed method uses a novel convolutional neural network
(CNN) architecture to automatically extract features from medical images,
followed by classification based on severity of the disease. To validate the
performance of CNN, different pre-trained models such as DenseNet, Mo-
bileNetV2 and the InceptionResNetV2 were fine-tuned and their scores are
compared. The proposed method is evaluated using a large dataset of endo-
scopic images. The 90% validation and 86% training scores demonstrate that
the proposed method achieves high accuracy in the classification of IBD and
performs well when compared with the highly advanced pre-trained networks
which are trained on millions of such images. The proposed method has poten-
tial applications in clinical settings and can assist physicians in the accurate
diagnosis and treatment of IBD.
 Keywords: Chron’s disease, Computer Aided diagnosis, Convolutional Neural
Network, Inflammatory Bowel Disease, Ulcerative colitis.

1 Introduction

Inflammatory bowel disorder (IBD) is a chronic and debilitating gastrointestinal

disease that affects millions of people worldwide. The most common types of IBD are
Crohn's disease and ulcerative colitis, which are characterized by inflammation and
damage to the digestive tract. Early and accurate detection of IBD is crucial for effec-
tive treatment and management of the disease [1-4].
Conventional approaches for the UC diagnosis and classification comprise colono-
scopy, biopsy based on histopathological observation. But these methods are invasive,
lengthy and subjective. Deep Convolutional Neural Networks (CNNs) have shown to
be a recent solution for the automatic detection and classification of UC in recent
years. Convolutional Neural Networks (CNNs) are a class of artificial neural net-
works that draw from the functionality and structural organization within human
brains. They have been used to describe and analyse in a variety of medical imaging
applications including cancer detection/classification, diabetic retinopathy classifica-
tion/diagnosis, pulmonary diseases analysis. CNNs can automatically identify and
grade UC lesions in endoscopic images of the colon or rectum, which is crucial for
studying UC branches. [5-7].
In this paper, we proposed a deep CNN based system to detect and classify UC le-
sions. The method is trained and evaluated on a set of endoscopic images, publicly
available. Proposed Approach The general block of our approach consists of three
stages: pre-processing the images, training deep Convolutional Neural Network
(CNN) model and evaluation based on several metrics also compare the performance
of our model with finely tuned pre-trained models such as InceptionV3, Resnet50,
VGG19 and DenseNet121 for UC detection and classification.
The results of our study demonstrate the potential of deep CNNs for the automated
detection and classification of UC lesions. Our proposed method achieves high accu-
racy and outperforms traditional methods for UC detection and classification. The
findings of this research could have significant implications for the early diagnosis
and effective treatment of UC.
This paper is organized as follows, firstly we will review the relevant literature and
highlight the key findings and gaps in knowledge. Next, we will describe the proce-
dures used to collect and pre-process the data. Then we describe the methodology and
construction of the CNN architecture. The results of our model will then be presented
and discussed in detail. Finally, we will conclude with a summary of the main find-
ings, implications for practice, and suggestions for future research.

1.1 Related Work

For convenience of processing, the authors of [8] resized the image to 256 × 256
pixels. To increase the image's sharpness, adaptive gamma correction was utilized for
image recognition and reconstruction. Finally, they employed augmentation to in-
 Contribution Title (shortened if too long) 3

crease the amount of training samples. They also applied histogram equalization to
improve the image quality. From the results obtained via the performance metrics
used in [6] we can infer that classification of UC is more complex than CD as 94% of
CD patients were accurately labelled whereas only 65% of the UC patients.
The lack of data presented a challenge to the writers of [9]. In their suggested
method, they used the FastGAN few shot generator to artificially create new data
from a real dataset containing UC colonoscopy data. To tackle class imbalance in
their dataset, the main objective was to produce high resolution synthetic images and
to introduce variance within the data.
The authors of [5] developed an automated method for diagnosing IBD (UC and
CD). The patient data was pre-processed, and important variables were chosen before
being exposed to the SVM, which was assessed using the generated binary classifica-
tion quality metrics. The objective is to map the n-dimensional input space to a
higher-dimensional space. A linear classifier is then used to classify the newly created
feature space.
The backbone network used by the authors in [10] was the DenseNet201 design. It
consists of five dense layers, with a feed-forward connection between each layer.
Features that are recovered by the DenseNet are partitioned and input into indepen-
dently recurrent neural networks (IndRNN) and an improved attention mechanism
module (EAM-Net) to generate attention maps and knit them together to emphasize
the extracted features. To optimize the computation space and lower the number of
calculations needed, the output of EAM- Net is added to the global average pooling
layer to optimize the calculations by reducing the number of calculations needed to be
performed. Additionally, it can help retain more background characteristics by reduc-
ing the errors brought on by the rise in estimation variance.
Ensemble models powered by pre-trained networks through transfer learning can
be utilized to generate a model that can be practically applied in the detection of GI
diseases with high accuracy which can help reduce burden on healthcare professionals
and lead to quicker diagnosis [11]. The authors suggested a UC-NfNet architecture in
[12-13]. Their network accepts as input an RGB image of HW resolution that has
been channel-wise normalized using the standard deviation and mean obtained from
ImageNet. By adding a Spatial Attention Block (SAB) following the initial convolu-
tion, using 2 convolutions with 16 channels, 1 with 32 channels and other with 64
channels, and then performing 2 convolutions with 128 channels, UC- NfNet alters
the main block of the original system. By essentially concentrating on areas that are
more important therapeutically, they developed the SAB to improve functionality of
the UC-NfNet.
In the proposed work the imbalance in the dataset is handled through class-wise
augmentation resulting in sufficient amount of data required to feed the model. The
model comprises of different convolutional blocks each of which contains a unique
setof filters to aid in feature extraction. The model’s performance is very competitive
compared to the different approaches mentioned above and is a brilliant learner that
can be trained on any medical dataset for custom implementation. The regularization
techniques used for handling overfitting assure the integrity of the model’s predic-
tions, which is of utmost importance when dealing with medical data.
2 Methodology

The framework for the proposed method is depicted as given in Fig. 1. The dataset
once loaded is visualized and augmented for the purpose of scaling the dataset hence
leading to a more generalized model when trained. The CNN architecture is con-
structed and learned over many iterations until the best possible weight combination
is achieved. Finally, the test data is loaded and the model is evaluated via multiple
sets of predictions.

Fig. 1. Block diagram of the proposed methodology

Some of the tools used are TensorFlow, OpenCV, Pandas, NumPy, Matplotlib. Coded
entirely in python using the Google Collab environment with GPU for training the
deep neural network. First, we observe the importance of balancing our dataset. The
dataset used in this project is downloaded from an open online repository. This
dataset contains 4 classes ranked from Mayo 0 to Mayo 3 which is in the increasing
order of the severity of the disease as classified by gastroenterologists. Number of
images in, Mayo 0: 5180; Mayo 1: 2588; Mayo 2: 1077; Mayo 3: 745. The dataset has
endoscopic images from different parts of the colon. The purpose of balancing the
dataset is to remove any bias that may be introduced into the model which may lead
to irregular pattern of classification. The dataset is relatively small hence it is also
scaled 4 times in size, thus by introducing new images into the sample space the
model has more features and variants to learn from leading to a more generalized
predictor.
We balance the dataset and scale it to 10,000 images per class through the application
of class-wise augmentation using a library known as Albumentations. The techniques
used are horizontal and vertical flips, rotations, brightness, and color jitter etc. On
 Contribution Title (shortened if too long) 5

training the same model using this new and improved dataset we will now observe the
upgraded results obtained.

2.1 Model Architecture

Initially we started with a simple CNN model. This model didn’t use any regulariza-
tion techniques to prevent overfitting and with a simple single Conv2d and single
dense layer, the model’s learning ability was also limited. On training for 34 epochs
the training and validation accuracy saturated at approx. 69%. So even though there
was no overfitting, and the fluctuations were mild the model simply was not powerful
enough to learn all the important features. So, we took it to the next level, by adding
another conv2d block with double the number of filters (32, original conv2d had 16)
and also adding regularization, batch normalization per convolutional layer and
dropouts to the dense layer to curtail the overfitting with what is now a more powerful
model. This new improved model produced an accuracy of 82% and validation score
of 76% on training for 34 epochs, so even with the regularization the suspected over-
fitting could not be handled effectively as the model probably still wasn’t complex
enough to be generalized effectively by the techniques implemented. So, we decided
to further increase the model complexity to raise the accuracy and observe how the
model performs on the validation data. With a total of now 3 Convolutional blocks
with 2 Conv2d layers per block with increasing number of filters per layer per block
starting from 32 going all the way up to 128 in the last convolutional layer in the third
block, a (2,2) max pooling at the end of each block output of which is flattened using
the GlobalAveragePooling2d layer and fed to a 512-neuron dense layer for learning.
The 4 neuron SoftMax layer performs the classification with a now improved training
accuracy of 90% at the 34th epoch and a validation accuracy of 86%. Here we can
finally see the importance of using regularization to reduce the degree of overfitting
as the complexity of the model increases, if we did not go for it then the validation
score would still be around the 70% mark whereas the training would be in the 90s.

Optimization- The process works on the principle of iterative comparison of dif-

ferent results. The goal of this process is to help find the best solution possible.
Through neural network hyperparameter adjustment, it is employed in deep learning
to reduce the generalized loss function. To reduce overfitting, we have implemented
various regularization techniques such as l2 regularization on the convolutional layers
and dropout on the dense layer.

Batch Normalization- Batch Normalization is one of the types of normalization

techniques used in deep learning for the input layer. It involves re-cantering and res-
caling for each of the mini-batches. One of the benefits of this technique is accelerat-
ing the training process. The concept is rather straightforward and is based on the
normalization of the defined value. If the covariate shift is reduced, the model learns
quickly, and the training process accelerates. On the other hand, if no normalization
of the input value is provided, the model has a number of problems with learning, The
statistic of each input is varied depending on the previous inputs, and the learning is
slow.

L2 Regularization: L2 regularization or weight decay, as it is also known in deep

learning, a standard procedure to prevent overfitting. During training, a penalty term
is added to the loss that encourages small weights. In practice, L2 regularization
causes the algorithm weights to be pushed closer and closer to zero (but typically not
exactly 0) for increased regularization strength which reduces some features contribu-
tion on prediction outputs thus is applied in order also by that way decrease overfit-
ting chance as well.

Dropouts: Another regularization method in deep learning is called "dropout,"

which involves temporarily removing random neurons from the neural network as it is
being trained. This forces the remaining neurons to learn more robust features that can
still make accurate predictions even when some of the inputs are missing. Dropout
has been shown to be an effective way to reduce overfitting in neural networks, espe-
cially when dealing with large and complex datasets. The dropout rate controls the
fraction of neurons that drop out during training.

We utilized an early stopping monitor which kept an eye on the valida-

tion score and stopped training when there was no significant improve-
ment after a certain number of epochs and restored the best weights on
completion. The batch size was set to 16 with a learning rate of 0.001
on the Adam optimizer with no decay.

3 Results and Discussion

The novel CNN model hit a training accuracy of 90% and a validation score of
86% highlighting the fact that the model has handled overfitting which implies that
the model has performed very well on fresh unseen data. On implementing transfer
learning and fine- tuning the pre-trained models we get the following results.

Table 1. Comparison of Model performance based on accuracy and F1 score

Model Validation Accuracy Training Accuracy

Proposed CNN 86.15% 90%
Inception_Resnet50 82.01% 88.88%
Mobilenetv2 84.13% 93.12%
Dense net 121 84.25% 89.77%
 Contribution Title (shortened if too long) 7

It can be observed that the pre-trained models did very well but not better than the
novel implementation, in fact the proposed approach did not overfit quite as much as
the pre- trained models, this is due to the fact that the novel model was trained on the
dataset from scratch and hence is more generalized whereas the pre-trained models
were trained on the ImageNet database and the weights of which were fine tuned to
the current dataset with the help of a single dense layer.

(a) (b)

Fig. 1. Performance of the proposed model and Transfer learning model (a) Proposed (b) Incep-
tion_Resnet_V2.
 (a) (b)

Fig. 2. Performance of the transfer learning-based models (a) DenseNet (b)

Inception_Resnet_V2.

From the Fig 1 and Fig 2 it can be observed that the frequency of fluctuations is lesser
in the fine- tuned pretrained models. Since these models are trained over millions of
images of different kinds the probability of randomized predictions is few and far
between. The ROC curve and Confusion Matrix depicts the class-wise performance of
the model, and as we can observe the model performs very well on both these metrics.
It can be inferred that the Mayo 2 class has relatively the least accurate predictions,
which makes sense as it is sandwiched between Mayo1 which is light infection and
Mayo 3 which is serious, resulting in some images from Mayo 2 being ambiguous and
thereby resulting in some confusion in the predictions.
 Contribution Title (shortened if too long) 9

(a)

(b)

Fig. 3. Performance of the proposed IBDNet (a) Confusion Matrix (b) ROC curve

4 Conclusion
This research work will greatly benefit doctors who now do not need to sit and analyze each n
every image to search for an issue, the computer will give the verdict with a high confidence
level and the doctor can now focus his attention on deciding the treatment plan going forward
for his/her patients thereby saving a lot of time and resulting in a faster diagnosis without com-
promising the quality of care given to the patients.

In the future we can focus on improving the performance of the proposed method by exploring
different deep learning architectures and transfer learning models. For instance, more recent
architectures such as EfficientNet and ViT (Vision Transformer) can be evaluated for their
suitability in the classification of IBD. Additionally, the proposed method can be extended to
incorporate other clinical data such as patient history, laboratory results, and endoscopy find-
ings to improve the accuracy of the diagnosis. Finally, the proposed method can be evaluated
on larger and more diverse datasets to ensure its generalizability and applicability to different
patient populations.

Disclosure of Interests. The authors declare that they have no competing interests.

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