Skin Lesion Classification Using Convolutional Neural Network For Melanoma Recognition

medRxiv preprint doi: https://doi.org/10.1101/2020.11.24.20238246; this version posted November 26, 2020.
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Skin Lesion Classification Using Convolutional

Neural Network for Melanoma Recognition
Aishwariya Dutta1 , Md. Kamrul Hasan2 , and Mohiuddin Ahmad2

1
Department of Biomedical Engineering, Khulna University of Engineering &
Technology, Khulna-9203, Bangladesh.
[email protected]
2
Department of Electrical and Electronic Engineering, Khulna University of
Engineering & Technology, Khulna-9203, Bangladesh.
{m.k.hasan, ahmad}@eee.kuet.ac.bd
Abstract. Skin cancer, also known as melanoma, is generally diagnosed

visually from the dermoscopic images, which is a tedious and time-
consuming task for the dermatologist. Such a visual assessment, via the
naked eye for skin cancers, is a challenging and arduous due to different
artifacts such as low contrast, various noise, presence of hair, fiber, and
air bubbles, etc. This article proposes a robust and automatic framework
for the Skin Lesion Classification (SLC), where we have integrated image
augmentation, Deep Convolutional Neural Network (DCNN), and trans-
fer learning. The proposed framework was trained and tested on publicly
available IEEE International Symposium on Biomedical Imaging (ISBI)-
2017 dataset. The obtained average area under the receiver operating
characteristic curve (AUC), recall, precision, and F1-score are respec-
tively 0.87, 0.73, 0.76, and 0.74 for the SLC. Our experimental studies
for lesion classification demonstrate that the proposed approach can suc-
cessfully distinguish skin cancer with a high degree of accuracy, which
has the capability of skin lesion identification for melanoma recognition.
Keywords: Skin cancer · Image augmentation · Deep convolutional neu-

ral network · Transfer learning · Melanoma recognition.
1 Introduction
Skin cancer is a common type of cancer that originates in the skin’s epidermis
layer by the irregular cells due to ultraviolet radiation exposure [1]. Every fifth
person in the United States (US) has a risk of skin cancer in a region under
strong sunshine [2]. Among all skin cancer types, melanoma is the nineteenth
most frequently cancer, where approximately 3.0 million new cases were iden-
tified in 2018. On average, 2, 490 females and 4, 740 males lost their lives due
to melanoma in 2019 [3] in the US alone. It is estimated that approximately,
in 2020, 1.0 million of newly affected melanoma patients will be diagnosed. An
approximated 6, 850 new case of deaths due to melanoma are anticipated in 2020
in the US alone, which will comprise 4, 610 males and 2, 240 females [4]. Skin
NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice.
medRxiv preprint doi: https://doi.org/10.1101/2020.11.24.20238246; this version posted November 26, 2020. The copyright holder for this
2 A. Dutta et al.
cancer deaths in Bangladesh reached 0.04 % of total deaths in 2017, which is

ranked 182 in the world [5]. However, a precise and robust early recognition
is significant as the survival rate was as high as apparently 90 % in advance
recognition [6]. Several imaging techniques like dermoscopic image, optical co-
herence tomography, magnetic resonance imaging, and confocal scanning laser
microscopy are currently being used to diagnose skin cancer. Those images are
visually inspected by the dermatologists [7], which is often a tedious and time-
consuming process. To relieve the dermatologist’s tediousness by improving the
preciseness in recognition, Computer-aided Diagnosis (CAD) systems are being
used [8]. Currently, CAD is an integral part of the routine health checkup in the
clinic, which consists of raw image acquisition, preprocessing, Region of Interest
(ROI) & feature extraction, and finally, recognition [8, 9]. The final step, also
known as the classification, is a crucial component, which is a challenging task
due to the diverse size of the lesion area, texture, skin color, and the presence
of various artifacts like reflections, hair, rolling lines, air bubbles, non-uniform
vignetting, shadows, and markers [8, 10], which are shown in Fig. 1.
Marker Sign
Hair Dark Corner

LED Illumination
Ruler Marker
Non-uniform Gel
Water Bubble Ink Marks
Vignetting
Fig. 1: An example of the challenging images, in the ISIC dataset [11], for the
accurate SLC.
Nowadays, several methods are being used for the SLC [12, 13]. The sen-
sitivity and specificity of the practitioners are 62 %, and 63 %, while for the
dermatologists are 80 % and 60 % respectively for melanoma recognition [14].
In [15], the authors presented a CAD system for the SLC, where they used
boarder and wavelet-based texture features with the Support Vector Machine
(SVM), Hidden Naı̈ve Bayes (HNB), Logistic Model Tree (LMT), and Random
Forest (RF) classifiers. In [16], the authors proposed a model for the SLC, which
comprises a Self-generating Neural Network (SGNN), a feature (texture, color,
and border) extraction, and an ensembling classifier. A deep residual network
(DRN) was presented in [17] for the SLC, where they demonstrated that DRN’s
have the capability to learn distinctive features than low-level hand-crafted fea-
tures or shallower CNN architecture. CNN architecture, along with the transfer
learning paradigm, was employed for the SLC in [18]. A 3-D skin lesion re-
construction technique was presented in [19], where depth and 3-D shape fea-
Skin Lesion Classification Using CNN for Melanoma Recognition 3
tures were extracted. Besides, they also extracted regular color, texture, and
2-D shape features. Different machine learning classifiers ( SVM and AdaBoost)
were employed to classify those features. In [20], the authors proposed an ef-
fective iterative learning framework for the SLC, where they designed a sample
re-weighting strategy to conserve the effectiveness of accurately annotated hard
samples. The stacking ensemble pipeline based on the meta-learning algorithm
was proposed in [21], where two-hybrid methods were introduced to combine the
mixture classifiers. The effect of dermoscopic image size based on pre-trained
CNNs, along with transfer learning, was analyzed in [22], where they resized
from 224 × 224 to 450 × 450. They proposed a multi-scale multi-CNN fusion
approach using EfficientNetB0, EfficientNetB1, and SeReNeXt-50, where three
networks architectures trained on cropped images of different sizes. An architec-
ture search framework was presented in [23] to recognize the melanoma, where
the hill-climbing search strategy, along with network morphism operations, were
employed to explore the search space.
This study proposes a framework for the SLC (multi-class task), where pre-
processing, geometric augmentation, CNN-based classifiers, and transfer learning
are the integrated steps. We have performed various types of geometric image
augmentations for increasing the training samples as in most of the medical
imaging domains, a massive number of manually annotated training images are
not yet available [24]. A CNN-based classifier has been used to avoid the tedious
feature engineering, which can learn features automatically during the forward-
backward pass of training images. Transfer learning of CNN is used to initialize
all the kernels in convolutional layers by leveraging the previously trained knowl-
edge rather than random initialization. Extensive experiments are conducted to
select different hyper-parameters like types of image augmentation, optimizer &
loss function, and metric to be maximized for training, the number of layers of
CNN to be frozen. We validate our proposed framework by comparing it with
several state-of-the-art methods on the ISBI-2017, where our proposed pipeline
achieved better results while being an end-to-end system for the SLC.
The remainder of this paper is set out as follows. Section 2 describes the
materials and the proposed framework. Section 3 presents detail results with
a proper illustration. Finally, the paper is concluded in section 4 with future
works.
2 Materials and Methods
The details description of the materials and the methods used in this literature
are represented as follows in several subsections:
2.1 Dataset and Hardware
The utilized dataset, for training, validation, and testing, is presented in Table 1,
where we use the ISIC-2017 dataset from the ISIC archive [11]. Table 1 presents
the class-wise distributions and a short description of the ISIC-2017 dataset. The
4 A. Dutta et al.
Table 1: Data distribution of the ISIC-2017 dataset.

SL # Class Types Description Train Validation Test
01 Melanoma (Mel) Malignant skin tumor obtained from melanocytic 374 30 117
02 Seborrheic Keratosis (SK) Benign skin tumor obtained from keratinocytes 254 42 90
03 Nevus (Nev) Benign skin tumor obtained from melanocytic 1372 78 393
Total Images 2000 150 600
proposed framework was implemented with the python programming language

with various python and keras APIs. The experiments were conducted on a
Windows-10 machine with the following hardware configuration: Intel® CoreTM
i7-7700 HQ CPU @ 2.80 GHz processor with Install memory (RAM): 16.0 GB
and GeForce GTX 1060 GPU with 6 GB GDDR5 memory.
2.2 Proposed Framework
In the proposed framework, as shown in Fig. 2, the feature extraction and classi-
fication of the skin lesion for melanoma recognition have been automated using
an end-to-end CNN architecture, where the image augmentation and normal-
ization are the crucial and integral parts of the proposed framework. The deep
Fig. 2: Block diagram of the proposed framework for an automatic SLC towards
melanoma recognition using CNN-based classifiers, preprocessing, and transfer
learning.
CNNs are widely used in both medical and natural image classification, which has
achieved tremendous success since 2012 [25]. It often rivals human expertise [26].
In CheXNet [27], a CNN was trained on more than 1.0 million frontal-view of
the chest X-rays, where it was able to achieve better recognition results than the
average recognition by the four experts.
However, in this article, the CNN model is shown in Fig. 3, which has 13
convolutional layers in the 5 convolutional blocks. Each block ends up with a
Mel
SK
Nev
HOut ϵ𝑅3
H3 ϵ𝑅64
H2 ϵ𝑅128
H1 ϵ𝑅256
Fig. 3: The CNN network for the SLC, where Hm ∈ Rn is the mth hidden layer
in n-dimensional space. The output layer, HOut lies in 3-dimensional (Mel, SK,
and Nev) space.
max-pooling layer to lower the computational complexity by reducing the num-

ber of connections between convolutional layers, accelerating the CNN models
to be generalized by reducing the overfitting. The convolutional layers’ output is
fed to the Fully Connected (FC) layers, where we use 3-FC layers and 1-output
layer (3 neurons for Mel, SK, and Nev classes). Global average pooling (GAP)
was used between convolutional layers and FC layers in place of the traditional
flatten layer due to state-of-the-art performance for the image classification [28].
In GAP, only one feature map is generated for each corresponding category,
which has an extreme dimensionality reduction to avoid overfitting. In GAP,
height × weight × depth dimensional tensor reduced to 1 × 1 × depth, where
each height × width feature map transfers to a single number by averaging the
height.width values. Additionally, GAP also provides a lightweight SLC network,
which makes it suitable for the real-time SLC-CAD systems for the dermatol-
ogists. However, for the fine-tuning the convolutional layers, different layers of
feature extractor were frozen to select the optimum number layers to be frozen
by maximizing the AUC for the SLC.
The scarcity of the training images, especially where the annotation is ardu-
ous and costly, can be overcome using a transfer learning [29]. The kernels of the
feature extractor (2-D convolutional layers), as shown in Fig. 3, were initialized
using the previously trained weights from the ImageNet [30]. The kernels in FC
layers were initialized using a glorot uniform distribution [31]. Glorot distribu-
tion, also called
p Xavier distribution, is centered on the mean of 0 with a standard
deviation of (2/(Fin + Fout )), where Fin and Fout are the number of input and
output units respectively in the weight tensor. Different image augmentation
was employed to improve the proposed framework’s generalization ability to the
unseen test data, which also makes sure validation error continues to decrease
with the training error. Random rotation (0 ∼ 90◦ ), width shift (10 %), height
shift (10 %), random shearing (20 %), zooming (20 %), and horizontal & vertical
6 A. Dutta et al.
flipping were used as an image augmentation, in the proposed pipeline, where

the outer pixels were filled using a reflection method. The images were also trans-
ferred to [0 1] before feeding them into the CNN network. As we saw from the
Aspect Ratio (AR) distribution of the ISIC-2017 images, AR lies in 3 : 4. So, we
resized the input images to 192 × 256 pixels using the nearest-neighbor interpo-
lation technique [8]. Categorical cross-entropy was the loss function, which was
optimized to maximize the average accuracy of lesion classification in our frame-
work. The loss function was optimized using the Adam [32] optimizer with initial
Learning Rate (LR), exponential decay rates (β 1 , β 2 ) as LR = 0.0001, β 1 = 0.9,
and β 2 = 0.999 respectively without AMSGrad variant. The initial learning rate
was reduced after 5 epochs by 20.0 % if validation loss stops improving. The pro-
posed pipeline was trained in a machine, as mentioned in subsection 2.1, with a
batch size of 8.0.
2.3 Evaluation Criterion

The proposed pipeline was evaluated using the confusion matrix of True Positive
(TP), False Positive (FP), False Negative (FN), and True Negative (TN). The
recall, precision, and F1-score were also used, where the recall quantifies the
type-II error (the sample with target syndromes, but wrongly fails to be refused)
and the precision measure the percentage of correctly classified positive patients
from all positive recognition. The F1-score indicates the harmonic mean of recall
and precision, which shows the tradeoff between them. Additionally, how well
lesion prediction is ranked rather than their absolute value is measured using
the AUC.
3 Results and Discussion

In this section, the results on the ISIC-2017 test dataset (see in Table 1) for
the SLC are presented. At the end of this section, state-of-the-art methods are
compared against the proposed framework on the same dataset.
A classification report, to visualize the precision, recall, F1-score, and support
scores per-class basis, is shown in Table 2. A classification report is a deeper
Table 2: Classification report for the SLC, where the weights of the classes were
calculated from the supported samples for averaging the metrics.
Class Precision Recall F1-score Support
Mel 0.53 0.62 0.57 117
Nev 0.87 0.76 0.81 393
SK 0.55 0.73 0.63 90
Weighted Average 0.76 0.73 0.74 600
intuition for the quantitative evaluation of the classifier, which can also show
the weaknesses in a particular class of a multi-class problem. The results, as

shown in Table 2, show that the correctly classifying samples of Mel, Nev, and
SK are 62.0 %, 76.0 %, and 73.0 % respectively, while the respective type-II error
(false-negative rate) is 38.0 %, 24.0 %, and 27.0 %. The support-weighted recall,
73.0 % indicates that 27.0 % samples having target symptoms, but erroneously
fails to be rejected by the proposed framework. The support-weighted precision,
76.0 % indicates that only 24.0 % samples are wrongly classified among all the
recognized true classes. The F1-score reveals that both the precision and recall
are better from the proposed framework for the SLC of the ISIC-2017, although
the uneven class distribution was being used for training. The more details the
class-wise investigation, of the proposed SLC, has been present in the confusion
matrix in Table 3. The confusion matrix, as shown in the Table 3, presents the
Table 3: Confusion matrix of the test results, where each column and row rep-
resent the instances in a predicted and actual class respectively.
Predicted
Mel Nev SK
Mel 72 28 17
Actual Nev 57 300 36
SK 8 16 66
number of correct and incorrect predictions by the proposed framework with

a count value. Table 3 shows that among 117, 393, and 92 samples of Mel,
Nev, and SK classes are classified as (72, 28, and 17), (57, 300, and 36), and
(8, 16, and 66) respectively to Mel, Nev, and SK. Among 117 samples of the
Mel classified as the Nev, which is undesirable FN. Table 1 shows that a more
number of samples are in the Nev class in the training dataset, which makes the
biased classifier towards Nev. The results, as shown in Table 3, also depicts that
a significant number of the Mel and SK samples are predicted as Nev. Some of
the miss-classified images by the proposed pipeline is shown in Table 4, where
we show the difficulties for the correct classifications. From Table 4, it is seen
that images (first two rows) having a true class of Mel are classified as SK and
Nev with respective confidence probability of 0.934 and 0.88. Similarly, all other
images in Table 4 are wrongly classified with a degree of confidence probability.
If we visually inspect those images, it seems those images, especially in the fifth
row, seem like a Mel as the texture of the lesion area is more complex. However,
the dermatologist tells that it is Nev. The probable reason behind such a wrong
classification by the proposed framework is the lack of diversity in the training
samples, inter-class diversity, and intra-class similarity.
The ROC and precision-recall curves are shown in Fig. 4 (a) and Fig. 4 (b),
respectively. It is observed from Fig. 4 (a) that for a 10.0 % false-positive rate,
the true-positive rates for the SLC is approximately 62.0 %. The corresponding
macro-average AUC from the ROC curve is 0.873, which indicates that for any
8 A. Dutta et al.
Table 4: Several examples of wrongly classified images, from the proposed frame-
work, with confidence probability.
Example Images Predicted Class with Confidence
Actual Class: Mel

Predicted Class: SK
Confidence Probability: 0.934
Actual Class: Mel

Predicted Class: Nev
Actual Class: SK
Predicted Class: Nev
Actual Class: SK
Predicted Class: Mel
Actual Class: Nev

Predicted Class: Mel
Actual Class: Nev

Predicted Class: SK
given random sample, the probability of accurate recognition as Mel, Nev, and
SK is as high as 87.3 %. The precision-recall curve, as shown in Fig. 4 (b), shows
the tradeoff between precision and recall for different thresholds, where the high
area under the curve represents both high recall and precision. High scores for
both show that the proposed pipeline is a blessing with the accurate results
as well as returning a majority of all positive results (high recall). The macro-
average precision from the proposed pipeline is 80.6 %, which indicates that the
proposed pipeline is well-suited for the SLC for melanoma recognition.
Table 5 shows the state-of-the-art comparison of our proposed pipeline with
recent works, where AlexNet [33] and ResNet-101 [34] were implemented in [35]
for the SLC. The proposed framework produces the best classification of the skin
lesion, as shown in Table 5. Our pipeline produces the best results concerning
1.0
0.9
0.8
True Positive Rate

0.7
0.6
0.5
0.4
0.3
0.2 Macro-avg ROC with AUC = 0.873
0.1 Random Classifier with AUC = 0.5
0.0
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
False Positive Rate
(a)
1.0
0.9
0.8
0.7
Precision
0.6
0.5
0.4
0.3
0.2
0.1
0.0
0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
Recall
(b)
Fig. 4: (a) ROC curve to summarize the trade-off between the true-positive rate
and false-positive rate, and (b) Precision-recall curve to summarize the trade-off
between the true-positive rate and the positive predictive value.
the recall and precision beating the state-of-the-art works in [36] by a 12.0 %
margin, and in [34] by a 5.0 % respectively. Our method beats method in [34] by
the margin of 39.0 %, and 5.0 % in terms of the recall and precision respectively,
although the AUC is same in both the methods.
4 Conclusion
In this article, an automatic and robust framework for melanoma recognition has
been proposed and implemented. The potentiality of the proposed framework
has been validated via several comprehensive experiments. The scarcity of using
10 A. Dutta et al.
Table 5: The state-of-the-art comparison with proposed framework, which were

trained, validated, and tested on the ISIC-2017 dataset.
Authors Year Recall Precision F1-Score AUC
AlexNet [33] 2018 0.34 0.65 - 0.86
ResNet-101 [34] 2018 0.34 0.71 - 0.87
Method-1∗ [36] 2018 0.61 - - 0.84
Method-2† [37] 2018 0.57 0.68 - 0.85
GR‡ [38] 2019 - - - 0.78
Our Proposed 2020 0.73 0.76 0.73 0.87
*ResNet50 + RAPooling + RankOpt [36]
†ResNet50 + Eigen Decomposition + SVM [37]
‡Gabor Wavelet-based CNN [38]
fewer manually annotated dermoscopic images to build a generic framework

was overcome by employing a transfer learning, previously trained weights, and
geometric augmentation. Additional tuning the hyper-parameters and the more
related augmentations may yield better recognition results for the SLC. The
proposed framework will be tested on other different datasets of dermoscopic
images for the SLC in the future. The proposed pipeline will be employed in
other domains for recognition to verify the adaptability and generality.
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Skin Lesion Classification Using Convolutional Neural Network For Melanoma Recognition

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medRxiv preprint doi: https://doi.org/10.1101/2020.11.24.20238246; this version posted November 26, 2020.

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