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Keywords: convolutional neural networks (CNNs), deep learning, computer-aided diagnosis, colorectal polyps,
colorectal cancer, colonoscopy
I. Introduction
Machine learning is an artificial intelligence method that a computer learns to do
specific tasks from available data without anyone explicitly programming it. Machine learning
approaches are divided into three core methods: supervised learning, unsupervised learning,
and reinforcement learning. Supervised learning is most broadly used among other core
methods, and popular algorithms, include linear regression, logistic regression, artificial neural
networks, support vector machines, decision trees, and decision forests. In these algorithms,
the goal is to find a relationship between an (x, y) pair and determine the function f , f(x)= y,
using available samples of (x, y) shapes [1]. In an (x, y) pair, x and y can be regarded as an
input and output of a system, respectively.
Artificial neural networks, or simply called neural networks, is a subclass of machine
learning in which the learning process is inspired by the mathematical modeling of nerve cells
in the human body. The overall structure of neural networks is layered. Each layer consists of
several nodes connected in two consecutive layers (Figure 1). Each node models a neuron in
the nerve system and connections among them represent synapses in the nerve system that
transmit information between two nodes [2]. This method is called deep learning when the
number of hidden layers in the neural network exceeds a certain amount (5 to 20 layers) [3].
1
e-mail: [email protected]
details the limitations of CNN models and the approaches that can lead to improving the
diagnostic performance of these models in future studies. Finally, conclusions are drawn in
section IX.
II. What are the differences between conventional machine learning models and CNNs?
In most medical studies, conventional or traditional models like logistic regression [22],
linear regression, artificial neural networks [23], support vector machines [24], and random
forest [25] are used for diagnostic purposes. In these models, features are extracted manually,
and this technique is called hand-crafted feature extraction [26]. These features are chosen
based on methods such as histogram of oriented gradient (HOG) or hue histogram in images
by persons [27]. However, CNNs extract features automatically, and features are learned by
the CNN model (Figure 2), achieving superior accuracy than conventional models, especially
when data is in the form of images [26].
Figure 2. Comparison between workflow of conventional or traditional models and deep learning or CNN models. Figure
from [28].
On the other hand, we need more data to train CNN models than conventional models
since CNNs have millions of learnable features or parameters [26]. In contrast, the number of
features in conventional models (less than a dozen) is much less than CNNs. Thus, the
computational volume and cost go higher. To solve this problem, it is better to exploit the
graphical processing unit (GPU) instead of the central processing unit (CPU) for training
CNNs. GPU or graphic card processor consists of more cores than the CPU, whereas the
computation power of the GPU core is less. Hence, GPUs process faster in matrix computing,
and computations in the training process are of the same type.
the values of which are calculated in the training process. Then, the input image matrix
convolves with the kernel, or in other words, the kernel matrix sweeps through the entire input
matrix in the length and width directions where these two matrixes overlap (Figure 3). In the
next step, the elements of the feature map matrix are summed with a constant value, called
bias. Here, a non-linear activation function like ReLU (Rectified Linear Unit), sigmoid, or tanh
(hyperbolic tangent) is applied to each acquired matrix element. A significant variation exists
between the values of the feature map matrix elements, and the activation function diminishes
variation between these values since the activation function range is limited. For instance, for
all input values, the hyperbolic tangent or sigmoid outputs are between minus one and one, or
zero and one, respectively (Figure 4). Between the convolutional layers, there are pooling layers
that, through down-sampling, reduce the computation volume and remove redundancy from
the input matrix of pooling layers by decreasing matrix dimensions. In these layers, a window
with a specific size moves through the input matrix. Wherever the window is located, the
maximum value of elements in the window (Max pooling) or the average of the elements’ value
in the window (Average pooling) creates each element of the output matrix of the pooling
layers (Figure 5). Finally, the last convolutional layer’s output matrix is converted to a vector
(a kind of matrix with only one column) before being fed into fully connected layers as inputs
or features extracted by the convolutional and pooling layers. Fully connected layers, as an
artificial neural network, perform classification [29]. The overall structure of CNN, along with
the types of layers described above, is shown in Figure 6.
Figure 3. Three sample steps of the convolution operation. Wherever the kernel is located, the values of the corresponding
elements in the two matrices are multiplied. Then, the resulting values are added together to form the corresponding
element in the output matrix, called the feature map matrix. Figure from [26].
Figure 4. Sigmoid function graph (right-side) and hyperbolic tangent graph (left-side)
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Figure 5. Steps of max pooling operation with a filter size 2*2 and a stride of 2. At each step, the maximum value is
extracted in a 2*2 patch from the input matrix and creates an element of the output matrix.
Figure 6. The overall structure of a CNN model, which classifies colonoscopy images into hyperplastic (Hp), adenomatous
(Ad), serrated (Sr), and normal groups. Figure from [30].
In the related primary studies, the output of the CNN model can be divided into four
overall categories, polyp classification, polyp detection, polyp localization, and polyp
segmentation. In polyp classification, the CNN model recognizes the type of polyp (e.g.,
adenomatous, hyperplastic, serrated, or normal) in a colonoscopy image (Figure 6). In polyp
detection, the CNN model only recognizes whether a colonoscopy image contains at least one
polyp or not. In polyp localization, the CNN model marks the position of each polyp in a
colonoscopy image with a rectangle but not with its exact shape (Figure 7). In polyp
segmentation, the CNN model draws a margin around each polyp that it detects (Figure 8) [31].
CNN models have different architectures; each model has a specific name, such as U-Net [32],
VGG [33], ResNet [34], and Faster R-CNN [35].
Figure 7. Samples of polyp localization. Green boxes show ground truth (gold standard), and white boxes show polyp
localization by the CNN model. Figure from [17].
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Figure 8. Samples of polyp segmentation. Blue contours represent ground truth (gold standard), and red contours represent
polyp segmentation by the CNN model. Figure from [36].
Figure 9.A schematic representation of the gradient descent algorithm. The gradient of the loss function means the
direction of the steepest slope as the loss function increases. Therefore, moving in the opposite direction of the gradient
with a learning rate step size leads to obtaining the loss function’s minimum or local minimum point. The learnable
parameter (w) value is updated iteratively until the gradient of the loss function reaches zero or the loss function reaches a
minimum value. At this point, the optimal value of the learnable parameter is obtained, and our model has been trained on
the dataset. Figure from [26].
a value and remains stable after at least 20 consecutive epochs. Also, α denotes the learning
rate, a minute positive constant number usually between 0 and 1 [26].
In the validation phase, hyperparameters such as learning rate, mini-batch size, number
of epochs, and type of loss function and optimizer are tuned, and the values are determined
[26].
The CNNs performance is evaluated in the testing phase by measuring the evaluation
metrics defined in section V [26]. Testing is divided into internal and external categories, based
on whether the testing dataset and the training dataset are from the same place or not,
respectively. An important note to consider is that in some papers, especially in medical science
criteria, the testing phase is called the validation phase, which differs from the validation phase
described above.
Sometimes, the CNN model performs astounding on the training dataset but does not
perform well on the testing dataset or other datasets. In other words, there is a considerable
interval between the test accuracy value and the training accuracy value. In this case, overfitting
has occurred, and to overcome this issue, we can exploit various methods like data
augmentation, transfer learning, dropout, regularization, and batch normalization [11].
V. Evaluation metrics
After the CNN model is trained on the training dataset, we have to evaluate our CNN
model performance on another dataset (testing dataset). This evaluation is accomplished by
measuring accuracy, sensitivity, specificity, positive predictive value (PPV), and negative
predictive value (NPV), which are defined below.
𝑇𝑃 + 𝑇𝑁
𝐴𝑐𝑐𝑢𝑟𝑎𝑐𝑦 =
𝑇𝑃 + 𝐹𝑃 + 𝑇𝑁 + 𝐹𝑁
𝑇𝑃
𝑆𝑒𝑛𝑠𝑖𝑡𝑖𝑣𝑖𝑡𝑦(𝑅𝑒𝑐𝑎𝑙𝑙) =
𝑇𝑃 + 𝐹𝑁
𝑇𝑁
𝑆𝑝𝑒𝑐𝑖𝑓𝑖𝑐𝑖𝑡𝑦 =
𝑇𝑁 + 𝐹𝑃
𝑇𝑃
𝑃𝑃𝑉(𝑃𝑟𝑒𝑐𝑖𝑠𝑖𝑜𝑛) =
𝑇𝑃 + 𝐹𝑃
𝑇𝑁
𝑁𝑃𝑉 =
𝑇𝑁 + 𝐹𝑁
Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 8 October 2021 doi:10.20944/preprints202110.0135.v1
There are four indicators in these metrics, including True Positive (TP), False Positive
(FP), True Negative (TN), and False Negative (FN). These indicators can be defined in the
form of a two-by-two table, also called a diagnostic table.
Ground Truth
Disease Normal
Positive TP FP
Model Output
Negative FN TN
The TP index indicates the number of images containing at least one polyp that the
CNN model has correctly classified or detected, or the number of images in which the type of
polyp is malignant and the model has correctly diagnosed the polyp type. The FN index
represents the number of images containing at least one polyp while the CNN model cannot
classify or detect it (or them), or the number of images containing malignant polyps falsely
diagnosed as benign. The TN measure indicates the number of images without any polyps
correctly classified by the CNN model as non-polyp images, or the number of images
containing benign polyps correctly diagnosed as the benign type. Finally, FP represents the
number of images without any polyps falsely classified by the CNN model as having at least
one polyp, or the number of images in which the polyp is benign while the model has falsely
diagnosed it as malignant.
IX. Conclusions
In recent decades, CNN models have accomplished many computer vision tasks like
object detection, image reconstruction, and medical imaging with notable results. In this paper,
I have discussed the applications of CNN in diagnosing colorectal polyps or cancer while
explaining the differences and advantages of CNN over conventional models. knowing the
applications and benefits of the CNN models, as well as their limitations and drawbacks, will
help develop computer-aided diagnosis tools. Such tools can enhance the endoscopists’
performance during colonoscopy, ultimately increasing the colorectal cancer survival rate by
reducing the polyps missing rate.
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