SelvarasaM w1654542 2016131 AutoSkreenr Automated Skin Cancer Screening Using Optimized CNN

Informatics Institute of Technology
In Collaboration With
University of Westminster, UK
AUTOSKREENR
AUTOMATED SKIN CANCER SCREENING USING
OPTIMIZED CNN
A dissertation by
Mr. Minoj Selvarasa
Supervised by
Mr. Achala Chathuranga Aponso
Submitted in partial fulfillment of the requirements for the

BSc (Hons) Computer Science
Department of Computing.
W1654542 | 2016131
May 2020
© The copyright for this project and all its associated products resides with Informatics Institute of
Technology
AutoSkreenr – Automated Skin Cancer Screening using Optimized CNN
Declaration
I hereby certify that this project report and all the artefacts associated with it is my own
work and it has not been submitted before nor is currently being submitted for any degree
programme.
Full Name of the Student: Minoj Selvarasa
IIT Registration ID: 2016131
UoW Registration ID: w1654542
Signature:……………………. Date:…………………….
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Abstract
Cancer is one the deadliest diseases known to mankind and skin cancer is a common form
of cancer that mainly occurs in people with lighter skin due to lack of melanin
pigmentation. It is less fatal in its benign form but deadly if malignant. Survival rate for a
malignant skin cancer is high if diagnosed at an early stage but significantly drops when
diagnosed at a later stage. Statistics show that the number of skin cancer cases are on the
rise in many western countries while the number of experienced dermatologists have stayed
constant resulting in a shortage.
Due to this, there is an increased need an automated skin cancer screening tool that can aid
a dermatologist in the screening process. In this project, the various aspects involved in
building an automated tool for skin cancer screening is well researched. Segmentation
model was built to improvise the segmentation accuracy on the ISIC 2018 dataset by using
the newer SOTA architecture, EfficientNet. Experiments were carried out to identify how
preprocessing and segmentation affects the prediction capabilities of the classification
model. Two experiments were carried out where one experiment involved the use of
preprocessed and segmented images while the other experiment involved the use of non-
preprocessed images. The classifier was optimized via the use of bio-inspired optimization
algorithms. COA and GA were compared for this purpose where the results showed that
GA tends to perform well. The proposed GA has a new variation called population variance
which intended to improve the diversity of the solutions produced by the algorithm. The
VGG-16 architecture was optimized using the GA algorithm and trained on both the sets
of data to identify the better approach. Segmentation model shows promising results while
further research needs to be conducted to investigate the classification model.
Finally, a web application was built for dermatologists to upload dermoscopic images and
get predictions on and also receive a visual reasoning for the prediction made.
Keywords
Deep Learning, CNN, Hyperparameter Tuning, Genetic Algorithm, Coyote Optimization

Algorithm, Segmentation, Augmentation.
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Acknowledgement
To do a good research, it requires a lot of effort and will. Researchers are challenging and
therefore, a lot of challenges need to be faced with confidence. And that confidence, not
only comes from within but also from around us. I owe a great many thanks to a great
number of people who helped me and put up with me throughout this project. It would not
have been possible to complete this research without their support and guidance.
I thank Mr. Achala Chathuranga Aponso for providing me with all the guidance I needed
throughout the research to make this project a success. Without his guidance, advice and
support this project would not have been possible.
I would like to extend my gratitude to the management of Informatics Institute of

Technology, my lecturers, colleagues, and friends at Informatics Institute of Technology
for supporting me in numerous ways to successfully complete this research. I would also
like to extend my sincere gratitude to my parents and sisters for pushing me towards the
targets of my life.
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Publication
A Critical Analysis of Computer Aided Approaches for Skin Cancer Screening
Conference: International Conference on Image Processing and Robotics, 2020
Venue: Negombo, Sri Lanka
Publication: IEEE Xplore
Content: A review on the steps involved in building an automated skin cancer screening
tool and existing approaches that have been explored.
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Table of Content
Declaration .......................................................................................................................... 2
Abstract ............................................................................................................................... 3
Acknowledgement .............................................................................................................. 4
Publication .......................................................................................................................... 5
Table of Content ................................................................................................................. 6
List of Figures ................................................................................................................... 12
List of Tables .................................................................................................................... 13
List of Abbreviations ........................................................................................................ 14
1. Chapter 1: Introduction ............................................................................................. 15
1.1. Chapter Overview .............................................................................................. 15
1.1. Background ........................................................................................................ 15
1.2. Problem Statement ............................................................................................. 17
1.3. Research Question .............................................................................................. 18
1.4. Research Aim ..................................................................................................... 19
1.5. Research Motivation .......................................................................................... 19
1.6. Research Objectives ........................................................................................... 19
1.7. Related Work...................................................................................................... 20
1.8. Project Scope ...................................................................................................... 21
1.9. Rich Picture ........................................................................................................ 22
1.10. Resource Requirements .................................................................................. 23
1.10.1. Software Requirements ........................................................................... 23
1.10.2. Hardware Requirements .......................................................................... 23
1.10.3. Data Requirements .................................................................................. 23
1.11. Chapter Summary ........................................................................................... 23
Chapter 2: Literature Review ............................................................................................ 24
2.1. Chapter Overview .................................................................................................. 24
2.2. Conceptual Graph .................................................................................................. 24
2.3. Domain Justification .............................................................................................. 24
2.4. Literature Review of the Domain .......................................................................... 25
2.4.1. Skin Cancer Screening Techniques ................................................................ 25
2.4.2. Computer Aided Skin Cancer Screening ........................................................ 27
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2.4.3. Machine Learning in Skin Cancer Screening ................................................. 28

2.4.4. Deep Learning in Skin Cancer Screening ....................................................... 29
2.4.5. Preprocessing of Skin Cancer Images............................................................. 34
2.4.6. Segmentation of Skin Cancer Images ............................................................. 35
2.5. Algorithmic Analysis ............................................................................................. 39
2.5.1. Image Segmentation........................................................................................ 39
2.5.2. Feature Extraction ........................................................................................... 41
2.5.4. Image Classification........................................................................................ 42
2.5.5. Hyperparameter Optimization ........................................................................ 45
2.6. Chapter Summary .................................................................................................. 46
Chapter 3: Methodology ................................................................................................... 47
3.2. Research Paradigm................................................................................................. 47
3.2.1. Positivist Paradigm ......................................................................................... 47
3.2.2. Interpretivism Paradigm.................................................................................. 47
3.3. Research Approach ................................................................................................ 47
3.3.1. Top-Down ....................................................................................................... 47
3.3.2. Bottom-Up ...................................................................................................... 48
3.4. Design Methodology .............................................................................................. 48
3.5. Software Development Methodology .................................................................... 48
3.6. Chapter Summary .................................................................................................. 48
Chapter 4: Project Management........................................................................................ 49
4.2. Time Management ................................................................................................. 49
4.3. Work Breakdown Structure ................................................................................... 49
4.4. Gantt Chart ............................................................................................................. 49
4.5. Risk Assessment and Mitigation Plans .................................................................. 49
4.6. Compliance with BCS Code of Conduct ............................................................... 50
4.7. SLEP Analysis ....................................................................................................... 51
4.8. Chapter Summary .................................................................................................. 51
Chapter 5: Software Requirement Specification............................................................... 52
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5.2. Stakeholder Analysis ............................................................................................. 52

5.3. Requirements Elicitation Methodologies ............................................................... 54
5.3.1. Observing Existing Systems ........................................................................... 54
5.3.2. Questionnaire .................................................................................................. 54
5.3.3. Brainstorming ................................................................................................. 55
5.3.4. Literature Review............................................................................................ 55
5.4. Questionnaire Findings .......................................................................................... 56
5.5. Functional & Non-Functional Requirements ......................................................... 58
5.5.1. Functional Requirements ................................................................................ 58
5.5.2. Non-Functional Requirements ........................................................................ 59
5.5. Use Case Diagrams ................................................................................................ 61
Chapter 6: Design ............................................................................................................. 63
6.2. Design Goals .......................................................................................................... 63
6.2. High Level System Architecture ............................................................................ 63
6.3. Class Diagram ........................................................................................................ 64
6.4. Sequence Diagram ................................................................................................. 66
6.5. Activity Diagram ................................................................................................... 67
6.6. Flowcharts .............................................................................................................. 68
6.6.1. Genetic Algorithm .......................................................................................... 68
6.6.2. Coyote Optimization Algorithm (COA) ......................................................... 69
6.7. E.R. Diagram ....................................................................................................... 70
6.8. Chapter Summary ................................................................................................. 70
Chapter 7: Implementation ............................................................................................... 71
7.2. Selection of Tools .................................................................................................. 71
7.2.1. Libraries .......................................................................................................... 71
7.2.2. Dataset............................................................................................................. 71
7.3. Optimization Algorithm ......................................................................................... 72
7.3.1. Hyperparameters Optimized ........................................................................... 72
7.3.3. Fitness Evaluation ........................................................................................... 73
7.3.4. Genetic Algorithm (GA) ................................................................................. 73
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7.3.5. Coyote Optimization Algorithm (COA) ......................................................... 75

7.3. Model Building ...................................................................................................... 77
7.3.1. Preprocessing .................................................................................................. 77
7.3.2. Augmentation .................................................................................................. 78
7.3.3. Semantic Segmentation ................................................................................... 79
7.3.4. Classification................................................................................................... 83
7.4. Web Application .................................................................................................... 85
7.4.1. Add New Patient ............................................................................................. 85
7.4.2. View Patient .................................................................................................... 86
7.4.3. Obtain Prediction ............................................................................................ 86
7.4.4. Validate Prediction.......................................................................................... 86
7.5. Chapter Summary .................................................................................................. 86
Chapter 8. Testing ............................................................................................................. 87
8.2. Objectives & Goals ................................................................................................ 87
8.3. Testing Criteria ...................................................................................................... 87
8.3.1. Black Box Testing........................................................................................... 88
8.3.2. White Box Testing .......................................................................................... 89
8.3.3. Integration Testing .......................................................................................... 91
8.4. Non-Functional Requirement Testing.................................................................... 92
8.4.1. Segmentation................................................................................................... 92
8.4.2. Classification................................................................................................... 93
8.5. Benchmarking ........................................................................................................ 95
8.5.1. Segmentation................................................................................................... 95
8.5.2. Classification................................................................................................... 95
8.6. Chapter Conclusion ................................................................................................ 96
Chapter 9. Evaluation........................................................................................................ 97
9.2. Evaluation Criteria ................................................................................................. 97
9.3. Selection of Evaluators .......................................................................................... 98
9.4. Evaluation Methodology and Approach ................................................................ 98
9.5. Evaluation of Survey Findings............................................................................... 98
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9.5.1. Overall Concept and Project Idea ................................................................... 98

9.5.2. Scope and Depth of the Project ....................................................................... 99
9.5.3. System Design and Architecture ................................................................... 100
9.5.4. Accuracy of the Implementation ................................................................... 100
9.5.5. Further Enhancements & Feedback .............................................................. 101
9.5.6. Usefulness of the Visual Reasoning ............................................................. 102
9.5.7. Usability of the GUI...................................................................................... 102
9.5.8. Usability of the tool in the Screening Process and Opinion on the system .. 103
9.6 Self Evaluation ...................................................................................................... 103
9.7. Completion Status of Functional Requirements .................................................. 105
9.8. Chapter Summary ................................................................................................ 105
Chapter 10. Conclusion ................................................................................................... 106
10.1. Chapter Overview .............................................................................................. 106
10.2. Achievement of Aims and Objectives ............................................................... 106
10.2.1. Aim of this Project ...................................................................................... 106
10.2.2. Completion of Objectives ........................................................................... 106
10.3. Utilization of Knowledge from Course Modules............................................... 107
10.4. Use of Existing Skills......................................................................................... 108
10.5. Learning Outcomes ............................................................................................ 108
10.6. Problems and Challenges Faced ........................................................................ 109
10.7. Research Contribution ....................................................................................... 110
10.8. Limitations ......................................................................................................... 110
10.9. Future Enhancements ......................................................................................... 111
10.10 Concluding Remarks ......................................................................................... 111
References ....................................................................................................................... 112
Appendices ...................................................................................................................... 121
Appendix A – Conceptual Graph ................................................................................ 121
Appendix B – Time Management ............................................................................... 122
Appendix C – Work Breakdown Structure ................................................................. 123
Appendix D – Gantt Chart .......................................................................................... 124
Appendix E – Onion Diagram .................................................................................... 125
Appendix F – SRS Questionnaire ............................................................................... 126
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Appendix G – Use Case - Process Image ................................................................... 127

Appendix H – Sequence Diagram............................................................................... 128
Appendix I – GA Hyperparameter Encoding ............................................................. 129
Appendix J – COA Hyperparameter Encoding .......................................................... 129
Appendix K – Prediction Function Web App ............................................................. 130
Appendix L – Metric Definitions................................................................................ 131
Appendix M – Evaluation Forms ................................................................................ 132
Domain Evaluator ................................................................................................... 132
Technical Evaluator ................................................................................................ 133
Appendix N – Evaluation Emails ............................................................................... 134
Appendix O – Published Review Paper ...................................................................... 136
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List of Figures
Figure 1 Rich Picture ........................................................................................................ 22
Figure 2 High level use case diagram. .............................................................................. 61
Figure 3 High Level Architecture diagram of the proposed system. ................................ 64
Figure 4 Class Diagram for the proposed solution. .......................................................... 65
Figure 5 Sequence Diagram for Classify Image Use Case ............................................... 66
Figure 6 Activity diagram of the proposed system. .......................................................... 67
Figure 7 Vanilla Genetic Algorithm ................................................................................. 68
Figure 8 Coyote Optimization Algorithm ......................................................................... 69
Figure 9 ER Diagram for the Web Application Database ................................................ 70
Figure 10 Convolution Dense Block Representation........................................................ 73
Figure 11 Single-Point Crossover ..................................................................................... 74
Figure 12 Original Image of Skin Lesion ......................................................................... 78
Figure 13 Contrast Enhancement of Image ...................................................................... 78
Figure 14 Original Image - Not Preprocessed .................................................................. 78
Figure 15 Preprocessed Image - Post Artifact Removal ................................................... 78
Figure 16 Preprocessing of a Single Image Function ....................................................... 79
Figure 17 UNet Architecture described ............................................................................ 80
Figure 18 Hyperparameters of the UNet - EfficientNetB3 Model ................................... 81
Figure 19 UNet Model Define with EfficientNetB3 Feature Extractor ............................ 81
Figure 20 UNet Model Compile with Optimizer, Loss Function and Metrics ................. 81
Figure 21 UNet Model Training with Callback to save weights if any improvement ...... 81
Figure 22 Semantic Segmentation Results – ISIC 2019 ................................................... 82
Figure 23 Enhance the Mask and Apply on original image.............................................. 82
Figure 24 Preprocessed Image – ISIC 2019 ..................................................................... 83
Figure 25 Generated Mask – ISIC 2019 ........................................................................... 83
Figure 26 Mask applied on preprocessed image. .............................................................. 83
Figure 27 Visual Reasoning – ISIC 2019 ......................................................................... 83
Figure 28 Statistical test results for the Segmentation Model. ......................................... 93
Figure 29 Segmentation model result on an image from ISIC 2018 Dataset. .................. 93
Figure 30 Segmentation model result on an image from ISIC 2019 Dataset. .................. 93
Figure 31 Statistical test results for Classification Model. ............................................... 93
Figure 32 Model Accuracy - Train vs Validation ............................................................. 94
Figure 33 Model Loss - Train vs Validation ..................................................................... 94
Figure 34 Model F1-Score - Train vs Validation.............................................................. 94
Figure 35 Model Recall - Train vs Validation .................................................................. 94
Figure 36 Model Evaluation - Train Data ......................................................................... 94
Figure 37 Model Evaluation - Test Data........................................................................... 94
Figure 38 Evalaution Criteria to evalaute the project. ...................................................... 97
Figure 39 Self Evaluation of the Project ......................................................................... 105
Figure 40 Completion Status of the Functional Requirements of the Project ................ 105
Figure 41 Utilizing knowledge from the degree. ............................................................ 108
Figure 42 The equation to calculate Intersection Over Union ........................................ 131
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List of Tables
Table 1 In Scope and Out of Scope .................................................................................. 22
Table 2 Software Requirements of Project. ...................................................................... 23
Table 3 Hardware Requirements of Project. ..................................................................... 23
Table 4 Summary of findings based on existing work – Image Classification. ............... 33
Table 5 Summary of findings based on existing work - Image Segmentation. ................ 38
Table 6 Risk assessment and Mitigation ........................................................................... 49
Table 7 Compliance with BCS Code of Conduct. ............................................................ 50
Table 8 SLEP Analysis ..................................................................................................... 51
Table 9 Stakeholders, their roles and how they benefit from the proposed tool. ............. 53
Table 10 Analysis of requirements elicitation by Observing existing systems. ............... 54
Table 11 Analysis of requirements elicitation by distributing Questionnaires. ................ 54
Table 12 Analysis of requirements elicitation by Brainstorming. .................................... 55
Table 13 Analysis of requirements elicitation by Literature review. ................................ 55
Table 14 Findings of the Interviews. ................................................................................ 58
Table 15 Functional Requirements of the Proposed System and Algorithm. ................... 59
Table 16 Non-Functional Requirements of the Proposed System and Algorithm............ 60
Table 17 Use case for description for Classify Image. ..................................................... 62
Table 18 Design Goal intended to achieve via this research. ........................................... 63
Table 19 ISIC 2018 and 2019 Dataset Description .......................................................... 72
Table 20 Hyperparameters to Tune the Architecture. ....................................................... 73
Table 21 Parameters that manipulated the Genetic Algorithm optimization. ................... 75
Table 22 Results of carrying on the hyperparameter tuning on the MNIST dataset. ....... 75
Table 23 Parameters that manipulated the Coyote Optimization Algorithm. ................... 76
Table 24 Results of carrying on the hyperparameter tuning on the MNIST dataset. ....... 76
Table 25 Summary of steps involved in Experiment 1 and 2. .......................................... 83
Table 26 Performance of all the models tried out. ............................................................ 84
Table 27 Hyperparameters optimized and the search space. ............................................ 84
Table 28 Parameters and Values of Genetic Algorithm ................................................... 85
Table 29 Values obtain for parameters upon hyperparameter tuning completion. ........... 85
Table 30 Web App code to add a new patient to the database. ........................................ 85
Table 31 Web App code to view a single patient with all the predictions........................ 86
Table 32 Web App code to validate a prediction made via the application. .................... 86
Table 33 Black Box Test Cases, Expected and Actual Outputs and the status of each test
case. ................................................................................................................................... 89
Table 34 White Box Test Cases, Expected and Actual Outputs and the status of each test
case. ................................................................................................................................... 91
Table 35 Feedback on the overall concept and project idea. ............................................ 99
Table 36 Objectives Completeness ................................................................................. 107
13
List of Abbreviations
Abbreviation Definition
USA United State of America
UV Ultra-Violet
ANN Artificial Neural Network
CNN Convolutional Neural Network
GA Genetic Algorithm
COA Coyote Optimization Algorithm
PSO Particle Swarm Optimization
TL Transfer Learning
WHO World Health Organization
SOTA State of the Art
ABCD Asymmetry, Border, Color and Diameter
ROI Region of Interest
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1. Chapter 1: Introduction
1.1. Chapter Overview
The introduction chapter provides an overview of the project been undertaken. The project
background and the problem background are both defined. The importance of the project
is addressed along with the research challenges. Related work is discussed before the
research challenges are discussed. The objectives that needs to be achieved to successfully
complete the project are defined. The project scope will also be defined. Finally, the
resource requirements will be discussed.
1.1. Background
Cancer is a disease that does not have any known cure and considered to be one of the
deadliest diseases in the world. One of the common forms of cancer is Skin Cancer. People
with ligher skin, those exposed to UV for prolonged period and people with higher count
of moles on skin are known to be at higher risk of skin cancer. This is due to the lack of
melanin pigmentation on their skin. Melanin is known to protect the skin from UV light,
which is a direct cause for skin cancer (Oliveira et al., 2016), (Reliant Medical Group,
2019). Not all cancers of the skin are harmful. Skin cancer can be either benign or
malignant where benign skin lesions are less or not harmful whereas malignant skin lesions
are cancerous and therefore harmful. Melanoma of the skin is the most common form of
malignant skin cancer according to the AAD but is less common when compared to benign
skin lesions (American Association of Dermatology, 2019). Although benign skin lesions
are not harmful, they do come with cosmetical disadvantages to the patient. In the USA,
the deadliest form of skin cancer is the Melanoma of the skin and has a high mortality rate
of 1.62% (American Cancer Society, 2020). The survival rate for a patient with malignant
skin cancer is high when diagnosed at early stages but drops significantly to as low as 23%
as time passes (The Skin Cancer Foundation, 2020). One of the common causes for skin
cancer is the exposure to UV rays for prolong period of time (Penta, Somashekar and
Meeran, 2017). Most cases of malignant skin cancer can be cured by surgical excision if
detected at an early stage (Herath et al., 2018). Benign skin lesions can be surgically
removed if required as well. Benign skin lesions account for the vast majority of the skin
lesion cases that are reported and only a small portion of the reported cases are cancerous,
15
melanoma. Therefore, distinguishing between the benign skin cancer and melanoma is very
important. Cases of skin cancer have seen a sharp rise since the 1970s, especially in the
UK. Cases related to malignant melanoma has increased by 50% in the last decade in the
UK (Robertson and Fitzgerald, 2017). In Brazil, skin cancer accounts for upto 30% of all
the reported malignancies (Minango et al., 2019). According to WHO, globally the number
of reported skin cancer cases are on the rise for the past few decades (WHO, 2020).
A person suspected to have a benign or malignant skin lesion undergoes a screening

process where the suspicious part of the skin is visually inspected by dermatologists. The
visual inspection alone is not used to make a diagnosis. The visual inspection process can
be carried out with and without an aid. Distinguishing between healthy tissues and skin
lesions via unaided visual inspection is not always accurate (Al-masni et al., 2018). The
accuracy of unaided visual inspection of skin lesions is only about 60% (Kittler et al.,
2002). Sch a low accuracy is not acceptable as it is important to not make any false
diagnosis. Therefore, tools to aid a dermatologist in the screening of skin lesion have been
introduced. Some of these tools are used together with other tools as they complement each
other. One such tool that is common and popular is the dermoscopy. Dermoscopy is a non-
invasive technique that is used for visual inspection of skin lesions. This imaging tool
acquires a magnified image of the skin lesion and helps to visualize the deeper details of
the skin structure (Kittler et al., 2002), (Al-masni et al., 2018). It has a higher accuracy than
manual visual inspection but is still very complex, time intensive and error prone (Al-masni
et al., 2018). The accuracy of inspection of dermoscopic images also depends on
experience (Rubegni et al., 2002). Clinicians have failed to adopt the algorithms that were
developed to improve scalability in favor of experience (Carli et al., 2003), (Gachon et al.,
2005). A rising shortage in the number of experienced dermatologists in the USA over the
past years can be observed (Codella et al., 2018), (Glazer, Rigel, Winkelmann and Farberg,
2017). A study carried out in medical schools and residency programs in the USA show
that 75.8% of doctors were never trained and 55.3% had never observed a skin cancer
screening examination (Herath et al., 2018). Providing appropriate training has shown to
improve the diagnostic accuracy (Mikkilineni et al., 2001). A study was performed by
Herath et al. in Sri Lanka to identify the knowledge and skills of doctors. It was identified
that only 10 out of the 123 respondents had received formal training to perform total body
16
examination and that the majority of the doctors have never performed a total body
examination in their career (Herath et al., 2018). All these indicate the need for an
automated approach for the skin lesion screening due to the lack of experts in the domain
(Codella et al., 2018), (Mishra and Celebi, 2016).
The advent of large datasets and more computational power, a surge in computer vision
research is being experienced. Deep Learning, a technique commonly used to solve
computer vision problems, shows breakthrough performance in several areas (Hongtao and
Qinchuan, 2019). CNNs, a variation of Neural Networks, is a Deep Learning algorithm
used to solve computer vision problems and considered to be the SOTA. They are known
to have surpassed human experts in several benchmarking tests (Sermanet and LeCun,
2011). Manual architecture/network design (Sermanet and LeCun, 2011), (Liu et al., 2019),
using existing architectures (Minango et al., 2019), and using Transfer Learning (Shin et
al., 2016). Transfer Learning is a technique where a pretrained network, usually trained on
a larger generalized dataset, is retrained on a more specific dataset. Although popular
architectures such as ResNet, VGGNet have emerged, they have their own defects and it
takes time to fix them (Weng et al., 2019). Tuning approaches have shown to improve the
accuracy as it allows to find the optimal network architecture for the dataset. The tuning
approach uses a search strategy to tune networks. Commonly used approaches are heuristic
search and RL (Liu et al., 2019).
1.2. Problem Statement

Studies show that the number of well experienced dermatologists are in shortage while the
number of reported skin cancer related cases are on the rise. This calls for an automated
tool that can aid dermatologists to carry out screening much faster. Such a tool can be used
by less experienced dermatologists as well. The use of clinical algorithms such as 7-point
checklist, ABCD are some of the commonly used algorithms that utilize clinical features.
These algorithms help extract clinical features from dermoscopy images. Commercial
products make use of such algorithms to aid a dermatologist in the screening of patients.
Popular machine learning algorithms such as SVM, kNN, Random Forest, Neural
Networks (Rubegni et al., 2002), (Codella et al., 2018), (Al-masni et al., 2018), (Yap,
Yolland and Tschandl, 2018) and Logistic Regression (Kawahara, BenTaieb and
17
Hamarneh, 2016) have been explored. These approaches require minimal human
intervention. Pretrained Neural Networks have been explored by several researches for the
classification of dermoscopic images of skin cancer/lesions (Bassi and Gomekar, 2019),
(Hosny, Kassem and Foaud, 2019), (Menegola et al., 2017), (Romero-Lopez et al., 2017).
Transfer learning shows better results when compared to training a network from scratch
(Romero-Lopez et al., 2017), (Menegola et al., 2017). Menegola et al. was able to achieve
an AUC score of 80.7% and 84.5% on two different datasets. Romero-Lopez et al. have
explored the use of transfer learning and compared it to training a network from scratch.
The results showed that using transfer learning with fine tuning of weights performs better
than freezing weights or training from scratch. Hosny, Kassem and Foaud have explored
the use of transfer learning across different datasets with a focus on data augmentation. The
accuracies achieved were 91.8%, 88.24% and 87.31% on MED-NODE, DermQuest and
ISIC 2017 respectively.
Lack of data and lack of hyperparameter tuning are some of the identified drawbacks
(Romero-Lopez et al., 2017). Menegola et al. suggest the further exploration of transfer
learning from a dataset related to the domain rather than a generalized dataset (Menegola
et al., 2017). The large publicly available dataset for skin lesions is the ISIC dataset (2019)
which contains images sourced from multiple sources. The images prohibit distortions and
artefacts (Majtner, Yildirim-Yayilgan and Hardeberg, 2016). Therefore, a robust pre-
processing pipeline is required. The dataset also lacks variation in terms of diseases, age
groups and ethnicities represented in the dataset (Codella et al., 2018). Another drawback
in the existing tools are the lack of reasoning provided which can be of use for less
experienced dermatologists and general physicians.
1.3. Research Question
Does the use of preprocessing for classification provide an accuracy improvement over not
using preprocessing with hyperparameter tuning and image segmentation involved in both
approaches?
How can the results of the model be interpreted to make medical decisions based on the
results provided by the model?
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1.4. Research Aim

The aim of this research is to design, develop & evaluate a system which should be capable
of carrying out skin cancer screening automatically using dermoscopic images.
Two experiments will be carried out to find out if certain preprocessing steps coupled with
segmentation helps improvise the prediction accuracy of skin cancer classification. A
robust set of pre-processing steps will be identified to preprocess the images. Feature
extraction and segmentation will be carried out to further improvise the images for
classification. The classification model will then be train on the preprocessed data and
compared against another classification model trained on the non-preprocessed data. Both
the experiments involve hyperparameter tuning and image segmentation.
1.5. Research Motivation

Cancer is a deadly disease that has a high mortality rate. Statistics show that in the United
States of America alone, a whopping 609,640 are estimated to die from the disease in 2018
(National Cancer Institute, 2019). The most common form of cancer is Skin Cancer
(American Association of Dermatology, 2019). A shortage in the number of dermatologists
is on the rise in western countries such as the USA (Codella et al., 2018), (Glazer, Rigel,
Winkelmann and Farberg, 2017). Also, a study done in Sri Lanka shows that the number
of skilled doctors is very less (Herath et al., 2018). The number of cases related to skin
cancer have seen an increase over the years in both Brazil (Minango et al., 2019) and the
United Kingdom (Robertson and Fitzgerald, 2017). A tool that enables dermatologist to
automatically carry out the screening with a high accuracy is therefore important. Existing
research has explored the application of manually crafted CNNs and utilization of Transfer
Learning for Skin Lesion classification. A solution that uses hyperparameter tuning can
improve the accuracy of existing work. Lack of preprocessing has been identified as a
limitation. Therefore, preprocessing is compared against not using preprocessing for
classification. Visual reasoning can prove to be useful for inexperienced dermatologists.
1.6. Research Objectives
1. To explore and identify the different image datasets available on Skin

Lesions/Cancer.
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2. To analyse the different image pre-processing techniques that can be applied.

3. To analyse the different data augmentation techniques that can be applied.
4. To analyse the different optimization algorithms that exist to optimize the network
to carry out the disease classification.
5. To compare the use of preprocessing with not using preprocessing to build a
classification model.
6. To design and develop an interface that can be used alongside the screening process
to perform the skin cancer classification.
7. To analyse the different techniques existing to interpret deep learning models to
provide reasonings for predictions.
1.7. Related Work

Dermoscopy is a technique that is regarded as the state-of-the-art for skin cancer screening.
This technique displays an accuracy higher than that of unaided visual inspection (Yap,
Yolland and Tschandl, 2018), (Kittler et al., 2002, p159-165) but also requires the
involvement of an experienced dermatologist. Number of skin cancer cases are on the rise
over the years (Minango et al., 2019), therefore an automated skin cancer screening tool
can aid dermatologists in the screening process.
The use of clinical algorithms such as 7-point checklist, Menzies method and ABCD rule
allows to visualize the clinical features better (Jain, Jagtap and Pise, 2015), (Mehta and
Shah, 2016). Such algorithms have also been used as the feature extraction algorithm for
more complex classification algorithms. Machine Learning algorithms such as SVM and
kNN have been explored for dermoscopic image classification (Majtner, Yildirim-
Yayilgan and Hardeberg, 2016), (Codella et al., 2018). These algorithms require a separate
feature extraction process. Clinical, Dictionary based, Hand-crafted and deep learning
based features have been explored for classification of skin cancer images (Barata, Celebi
and Marques, 2019).
CNNs are considered the SOTA for computer vision problems. They’ve been explored for
skin cancer classification and have displayed tremendous improvement in terms of
accuracy when compared against physicians and other class of algorithms (Yap, Yolland
and Tschandl, 2018). Different approaches for training CNNs have been explored
20
(Romero-Lopez et al., 2017), (Menegola et al., 2017). The advantages of transfer learning
and fine-tuning have been explored by the authors (Bisla et al., 2019). Model ensembling
is another approach explored for classification (Harangi, 2018).
The most common and important steps that are carried out in pre-processing skin cancer
images for classification have been presented by researchers (Mehta and Shah, 2016),
(Hoshyar, Al-Jumaily and Hoshyar, 2014), (Bisla et al., 2019). Segmentation has been
identified as an important step as it allows the classifier to focus only on the ROI (Mehta
and Shah, 2016). CNNs display good performance in image segmentation (Al-masni et al.,
2018, p221-231), (Jafari et al., 2016), (Hoshyar, Al-Jumaily and Hoshyar, 2014). Class
imbalances and lack of data can be addressed via augmentation. It is shown to improve the
classification accuracy for dermoscopic images (Bisla et al., 2019), (Perez et al., 2018).
Data augmentation has shown promising results for computer vision tasks (Perez and
Wang, 2017).
1.8. Project Scope
Based on the objectives and review of existing products, the scope is defined. The main
goal of the project is to improve the accuracy of skin lesion classification using a deep
learning approach and providing a way for the doctors to the interpret the results.
In Scope Out of Scope
Finding a dataset to be used for Including variation in the dataset by

segmentation and classification. gathering data from hospitals.
Identifying robust preprocessing steps and Complex architecture components such as

applying them. skip connections, regularization etc. in the
hyperparameter tuning algorithm.
Identifying and carrying out image Providing verbose reasoning for the
segmentation on the images. predictions obtained after classification.
21
Identifying image augmentation steps and

applying them to address class imbalance
and insufficient data.
Identifying suitable algorithms for

hyperparameter optimization.
Choosing the hyperparameters for

optimization and optimizing.
Carry out experiments to compare the

effectiveness of the chosen preprocessing
steps for classification.
Providing reasons for the prediction based

on the internal parameters of the chosen
algorithm.
Table 1 In Scope and Out of Scope
1.9. Rich Picture
Figure 1 Rich Picture
The Rich Picture shows the final web application. Input image is preprocessed, segmented,
and classified using both models. One model where only segmentation is applied while the
other, both segmentation and preprocessing. The generated prediction is displayed along
with the visual reasoning for the prediction.
22
1.10. Resource Requirements

The software, hardware, and data requirements identified are listed below.
1.10.1. Software Requirements

OS Ubuntu (VM)
Windows (Local PC)
Programming Language Python
IDE MSVSCode, Jupyter Notebookes (VM)
Package Manager Anaconda
Miscellaneous Software(s) MS Word, Zotero, Google Drive
Table 2 Software Requirements of Project.
1.10.2. Hardware Requirements

Processor 28 Core CPU
GPU 1*Nvidia Tesla T4
Memory 104GB
Disk Space 200GB
Table 3 Hardware Requirements of Project.
1.10.3. Data Requirements

• The following datasets were chosen: ISIC 2018 (Codella et al., 2018), HAM10000
(Tschandl, Rosendahl and Kittler, 2018), and ISIC 2019 and MNIST.
1.11. Chapter Summary

The chapter presents the background of the problem and the problem that this research
aims to solve. A Rich picture has been provided to depict the proposed solution. The
chapter presented the various decisions taken regarding the project initiation and
progression. The expectations, objectives, aims and deliverables have been well defined.
The requirements of the project have also been defined properly to be able to continue with
the research.
23
Chapter 2: Literature Review

Cancer is a major health risk and one of the common forms of cancer is skin cancer that
also happens to have a high mortality rate when diagnosed at a later stage. The existing
approaches used for skin lesion diagnosis are manual approaches and/or expensive
equipment. The application of artificial intelligence in the area of skin lesion diagnosis is
a popular area of research. In this chapter we explore the existing work carried out in the
area of skin lesion diagnosis using artificial intelligence. The pros and cons of these
existing systems are explored in terms of the features, and the accuracy (metric used to
measure the performance of the tool).
2.2. Conceptual Graph

The Conceptual Graph defines the scope to be covered. The areas were divided as review
on domain of the project, review of the technologies required and review on existing
systems. This was used to gather literature in a systematic manner. The use of Concept
Graph allows to ensure that we do not miss out any of the important areas.
The Conceptual Graph has been added to Appendix A.
2.3. Domain Justification

Cancer is a major health hazard with a high mortality rate (N et al., 2015) and the second
leading cause of deaths in the USA, 2016 (National Cancer Institute, 2019). Skin cancer,
common form of cancer, can be cured if diagnosed early but if left undiagnosed, it can
become fatal (National Cancer Institute, 2019). Lighter skinned people are at a higher risk
of cancer as they are more sun-sensitive due to less melanin pigmentation and are most
affected by UV (Reliant Medical Group, 2019). Another risk factor for skin cancer is the
presence of numerous large and atypical moles on the skin (American Cancer Society,
2020).
Skin cancer can be either benign or malignant where benign is not fatal and malignant is
fatal and if diagnosed at a later stage, the survival rate is very low. Malignant Skin Cancers,
especially melanoma only make up 1% of all the reported cases of skin cancer but
responsible for over 75% of skin cancer induced deaths (American Cancer Society, 2020).
24
The survival rate for melanoma when diagnosed early is around 92% but drops
significantly when diagnosed later. According to the WHO the number of reported cases
of skin cancer is on the rise for the past few decades (World Health Organization, 2020).
In the UK, the number of reported cases is seeing a sharp rise since the 1970s with a 50%
increase in just the past decade. According to Cancer Research UK, in the year 2013 14,509
cases of melanoma were found and it was predicted that the rate will increase further in the
upcoming years. Skin cancer is becoming very common in youngsters which poses a
serious issue to the future of the country (Robertson and Fitzgerald, 2017). In Brazil, skin
cancer accounts for upto 30% of all the reported malignancies (Minango et al., 2019). The
number of dermatologists per capita in the USA has drastically decreased in the past few
years while a demand for them has increased due to the rise in the number of cases of skin
cancer (Codella et al., 2018). It has been estimated that in the year 2020 there will 108,420
cases of skin cancer out of which 100,350 will be the melanoma of the skin. 10% of these
cases may also result in death (American Cancer Society, 2020). A study carried out by
Herath et al. show that the number of doctors with knowledge about skin cancer
examination is very low in Sri Lanka. Out of the 123 respondents to their survey, only 10
had received formal training on how to perform a total body examination and the majority
of the doctors have never performed a total body examination in their career (Herath et al.,
2018). This shortage of well-trained dermatologists in combination with rising number of
skin cancer cases calls for an interest in an automated tool for skin cancer examination that
can aid the dermatologists in the screening process.
2.4. Literature Review of the Domain

2.4.1. Skin Cancer Screening Techniques
Skin cancer classification is a challenging task that has been Cancer screening is when a
certain set of tests that are specific to the different types of cancer are carried out in order
to identify the patients at risk. This allows the doctors to focus their attention on those
patients that are at a higher risk of developing cancer and those that are currently
developing cancer. Skin cancer is no exception to this, and tests needs to be carried out to
accurately identify if a person is at risk or is currently developing any forms of skin cancer.
A complete body skin examination is the most common form of screening and usually
25
carried out regularly by dermatologists on patients. Patients may also carry out self-
examinations that may help them to identify any lesion on their body. Skin cancers are
known to change shape, size and color overtime, especially the malignant cancers.
Therefore, tracking the cancer is very important. Overdiagnosis is problem faced by
patients when dermatologists identify a false positive. As further tests may involve invasive
techniques, it is important to have a solid screening technique with very few or no false
positives.
2.4.1.1. Unaided Visual Inspection

Skin Screening always involves the visual inspection of the suspicious area of the skin by
a dermatologist. A well trained and experienced dermatologist will be able to accurately
identify if the suspicious skin lesion points towards a cancer. The earliest of the visual
examination that was also considered to be an early detection tool was carried out unaided.
Although this did perform well at the time it did have a very low accuracy compared to the
tools introduced later. An expert dermatologist is required to always carry out an unaided
visual inspection (Kittler et al., 2002, p159-165). The diagnostic accuracy amongst general
practitioners is very low. The accuracy measured for unaided visual inspection of skin
lesions is around 60% (Kittler et al., 2002). The accuracy of unaided visual inspection of
images are lower when compared to unaided visual inspection of the skin in person
(Cochrane, 2020). Diagnostic accuracy among dermatologists with training less than 5
years is still low but increases considerably in those who have training for over 10 years
(Dinnes et al., 2015). Tools to assist visual inspection exist. Some these tools are the ABCD
rule, Menzies checklist, and the 7-point checklist. Such tools still call for trained
dermatologists even though the tools are simple to use (Dinnes et al., 2015).
2.4.1.2. Aided Visual Inspection

Several image acquisition methods to carry out inspection exists. These include
Dermoscopy, Confocal Scanning Laser Microscopy (CSLM), Magnetic Resonance
Imaging (MRI), Ultrasound and Multi Spectral Imaging. The most commonly used
technique and fastest growing is dermoscopy (Masood and Ali Al-Jumaily, 2013).
Dermoscopy allows to obtain dermoscopic images of the skin that visualizes the details of
the skin so that a dermatologist can carry out a visual examination. Dermoscopy is a non-
26
invasive technique that uses a hand-held microscope and incident light to view the
subsurface image of the skin at an increased magnification. Dermoscopy is mainly used for
the early detection of melanoma. The tool is of two types, immersion contact dermoscopy
and non-contact dermoscopy. It is the most common tool used by clinicians to get an
accurate assessment of skin cancer (Kittler et al., 2002, p159-165), (Dinnes et al., 2015),
(Barata, Celebi and Marques, 2019). The tool allows to obtain a clear zoomed in image of
the skin lesion that clinicians can assess to make further decisions (Barata, Celebi and
Marques, 2019).
Macroscopic images are also a possibility. These images are obtained from standard
cameras and therefore do not visualize the deeper details like a dermoscopy would. Several
issues exist with macroscopic images such as an inconsistent distance between the camera
and skin, and poor resolution and bad lighting (Oliveira et al., 2016). Dermoscopy shows
a signification improvement in terms of accuracy when compared with unaided visual
inspection. This allows for an increase in accuracy from 60% to a 90% and therefore is a
tool that is used around the world (Kittler et al., 2002), (Dinnes et al., 2015), (Barata, Celebi
and Marques, 2019). But the accuracy highly depends on the expertise of the examiner.
The accuracy is no better than that of unaided visual inspection when used by a non-
experienced examiner (Dinnes et al., 2015). The main shortcoming identified with this tool
is the need for an experienced examiner. A study carried out by Kittler et al. (2002)
recommends the involvement of two or more dermatologists to yield the highest possible
accuracy. But with the undersupply of dermatologists, that can be very difficult (Glazer,
Rigel, Winkelmann and Farberg, 2017). Further biopsies are carried out to confirm the
prognosis.
2.4.2. Computer Aided Skin Cancer Screening

Aided visual inspection of skin cancer can benefit from the use of technology. As explored
earlier, CAD systems usually involve the above explored clinical algorithms for
visualization and screening. Newer CAD approaches involve the use of Machine Learning
and Deep Learning. As the focus of this research is more into Deep Learning and Machine
Learning, they’ve explored in depth. Some clinical algorithms include ABCD, Menzie’s
Scoring method and 7-points checklist
27
2.4.3. Machine Learning in Skin Cancer Screening

Use of Machine Learning in Medical Imaging is a very popular area of research and is
being carried out for the past few years to decades. Many Machine Learning algorithms
have been applied for a variety of problems to explore their effectiveness for each medical
imaging problem. Use of Machine Learning has allowed to achieve remarkable accuracies
that has even raised concerns as to whether such applications can replace human
radiologists (Radiology Business, 2020).
Researches have been carried out to explore the effectiveness of ML in classifying

dermoscopic images. The use of Machine Learning introduces more steps such as
Preprocessing, Segmentation, Feature Extraction into the pipeline in addition to
classification. The steps preceding the classification step improvises the data to allow for
an improved and accurate classification.
The use of Support Vector Machine (SVM) has been explored by Majtner et al. in their
research paper where manual feature extraction techniques have been used to extract the
features required to perform the classification. The effectiveness of the manual feature
extraction technique has been compared against automated feature extraction with
Convolutional Neural Networks. Results show that automated feature extraction
approaches work better then manual feature extraction (Majtner, Yildirim-Yayilgan and
Hardeberg, 2016), (Mahbod et al, 2019). Logistic Regression Classifier has been used to
test its effectiveness in images classification based on features extracted via automated
feature extracting using pretrained CNNs (Kawahara, BenTaieb and Hamarneh, 2016).
Linear Texture information and has been used for the identification of malignant
melanomas using SVMs. The proposed system was capable of achieving an accuracy of
70% (Yuan, Yang, Zouridakis and Mullani, 2006). Researchers have also utilized ABCD
rules for feature extraction before using Machine Learning algorithms such as SVM for
classification (Farooq, Azhar and Raza, 2016). Murugan, Nair and Kumar have explored
the use of algorithms such as Random Forest, kNN and SVM for skin cancer classification.
The approach involves segmentation and the use of manual feature extraction techniques
such as ABCD and GLCM to extract the required features to carry out the classification.
The SVM outperforms all the other classifiers by a large margin with an accuracy of
28
85.72% (Murugan, Nair and Kumar, 2019). The use of Random Forest, Naïve Bayes, K*
instance-based classifier and Attributional Calculus for the automatic diagnosis of
melanoma has been explored by Grzesiak-Kopeć, Nowak and Ogorzałek. ABCD has been
the chosen set of features to be extracted from the dermoscopic images. In this study,
Random Forest emerged as the best performing classifier with an accuracy of 86.53%
(Grzesiak-Kopeć, Nowak and Ogorzałek, 2015). Almaraz-Damian, Ponomaryov and
Rendon-Gonzalez have explored the use of SVM for classification with ABCD rule for
feature extraction and Morphological masking for the removal of artefacts from the image
and Segmentation. The accuracy of their system was 75.1% (Almaraz-Damian,
Ponomaryov and Rendon-Gonzalez, 2016).
The use of Delaunay triangulation for the segmentation and classification has resulted in a
sensitivity of 93.5% and specificity of 85.2% with an Adaboost classifier (Pennisi et al.,
2016, p89-103). Ferris et al. has explored the use of Decision Trees for classification using
ABCD features (Ferris et al., 2015). Although the performance is good, like all the previous
researches, the classifier is only trained to distinguish between melanoma and benign skin
lesions excluding other cancers have not been included. Comparing results from existing
research show that the use of segmentation has resulted in a higher accuracy than with no
image segmentation (Pennisi et al., 2016, p89-103). It is evident that SVM is the most
commonly used classifier.
2.4.4. Deep Learning in Skin Cancer Screening

The use of Deep Learning in computer vision problems have been gaining a lot of
momentum recently. Deep Learning is based on Neural Networks which are a set of
algorithms that mimic the human brain. These algorithms, unlike conventional machine
learning algorithms, require large amounts of data and computation resources.
An article published in the year 2017 in nature has shown that Deep Convolutional Neural
Networks (DCNN) based approaches provide better accuracy when compared to well-
trained dermatologists by a difference of almost 6% (Esteva et al., 2017). Premaladha and
Ravichandran have compared neural networks and other machine learning algorithms for
the classification of dermoscopic images. The results of the research show that SVM-
Adaboost hybrid algorithm performs better than the proposed ANN (Premaladha and
29
Ravichandran, 2016). Classification of segmented dermoscopic images using ANN has

resulted in better accuracy, 93.60%, when compared against kNN, 85.22%. The
improvement in accuracy of both the algorithms are also a result of the image segmentation
(Dalila, Zohra, Reda and Hocine, 2017). But it has to be noted that ANNs alone are not
considered the SOTA for computer vision. It is a variation of Neural Network,
Convolutional Neural Network (CNN), that is considered to be the SOTA for most
Computer Vision tasks (Shin et al., 2016), (Alom et al., 2019). Training a CNN from
scratch is an approach that has been explored for the classification of dermoscopic images.
The importance of robust preprocessing has been explored by Nasr-Esfahani et al. for
classification (Nasr-Esfahani et al., 2016). Although the result of the proposed method is
better than several other approaches but is easily outperformed by newer research and
proposed solutions.
Pomponiu, Nejati and Cheung proposed the use of CNNs with a Transfer Learning for
training for the classification of dermoscopic images. The Transfer learning approach used
for training the chosen architecture allows to initialize the networks weights using the
weights learnt from a much larger dataset such as ImageNet (Deng et al., 2009). The
approach involves augmentation of data to compensate for the lack of large datasets and
automated feature extraction via CNN. An accuracy of 83.95% was achieved. The
automated feature extraction approach has resulted in an accuracy higher than the use of
hand-crafted features (Pomponiu, Nejati and Cheung, 2016). Hosny, Kassem and Foaud
have proposed a method that uses a pretrained CNN architecture known as Alex-Net which
resulted in an accuracy of 87.31% on the original ISIC 2017 dataset and 95.91% accuracy
on the augmented ISIC 2017 dataset (Hosny, Kassem and Foaud, 2019).
Menegola et al. have explored different approaches such as no TL, TL from related dataset
and TL from a generalized dataset and also exploring how further tuning affects the
accuracy. Results show that TL without fine-tuning and training from scratch shows the
worst performance. TL from a more generalized dataset is the best approach. The authors
suggest further exploration of the application of TL. Romero-Lopez et al. have explored a
TL approach segmentation and classification of dermoscopic images. The TL approach had
been compared with training from scratch and further tuning of the CNN. The results of
30
the research on the test dataset show that the third approach, fine-tuning a pre-trained
model, has resulted in a higher accuracy of 81.33%. Although the used dataset is large, the
risk of overfitting is inevitable as the dataset is not large enough for Deep Learning. The
authors have noted the lack of hyperparameter tuning as another limitation (Romero-Lopez
et al., 2017).
Transfer learning for skin cancer classification has also been explored in the works of Bassi
and Gomekar. Their experiment involves preprocessing and segmentation of the image
using thresholding methods. Features such as the age and gender of the patient has also
been used in their experiment via a parallel network. Augmentation techniques were also
used due to the presence of class imbalances. Multiple CNN architectures had been trained
and the VGG16 architecture had emerged as the best with an accuracy of 82.8% on the
non-segmented data. The accuracy with the segmented dataset had dropped significantly
to 65.8% suggesting that the thresholding technique used for segmentation is not ideal and
recommending further research into supervised segmentation techniques (Bassi and
Gomekar, 2019). A hybrid approach by Mahbod et al. shows that CNNs can be used as the
feature extractor with algorithms such as SVM. The authors have used an ensemble of
pretrained models for the feature extraction proving that ensembles perform better than a
single model. The authors have also suggested exploring more advanced pretrained models
such as DenseNet (Mahbod et al., 2019).
Advanced pretrained models such as DenseNet and SqueezeNet have been explored by
Kadampur and Al Riyaee. The best performing out of the research is the SqueezeNet with
an AUC score of 99.77%. Although the dataset used in the research is large, it is not the
largest dataset available (Kadampur and Al Riyaee, 2020). Deep architectures such as
ResNet-101 and Inception-v3 has also been applied for the classification of skin cancers
into benign and malignant by Demir, Yilmaz and Kose. The results are promising with an
accuracy of 90% for the Inception-v3 model which marginally outperformed ResNet-101
by 1% (Demir, Yilmaz and Kose, 2019). A limitation of this research is the small dataset.
Complex architectures could result in model overfitting and regularization can be used to
address this. CNNs have been trained from scratch using the proposed regularizer to
31
achieve an accuracy of 97.49% placing it very close to the SOTA in the domain (Albahar,
2019). One of the limitations is the need to specify the lambda constant.
Dermatologists follow a hierarchical method to carry out the diagnosis for any form of skin
cancer. Barata and Marques imitate this method in their proposed solution where TL is
used. The first stage of the is to identify if the dermoscopic image consists of a melanoma
or non-melanoma and then the final diagnosis was carried out. The authors highlight the
importance of the image segmentation (Barata and Marques, 2019). The results show that
the hierarchical approach does offer improvements in terms of performance. The results
also show that fine tuning is superior to not fine tuning the pretrained model. A limitation
in this research is the size of the dataset (Barata and Marques, 2019). Hyperparameter
tuning is a suggestion made by some researchers as a potential area that requires more
exploring. Tan, Zhang and Lim have explored the effectiveness of hyperparameter tuning
of CNNs using PSO (Tan, Zhang and Lim, 2019). The limitation identified is similar to the
research by Barata and Marques, the use of a larger dataset should be explored.
Study Methodology Limitations

Majtner et al., 2016 Manual feature extraction • Lack of robust
compared with automated feature preprocessing.
extraction with SVM classifier. • Comparatively
smaller dataset.
• Lesser number of
skin cancers
classified.
Kawahara, Automated feature extraction with • Comparatively
BenTaieb and pretrained CNNs with Logistic smaller dataset.
Hamarneh, 2016 Regression for classification. • Weaker classification
algorithm.
Romero-Lopez et Exploring how Fine Tuning with • Lack of
al., 2017 Transfer Learning compares Hyperparameter
against non-fine-tuning Transfer Tuning.
32
Learning and training from • Using a larger dataset

scratch approaches. to mitigate the risk of
overfitting.
Bassi and Gomekar, Segmentation of the images via • Manual segmentation
2019 manual segmentation techniques. technique performs
This did not improve the accuracy poorly.
as expected.
Mahbod et al., 2019 Ensemble of Pretrained CNNs for • Comparatively
Feature Extraction with SVM smaller dataset.
Classifier. • No complex
architectures have
been explored. Ex:-
DenseNet101
Albahar, 2019 Pretrained CNN for classification • Only classifies a
of dermoscopic images with a dermoscopic image
novel regularization technique. into benign and
Classify images into two classes: malignant.
Benign and Malignant. • Lack of
hyperparameter
tuning.
Barata and Hierarchical CNN that mimics the • Lack of data and lack
Marques, 2019 process carried out in labs using of variation in the
segmented (cropped) types of benign skin
dermoscopic images of skin cancers.
cancer. Classify images into
melanoma and non-melanoma.
Tan, Zhang and Particle Swarm Optimization • Comparatively
Lim, 2019 (PSO) for optimal feature smaller dataset with a
selection and optimizing the CNN smaller number of
for melanoma classification. unique skin cancers.
Table 4 Summary of findings based on existing work – Image Classification.
33
2.4.5. Preprocessing of Skin Cancer Images

Existing research shows that the enhancement of images may result in an improvement in
terms of the classification and segmentation accuracy. Several researchers have explored
the different preprocessing steps that can be applied for the classification and segmentation
of skin cancer images. The importance of robust preprocessing steps has been explored by
Majtner et al. for the segmentation of dermoscopic images (Majtner et al., 2016), (Mehta
and Shah, 2016). But preprocessing steps should be carried out properly as errors could
propagate from this stage and result in a bad accuracy in terms of segmentation and
classification (Kawahara, BenTaieb and Hamarneh, 2016).
The important preprocessing steps for the detection of skin cancers in images has been
discussed by Hoshyar, Al-Jumaily and Hoshyar. The preprocessing steps involved in skin
cancer detection is mainly carried out to enhance the images (Hoshyar, Al-Jumaily and
Hoshyar, 2014), (Mehta and Shah, 2016). Full resolution images require more
computational resources to train. Resizing an image reduces the need for vast computation
resources (Hoshyar, Al-Jumaily and Hoshyar, 2014), (Mehta and Shah, 2016). The images
are known contain artefacts such as hair, gel and rulers that are left behind as a result of
the use of dermoscopy (Majtner et al., 2016), (Aziz, 2015), (Hameed, Ruskin, Abu Hassan
and Hossain, 2016), (Mehta and Shah, 2016). Therefore, artefact removal steps are used to
remove these artefacts from the images.
Hameed, Ruskin, Abu Hassan and Hossain suggest color space transformation as the RGB
color space consists of a range of colors. Transforming to a color space with less colors
may allow for better and accurate preprocessing (Hameed, Ruskin, Abu Hassan and
Hossain, 2016), (Hoshyar, Al-Jumaily and Hoshyar, 2014). LAB color space has been
identified as the optimal color space that results in very low error rate. Artefact removal
for skin cancer detection has been extensively explored by several researchers for skin
cancer classification and segmentation (Menegola et al., 2017), (Al-masni et al., 2018,
p221-231). Dullrazor is an artefact removal method invented in 1997 which uses
morphological edge operations (Lee et al., 1997) but doesn’t work well for thin hair. “E-
Shaver” is an improvement proposed by Kiani et al. (Jaworek-Korjakowska and
Tadeusiewicz, 2013) have proposed an artefact removal approach that involves the removal
34
of the artefacts from an image by first converting an image to grayscale and then applying
unsharp masking and Black top hat transform was then applied on the image. The next step
was to perform image inpainting. This approach was able to achieve an accuracy of 88.7%.
Generating binary mask and then applying inpainting is another artefact removal approach
but results in low accuracy (Aziz, 2015). As explored by Hoshyar, Al-Jumaily and
Hoshyar, Contrast Limited Adaptive Histogram Equalization (CLAHE) is considered to be
one of the best contrast enhancement approaches. CLAHE is designed for medical image
enhancement (Hoshyar, Al-Jumaily and Hoshyar, 2014).
2.4.6. Segmentation of Skin Cancer Images

Segmentation involves retrieving the Region of Interest (ROI) of an image and highlighting
it to allow a classifier to focus only on the ROI during classification. As explored by
Hoshyar, Al-Jumaily and Hoshyar, image segmentation is essential for skin cancer
classification (Hoshyar, Al-Jumaily and Hoshyar, 2014), (Mehta and Shah, 2016).
Segmentation steps can be both supervised and unsupervised. Both types of approaches
have been extensively explored by researchers for skin cancer detection. A comparison
between multiple segmentation approaches has been carried out by Hameed, Ruskin, Abu
Hassan and Hossain in their review on the approaches for skin cancer detection. Ganster et
al. have suggested the use of a fusion of three types of segmentation methods: dynamic
thresholding, global thresholding, and color clustering (Ganster et al., 2001). Jain, jagtap
and Pise, in their research on skin cancer detection, have proposed the use of automatic
thresholding and masking operations in each of the R, G and B planes. The 3-plane masking
accuracy had been proposed to improvise the accuracy over single plane masking. The
segmentation technique requires artefact removal as it focuses on the largest blob on the
image (Jain, jagtap and Pise, 2015). The Water-shedding algorithm has also been proposed
for skin lesion segmentation of dermoscopy images by Wang et al. The algorithm requires
robust preprocessing steps as it does not work well in the presence of artefacts such as hair
and black borders in the image (Wang et al., 2010). The watershed algorithm has been
compared against another segmentation approach known as the active contour method.
Watershed algorithm is comparatively a better region-based segmentation technique which
is also less sensitive to noise. Farooq, Azhar and Raza have explored the use of watershed
35
algorithm for segmenting dermoscopic images in the PH2 dataset. It is compared with
active contour and a combination of both. The combined approach is shown to work better
for segmentation of images. (Farooq, Azhar and Raza, 2016).
A Gradient and Feature Adaptive Contour model is proposed by Sreelatha, Subramanyam

and Prasad for the segmentation of skin cancers of dermoscopic images. A mathematical
modelling approach is used to detect melanoma in dermoscopic images. The results show
that the approach performs better than the compared approaches with a Similarity
Coefficient of 97.08% (Sreelatha, Subramanyam and Prasad, 2019). The research was
carried out using the PH2 dataset which is a small dataset and therefore, a limitation in the
researches that use this data would be the lack of data. The images present in the dataset
were gathered in a very controlled environment and therefore perfect images. This is noted
by Farooq, Azhar and Raza in their research.
The use of clustering algorithms for skin cancer image segmentation has been explored by
Nasr-Esfahani et al. The masks generated via this method was further enhancement via the
use of morphological operations. The generated masks are then applied on the images used
for classification with guassian filtering for smoothening the areas surrounding the skin
cancer (Nasr-Esfahani et al., 2016). The effectiveness of Ant-colony based segmentation
algorithm has been explored for the segmentation of skin cancer images. The algorithm is
applied on each of the three-color plane system, RGB, HSV and LAB, and the grayscale
image. The plane that results in the best plane was used. The effectiveness of the ACO
based algorithm is measured using the XOR metric. The average XOR error of 172 images
used to test the algorithm was 57.6% (Dalila, Zohra, Reda and Hocine, 2017). The proposed
approach was compared against manually crafted masks by using the images for
classification. The results show that the classification of images using the ACO based
segmentation is better with an accuracy of 93.60% than the classification of images using
the manual mask segmentation with an accuracy of 86.60%. A comparison between
Chan0vese segmentation algorithm and Expectation maximum algorithm has shown that
the Expectation maximum algorithm performs better with a Jaccard index of 71.2%. The
approaches have also been compared with the artefact removal approaches proposed by the
researchers. The results show that artefact removal improves the segmentation than not
36
applying any artefact removal technique (Majtner, Lidayova, Yildirim-Yayilgan and

Hardeberg, 2016).
Deep learning approaches that involve the use of CNNs have been explored with the advent
of larger datasets that contain dermoscopic images thus supporting supervised learning.
Jafari et al. have applied CNNs for the patch extraction or segmentation of dermoscopic
images of skin cancer. The approach uses a local and global window where the local
windows allows to identify the local texture around the pixel and the global window allows
to identify the lesion. The dataset being used for the research consists of a smaller number
of images and therefore very little variation. The approach is shown to perform better than
other approaches with an accuracy of 98.5% and recall of 95.0% (Jafari et al., 2016).
Mishra and Daescu have compared the Otsu thresholding method against the use of CNNs
for segmentation of dermoscopic images. Otsu thresholding is a clustering-based image
segmentation method. The comparison between the two approaches show that the CNN
based approach performs better than Otsu thresholding with a Jaccard index of 84.2% and
71.1% respectively (Mishra and Daescu, 2017). Fully Connected Networks for multi class
segmentation of dermoscopic images have shown to improve over existing approaches that
do not involve CNNs but doesn’t improve over an architecture such as the U-Net (Goyal,
Hoon Yap and Hassanpour, 2017). Youssef et al. have explored the use of Deep
Convolutional networks for skin cancer image segmentation. Encoder-decoder technique
for semantic pixel-wise segmentation has been used, resembling SegNet, a commonly used
Segmentation Architecture. The results show that the approach performs very well with an
F1-Score of 87.0% (Youssef et al., 2018). Results from the research by Murugan, Nair and
Kumar also show that the use of segmentation before performing classification indeed
helps improve the accuracy as the classifier can focus more on the ROI but comparison
between the two approaches have not been provided (Murugan, Nair and Kumar, 2019).
The use of FrCN for skin cancer segmentation has shown tremendous performance and is
shown to perform better than SegNet, U-Net and FCN (Al-masni et al., 2018, p221-231).
Study Methodology Limitation
37
Jafari et al., 2016 CNN architecture for both • Smaller dataset.

local feature extraction and
global feature extraction.
Mishra and Daescu, 2017 Preprocessed images, • No classification of
augmented and the images.
segmentation carried out • Comparatively
using U-Net CNN smaller dataset.
architecture.
Majtner, Lidayova, Expectation Maximum • Comparatively
Yildirim-Yayilgan and algorithm and Chan-Vese smaller dataset.
Hardeberg, 2016 Segmentation compared • Lower accuracy
with different artefact compared with other
removal methods to segmentation
explore if they add any algorithms.
value to segmentation.
Goyal, Hoon Yap and Pretrained Fully Connected • Lower accuracy
Hassanpour, 2017 CNN for dermoscopic compared with other
image segmentation. segmentation
algorithms.
• Lack of
preprocessing such
as artefact removal.
Youssef et al., 2018 Encoder-decoder technique • Lack of
for semantic pixel-wise Preprocessing.
segmentation of
dermoscopic images.
Al-masni et al., 2018 Full Res. Convolutional • Lack of data.
Networks
Table 5 Summary of findings based on existing work - Image Segmentation.
38
2.5. Algorithmic Analysis

2.5.1. Image Segmentation
Several segmentation algorithms have been explored by a lot of researchers for skin cancer
image segmentation. Segmentation of dermoscopic skin images depend heavily on
preprocessing due to the process of artefacts such as hair, rules, and gel. These artefacts
need to be removed before segmentation is applied on the images. As discussed earlier,
algorithms such as the Watershed algorithm, Chan-vese segmentation, Expectation
Maximum algorithm and CNNs have been explored for image segmentation by
researchers.
2.5.1.1. Watershed Algorithm

The Watershed algorithm is a region-based algorithm used for image segmentation. The
widespread use of watershed algorithms in medical imaging tasks origins from the success
achieved by Vincent and Soille when a variation of the algorithm was released that was
better than all the previous versions (Vincent and Soille, 1991). Murugan, Nair and Kumar,
Wang et al., and Farooq, Azhar and Raza have explored the application of the algorithm
for image segmentation. The results show that although the approach works better than
other known manual approaches, newer supervised approaches work better. The
disadvantages of the algorithm include Over-segmentation and under-segmentation
(Kumar, 2010). The results from the research by Farooq, Azhar and Raza show that the
Watershed algorithm performs almost similar to the Active Contour algorithm while a
combination of the algorithms outperform both (Farooq, Azhar and Raza, 2016).
2.5.1.2. Expectation Maximization

Expectation Maximization algorithm is an iterative algorithm used to perform likelihood
estimation. As explored previously the comparison of the algorithm with Chan-Vese
segmentation algorithm has shown that the Expectation Maximization algorithm performs
better (Majtner, Yildirim-Yayilgan and Hardeberg, 2016). The highest IoU obtained was
73.3%. A comparison of a variety of segmentation algorithms for melanoma diagnosis has
shown that the Expectation Maximization algorithm is second only to the Adaptive Snakes
(AS) algorithm. An improved Expectation Maximization was used, Expectation
Maximization – Level Set, by the authors in their comparison (Silveira et al., 2009). The
39
algorithm is known to have a very slow convergence with higher chances of being stuck in
the local minima. Another notable limitation of the use the two previously explored
algorithms are the use of additional feature extraction steps.
2.5.1.4. Convolutional Neural Networks (CNN)

CNNs do not require a separate feature extraction step as the Convolutional filters in a
CNN are capable of performing feature extraction automatically. Zahangir Alom, Aspiras,
M. Taha and K. Asari have explored the use of a novel architecture, NABLA-N, proposed
by the authors. The proposed architecture is based on the R2U-Net architecture and uses
more latent spaces and therefore reuses the learnt features. This reduces the number of
model parameters significantly. The proposed architecture is shown to perform better than
R2U-Net with an IoU score of 88.83%. The authors have also used Transfer Learning to
train the architecture due to the presence of a smaller dataset (Zahangir Alom, Aspiras, M.
Taha and K. Asari, 2019). The training has been performed for a longer, 250 epochs.
The application FCN-AlexNet, AlexNet architecture based FCN, and VOC-FCN, FCN
trained on the VOC dataset, on skin cancer segmentation has shown that they perform
better than most of the other approaches with an IoU score of 84% (Pour, Seker and Shao,
2017). Mishra and Daescu have stated that the use of architectures such as Fully Connected
Neural Network (FCN) and Deconvolutional Neural Network (DCN) would require more
computational resources due to the increased number of parameters.
Mishra and Daescu have suggested the more medical imaging related architecture, U-Net,
for the skin cancer image segmentation task (Mishra and Daescu, 2017). The result of their
research show that the chosen approach using the U-Net architecture has been able to
perform better than other segmentation techniques such as Otsu’s Segmentation with a IoU
score of 84.2%.
Attention U-Net is shown to be one of the best performers in terms of skin cancer image
segmentation on the ISIC 2018 dataset (Abraham and Mefraz Khan, 2018). The authors
have also implemented a novel loss function called the Focal Tversky Loss Function to
deal with the class imbalances the dataset by giving more importance to False Negatives
instead of both False Negatives and False Positives. The architecture trained with the
proposed loss function is compared against other variations of the U-Net architecture
40
proving that the proposed approach performs significantly better with an average difference
in recall of 15.9% (Abraham and Mefraz Khan, 2018).
2.5.1.5. Conclusion
It is clear from the above discussion that CNNs are better algorithms in terms of image
segmentation. This has also been proven by extensive research carried out by a lot of
researchers. Therefore, CNNs are chosen to carry out the image segmentation as part of
this project. It has also been identified that the U-Net architecture is the most suitable for
this task as it is an architecture introduced for medical imaging tasks.
2.5.2. Feature Extraction

Feature Extraction can be either manual or automatic. Manual Feature Extraction
techniques for Skin Cancer Segmentation have been explored by Majtner, Yildirim-
Yayilgan and Hardeberg. The use of Feature Extraction methods such as RSurf features
and Local Binary Patterns (LBP) were explored by the authors. This was compared against
automatic feature extraction and it was concluded that the automated approach
outperformed the manual approach (Majtner, Yildirim-Yayilgan and Hardeberg, 2016).
ABCD rules are also commonly used as feature extractors for skin cancer classification as
they are most suitable for such images. Clinical features such as ABCD is capable of
extracting features of melanoma (Grzesiak-Kopeć, Nowak and Ogorzałek, 2015),
(Almaraz-Damian, Ponomaryov and Rendon-Gonzalez, 2016). (Murugan, Nair and Kumar
have explored the use of GLCM and ABCD features for melanoma classification. The
algorithms are only capable of extracting features to classify melanoma (Murugan, Nair
and Kumar, 2019).
The most common candidate algorithm for automatic feature extraction in the presence of
sufficient data and ground truth labels is the Convolutional Neural Network. CNNs are
capable of extremely efficient feature extraction due to the presence of Convolutional
Filters which are capable of extracting low level features and learning the image
representations without human intervention (Tschandl et al., 2019). Transfer Learning is
also commonly used to address the lack of data. Transfer Learning is when CNNs are
initialized with weights learnt from much larger and general datasets and these weights are
either directly used or further fine-tuned for the problem in hand.
41
When CNNs were compared with manual feature extraction methods such as RSurf
features and Local Binary Patterns (LBP), pretrained CNNs were shown to perform better
(Majtner, Yildirim-Yayilgan and Hardeberg, 2016). The use of CNNs as feature extractors
have shown to result in better classification accuracy when compared with human
diagnostic results (Yap, Yolland and Tschandl, 2018). The use of CNN as feature extractors
with transfer learning is shown to perform very well for classification of images
(Kawahara, BenTaieb and Hamarneh, 2016). A comparison between hand-crafted features,
dictionary based features, clinically inspired features and deep learning features show that
deep learning features work well but only if there are large amounts of data while the other
approaches work well with even very little data (Barata, Celebi and Marques, 2019). With
the advent of data augmentation techniques, smaller dataset sizes can be artificially
increased to allow for the use of CNNs. A study carried out by Wu et al. on face skin
disease classification have shown that the use of pretrained CNNs doesn’t require any
additional feature extraction steps and this laborious task can therefore be automated (Wu
et al., 2019).
2.5.2.1. Conclusion
It can be concluded that CNN as a feature extractor is far superior and less laborious
compared to other feature extraction methods. In the presence of large datasets, CNNs are
shown to work well. In the presence of moderately large datasets, pretrained CNNs can be
used to learn features better and displaying performance significantly better than the other
feature extraction methods.
2.5.4. Image Classification

The classification of dermoscopy is an important function in many of the skin cancer
detection tools in existence. Several algorithms have been explored by past researchers.
Both Machine Learning algorithms and Deep Learning algorithms have been explored for
the classification of dermoscopic images.
2.5.4.1. Machine Learning Algorithms

Machine Learning algorithms such as Random Forest, K-Nearest Neighbor, Logistic
Regression and Support Vector Machines have been explored for the purpose of skin
cancer image classification. Random Forest compared was compared against k-Nearest
42
Neighbor algorithm for skin cancer image classification has shown that RF performs better
than kNN by approx. 10% in terms of accuracy (Murugan, Nair and Kumar, 2019). In the
study by Grzesiak-Kopeć, Nowak and Ogorzałek for the classification of skin cancer
images, RF was compared with Naïve Bayes classifier and K* instance-based classifier.
RF was once again the better performing algorithm with an (Grzesiak-Kopeć, Nowak and
Ogorzałek, 2015).
But SVMs were able to outperform RF in the study by Murugan, Nair and Kumar where
SVM trained on ABCD features had an accuracy of 89.43% while the RF had an accuracy
of 76.87% (Murugan, Nair and Kumar, 2019). SVM has also been used by Majtner,
Yildirim-Yayilgan and Hardeberg for classification of skin cancer using dermoscopic
images. The results show that the SVM is capable of achieving higher accuracies compared
to the other machine learning algorithms explored (Majtner, Yildirim-Yayilgan and
Hardeberg, 2016). 92.1% classification accuracy on classifying skin cancers into benign
and malignant have been achieved using SVM (Alquran et al., 2017). Comparison between
SVM and CNN for polyp classification shows that CNNs work better in terms of
classification and feature extraction (Shin and Balasingham, 2017).
2.5.4.2. Deep Learning Algorithms

Deep Neural Networks have recently seen a lot of popularity due to the breakthroughs
achieved in several areas. Convolutional Neural Network is a type of Deep Learning
algorithm, a variation of Neural Network. CNNs are mainly composed of Convolutional
Layers which is not present in ANNs.
Extensive research shows that CNNs are the SOTA for computer vision tasks. Variations
of CNNs exist that aid in different types of tasks. For the purpose of this research, we focus
mainly on the vanilla CNN. Romero-Lopez et al. have explored the use CNNs for
dermoscopic image classification and the results show that the network is capable of
producing highly accurate predictions (Romero-Lopez et al., 2017). Menegola et al. and
Romero-Lopez et al. have both explored the use of CNNs and Transfer Learning for
dermoscopic image classification. Bassi and Gomekar have explored pretrained CNN
models for dermoscopic image classification. The results show that the VGG-16
architecture has the highest F1-Score compared to other architectures: VGG-19,
43
Inceptionv3, and MobileNet (Bassi and Gomekar, 2019). ResNet101 has been compared
against Inception-v3 for classification of dermoscopic images. Inception-v3 is shallower
compared to ResNet101 and in this study Inception-v3 emerges as the better accuracy with
an accuracy of around 90% (Demir, Yilmaz and Kose, 2019). A comparison between the
accuracy of deep learning approach and human physicians have shown that CNNs
outperform human physicians for classification of dermoscopic images with accuracies of
42.94% and 81.59% respectively. This shows that using a computer aided approach,
especially deep learning improves the accuracy of the prediction by a huge margin (Hekler
et al., 2019). The authors also suggest a combined approach that performs better but only
marginally when compared with the CNN approach. Ensemble of pretrained CNNs have
shown to be capable of achieving SOTA performance with SVM classification (Mahbod
et al., 2019).
2.5.4.3. Conclusion
As CNNs are being used feature extractors, they can also be further extended to perform
the classification. Research also shows the CNNs work well for classification as well.
Therefore, CNNs have been chosen. Transfer Learning was also chosen as the training
approach as it allows to achieve a higher accuracy with a smaller dataset. Research shows
that transfer learning approaches with further fine tuning the network works better than no
fine-tuning or training the network from scratch (Romero-Lopez et al., 2017), (Menegola
et al., 2017).
An architecture is the order of the different types of layers that exist. Choosing an
appropriate architecture aids in achieving good performance. For the purpose of this
research a complex architecture, as suggested by Mahbod et al., and a shallow architecture
that has been well researched and shown to perform well was chosen (Romero-Lopez et
al., 2017). Therefore, pretrained VGG16 and DenseNet101 were chosen for the
implementation. Performance of both architectures was compared before finalizing on one
architecture.
44
2.5.5. Hyperparameter Optimization

Parameters can be either hyperparameters or model parameters. Hyperparameters can be
manually set by a person while the model parameters are learnt during the training process.
Hyperparameter Optimization can help in improving the accuracy.
The most commonly used approach for tuning CNNs is Reinforcement Learning (RL). RL
is shown to be capable of designing architectures that are on par with the SOTA
architectures (Baker, Gupta, Naik and Raskar, 2016). Asynchronous RL, a variation of RL,
is shown to be capable of designing architectures on the MNIST dataset with accuracies
over 95.8% without human intervention, and boundaries. (Neary, 2018). Evolutionary
algorithms are a class of algorithms that are quite often explored in the area of
hyperparameter tuning of CNNs. The algorithm is designed around the evolutionary theory
proposed by Darwin (Vikhar, 2016). Genetic Algorithm is the most commonly used type
of Evolutionary Algorithm. RL is more resource intensive and therefore, this has sparked
an interest in the use of evolutionary algorithms to search for architectures (Sun et al.,
2019). Sun et al. have proposed a GA implementation where the results show that the
proposed algorithm is capable of finding the architectures comparable with SOTA
architectures. Petroski Such et al. did a comparison between GA and RL for training neural
networks. The results show that GA is faster and equally capable as RL in less time
(Petroski Such et al., 2018).
Tan, Zhang and Lim have explored on using PSO for hyperparameter tuning of CNNs for
skin cancer classification. The authors have proposed a variation of PSO for
hyperparameter tuning called the Random Coefficient PSO (RCPSO). The algorithm is
capable of searching for every deep CNNs with a fixed set of different layers (Tan, Zhang
and Lim, 2019). The proposed algorithm is compared against other bio-inspired algorithms
and is shown to perform the best out of the lot. COA is a rather new meta-heuristic global
optimization algorithm that mimics the social organization of Coyotes and their adaptation
to the environment. The algorithm focuses on the social structure and the experiences
exchanged by the Coyotes (Pierezan and Dos Santos Coelho, 2018). Standard Benchmark
functions are used to evaluate the performance of the proposed COA compared to other
bio-inspired algorithms such PSO. The algorithm is shown to perform better than PSO.
45
2.5.5.1. Conclusion
Two of the bio-inspired algorithms chosen are GA and COA. Although GA has been
extensively applied in this area, it has not been applied in the domain of skin cancer and as
seen in (Sun et al., 2019), it shows a lot of promise in terms of hyperparameter tuning of
CNNs. COA is a rather new algorithm that has not been applied in the area of architecture
search. Therefore, it was decided to perform a comparison of the two algorithms in the area
of CNN hyperparameter tuning/architecture search and so both of the algorithms were
chosen for the optimization of CNN.

Existing work related to skin cancer screening using ML and DL approaches were analysed
and the limitations were identified. The algorithms that can be used to carry out of each of
the tasks involved in building such a tool was also explored and decisions were made.
46
Chapter 3: Methodology
This chapter covers the research methodologies that will be used to carry out this research.
The various methodologies are explored and the methodology most suitable for this
research is identified and justifications are provided for the choices.
3.2. Research Paradigm

A research paradigm is an approach to carry out a research that has been verified by
previous researchers and have been in use for very long.
3.2.1. Positivist Paradigm

Quantitative researches are positivist researches. Positivists believe in hypothesis testing
and that the findings of one study can be generalized to another study that is almost similar
to the previous study regardless of it is conducted in a different environment.
3.2.2. Interpretivism Paradigm

Qualitative researches are constructivist researches. Social constructivist is a philosophical
approach which holds that reality is not directly known and only be inferred or assigned
based on convention or consensus.
A mix-mode approach was chosen for this research as the data gathered for this research
was via questionnaires and the tool built at end of this research is measured using statistical
approaches and evaluated by experts.
3.3. Research Approach

Identifying the research approach allows to define the relationship between the theory and
the research and also the relevancy of the data collection approaches that are used.
3.3.1. Top-Down
This approach is also known as deductive. The researcher initially develops a hypothesis.
Data related to this hypothesis is then gathered. The researcher then studies the data and
tests the hypothesis that was previously developed to check if the hypothesis is valid or
not.
47
3.3.2. Bottom-Up
This approach is also known as inductive. The researcher begins by collecting data that is
relevant to the research that is being carried out and tries to tries to make sense of data via
analysis. In this approach the researcher develops a theory based on the data that has been
gathered. An example of a deductive is the research carried out by Herath et al. where the
knowledge and skill of doctors in Sri Lanka related to melanoma is low is the hypothesis.
3.4. Design Methodology

The design methodology chosen for this research is the Object-Oriented Design (OOD).
The reason for picking OOD is because it reduces complexity, improves the reusability,
and maintability of the solution. This is purely because the entities in the software are
separated into objects. The methodology follows the four Object-Oriented Design
concepts: Encapsulation, Abstraction, Polymorphism, and Inheritance which are useful.
3.5. Software Development Methodology

It is important to follow a proven methodology to develop the software as it ensures success
in the development. The methodology used in the development as part of this research is
the Agile Development Methodology. The reason for choosing this methodology is
because it enables to carry out several iterations in the development. This development
methodology allows for faster prototyping and improvements can be made iteratively. This
ensures stake-holder satisfaction as an actual working product will be available as soon as
the first few sprints are over. This approach also allows to incorporate changes that may
occur during the development process due to the identification of new functionalities and
or deviations in the research. A set of requirements can be chosen from a list of
requirements identified and incorporated into each sprint. The sprints were divided such
that each set of functionalities was developed to complete the development.

Research methodologies and development methodologies have been explored in this
chapter and the most appropriate methodologies for this research has been chosen.
Appropriate research methodologies and development methodologies to ease the
development were identified and picked as the ideal choice with justifications.
48
Chapter 4: Project Management

This chapter covers the different aspects of project management that has been covered in
this research. The tools used to cover the different project management aspects have been
explored in this chapter. The risks that could arise during the research have also been
covered while a mitigation has been decided on for the identified risks. The BCS Code of
Conduct has been understood and analysis has been carried out on how the research can
align with the BCS Code of Conduct.
4.2. Time Management

The Time Management table has been added to Appendix B.
4.3. Work Breakdown Structure

The Work Breakdown Structure has been added to Appendix C.
4.4. Gantt Chart

The Gantt Chart has been added to Appendix D.
4.5. Risk Assessment and Mitigation Plans

Risk Impact Probability Mitigation
Damage to data and/or High Low Take regular backups of all data related
devices being used for to research and development.
research and development.
Resource unavailability. Mediu High Use cloud VMs with required
m resources.
Inability to carry out a full High High Limit search space and the
hyperparameter tuning. hyperparameters that are optimized.
Unavailability of dataset High Low Few image datasets exist for both
segmentation and classification.
Similar research High Medium Therefore, it is important that the
research is as novel as possible.
Table 6 Risk assessment and Mitigation
49
4.6. Compliance with BCS Code of Conduct

The British Computer Society sets the professional standards of competence, conduct and
ethical practice for computing. The four important aspects of the BCS Code of Conduct
are: (1) Public Interest, (2) Professional Competence and Integrity, (3) Duty to the
Profession, (4) Duty to Employers and Clients
Public Interest Professional Competence and Integrity

This research project aims to find a tool The research problem, domain and the
that enables dermatologists to speed-up the background were initially defined as the
skin screening process with the aid of first step of the project. This was succeeded
computer vision techniques. In the process with the critical evaluation of existing
of building the tool different approaches work carried out by other researchers in the
were explored such as the optimization of research area. Related technologies were
Hyperparameters and ideal training also evaluated to identify the most suitable
approach. The general public can benefit approaches and technologies. This enabled
greatly from this tool if used by to identify the contribution of the research.
dermatologists. The approaches explored Suitable methodologies were chosen to
can be utilized by other researches in the perform design, development and
future based on the performance and evaluation of the research and its outcome.
quality of the explored approaches.
Duty to the Profession Duty to the Employers and Clients
It is important to maintain professional This research was carried out as a
standards and therefore, it was maintained requirement for the degree BSc (Hons)
throughout the research project by citing Computer Science. All the instructions that
work done by other authors. Code that was was provided by the supervisor, instructor
also obtained from open source was and institution was followed to maintain
credited to the respective authors. the professional standards. It is important
Feedback from domain and technical to ensure that any sensitive information is
experts have been garnered to ensure that kept confidentially. Therefore, this project
standards have been met to have a quality adheres to this rule and does not disclose
output. any confidential information.
Table 7 Compliance with BCS Code of Conduct.
50
4.7. SLEP Analysis

The Social, Legal, Ethical and Professional analysis is presented in Table 8.
Social Legal
Privacy is very important. None of the No violations should be attempted against
survey respondent’s details were added to laws setup for privacy, data and IT
the thesis but only the data collected from protection. All of the data used in the
them. It is important that unauthorized research are freely available datasets that
parties don not get access to confidential are public to use with citations. All patient
data as this is a medical related research. data are anonymized.
Ethical Professional
All feedbacks and responses were taken Medical practitioners did not divulge any
with the consent, orally or written. patient related information. The
application does not require the user to
input any information to reveal their
identity.
Table 8 SLEP Analysis

This chapter provides a summary on the work breakdown structure and the timeline of the
project. This allowed to adhere to a set timeline and work accordingly. Although, there
were slight deviations due to unexpected external factors, these were addressed, and the
research was brought back on path. As the resource requirements changed due to further
research and understanding of the research, the resource requirements were revised and
listed. It is important for the project to be compliant with the BCS Code of Conduct.
Therefore, how the project adheres to the BCS Code of conduct has been discussed. A
SLEP analysis was carried out to identify all the issues.
51
Chapter 5: Software Requirement Specification

This chapter focuses on the different system requirements gathering approaches that was
undertaken as part of this project. The stakeholders associated with the system are
identified. The functional and non-functional requirements have been identified based on
the gathered requirements.
5.2. Stakeholder Analysis

The stakeholders associated with the System have been identified and are represented in
the Onion Diagram. Descriptions of the stakeholders have been provided in Table 9.
The Onion Diagram can be found in Appendix E.
Stakeholder Role Benefits

Dermatologists Operational - Normal Makes use of the tool built
for skin cancer screening.
Maintenance Operator Operational – Maintenance Monitors and maintains the
system.
Patient Functional Beneficiary Get a skin cancer screening
to know if they have any
form of skin cancer.
Dermatologist Functional Beneficiary Wants to identify if the
patient is at risk of any form
of skin cancer.
Hospital Social Beneficiary Able to perform more tests.
Project Manager Managerial Beneficiary Looks over the project to
ensure that the project is
being carried out properly
to accomplish successful
completion.
Researcher Intellectual Beneficiary Research about the system
for development.
52
Developer Functional Beneficiary Develop the system based

on the findings by the
researcher.
Investor Financial Beneficiary Invests on the platform to
further advance the
development, marketing
etc.
Medical Experts Expert Decides whether the tool
meets a set of requirements
and performs well enough
for real world use.
Hospitals Operational - Maintenance Deploy the Skin
lesion/cancer screening tool
for use by dermatologists.
System Administrator Operational - Deploy the model in
Administration production environment.
Technical Writer Operational - Support Prepare documentation for
the deployed system.
Public Regulatory Provides feedback about
the implemented
application.
Competitor Negative Stakeholder Develops a tool that
addresses the defects and
limitations of the current
tool.
Supervisor Advisory Guides the research and
development.
Table 9 Stakeholders, their roles and how they benefit from the proposed tool.
53
5.3. Requirements Elicitation Methodologies

Requirements Elicitation is an important step in the development of a system. Several
methodologies exist to gather requirements based on the research paradigm chosen. The
different research methodologies have been explored below.
5.3.1. Observing Existing Systems

The initial step is requirements gathering is to identify the systems similar to the proposed
systems and learn how they function. This allows to identify how such similar systems
work and they can be analysed to find their advantages and limitations.
Advantage Disadvantage
The core features and the limitations of a Time taken to analyse all the systems is
skin cancer screening tool can be really high.
identified.
Table 10 Analysis of requirements elicitation by Observing existing systems.
Result: The existing commercial tools do not make use of deep learning and are mainly
based on clinical algorithms. Although the reported accuracy is good, deep learning
approaches can improve the accuracy further. Existing researches have explored the use of
deep learning but have dataset limitations and lack hyperparameter tuning.
5.3.2. Questionnaire
Questionnaires were prepared and were emailed to Dermatologists and Doctors. The
chosen individuals are a very small group as such domain experts are hard to come by.
Advantages Disadvantage
Minimal effort and time when compared The honesty of the respondent cannot be
with other elicitation methods. guaranteed.
Easy to obtain insights from the data. Smaller audience reach if the audience are
a very specific group.
No geographical barriers.
Table 11 Analysis of requirements elicitation by distributing Questionnaires.
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Result: Dermatologists considered that the system will be useful if made a reality can
indeed aid in the skin cancer screening process. This step was considered to elicit
requirements to gather requirements that turned out to be very useful for this research.
5.3.3. Brainstorming
Brainstorming sessions were carried out in the project initiation phase to define the problem
and propose a solution to the identified problem. This method goes along with observing
existing systems to identify the problem. Brainstorming helps to identify a variety of
requirements at each session, which can also be considered a disadvantage at times.
Ability to identify novel requirements that Contradicting requirements at each
may not have been considered by other brainstorming sessions.
researchers and existing systems.
Table 12 Analysis of requirements elicitation by Brainstorming.
Result: A lot of the decisions made in this research were based on brainstorming sessions.
This turned out to be very useful as several decision had to be made during the research
and quick brainstorming sessions made this possible.
5.3.4. Literature Review

One of the most commonly used requirements elicitation methodologies. Literature review
was performed on the domain, existing researches carried out and technologies to gather
requirements.
Provides the opportunity to identify well Very time consuming and needs to be
documented, critically evaluated performed throughout the project.
advantage and limitations of existing skin
cancer screening tools.
Table 13 Analysis of requirements elicitation by Literature review.
Result: Another main contribution to the requirements identified in this research is the
Literature Review. The several decisions that were taken and requirements identified have
been explored in the Literature Review chapter.
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5.4. Questionnaire Findings

Although questionnaires help reach a larger audience, considering the need for specialized
experts, only a small group of audience were reached with the help of questionnaires. The
questions and the results that was observed are listed in the table below, Table 8.
The questionnaire used to gather requirements can be found in Appendix F.
Question Result
1. Is the
examination
and
identification
of skin cancer
from
Based on the results, it was concluded that the examination process is
dermoscopy
not very time consuming as the majority of the respondents have
image time
mentioned.
consuming?
2. Does the
examination
and
identification
process require
a certain level
It can be concluded that the examination and identification process
of experience
does indeed require a certain level of experience to be carried out
for accurate
successfully.
identification?
3. Will an
automated tool
that can
examine and
identify the
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type of skin All the interviewees consider such a tool to be useful as it can ease the
cancer from identification process.
dermoscopy Objective: 2,3,4
image be
useful in the
screening
process?
4. Is it important
to be able to
interpret the
results
obtained from
the tool?
The interpretation was considered important but when used my expert
dermatologists, this will not be of much necessity due to their
experience.
Objective: 6
5. What are the
most important
types of skin
lesions out of
the list of skin
Melanoma and Squamous Cell Carcinoma was considered the most
lesions?
important as they are malignant.
Objective: 1
6. How likely is it
for such a tool
to attract the
interests of
dermatologists The interviewees consider this tool to be very useful in the prognosis
for use in the and are highly likely to use.
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screening Objective(s): 5
process?
7. What is your The results for this question can be found in the Appendix.
opinion on this
tool that The respondents feel that such a tool can aid in the prognosis. One
utilizes the respondent also claims that such a tool can help avert unnecessary
advances in invasive biopsies.
Artificial Objective(s): 4, 5
Intelligence for
medical
imaging?
Table 14 Findings of the Interviews.
Although questionnaires were distributed, only a small number of domain experts were
reached. This is due to the importance of only distributing the questionnaires to domain
experts, dermatologists in case of this research. Dermatologists are hard to come by and
therefore, only a few of them were reached and requirements were gathered from them.
5.5. Functional & Non-Functional Requirements

The system requirements that have been identified are listed below with their priority
levels. The prioritization is important to ensure that more focus is directed towards the
functionalities that have higher priority.
5.5.1. Functional Requirements

FR # Requirement and Description Priority
01 Upload Image High
Upload a dermoscopy to get predictions on.
02 Preprocess Image High
Carry out the required preprocessing steps to prepare the uploaded
image.
03 Segment Image High
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Segment the image so that the ROI is extracted from the image. The
image can then be fed to classifier as the classifier can focus on the
ROI.
04 Classify Image High
Classify the image into one of the several skin diseases that the tool
is capable of identifying.
05 Reason the prediction. High
Based on the image uploaded, identify the regions that correspond
to the classification and display this information.
06 Create and Manage Patients Medium
Create patients so that images can be uploaded under each patient.
This way keeping records of the images and classification can be
easier.
07 Provide technical information Low
Allow the user to access details about the steps involved in the
model building and the results. Ex:- Segmentation accuracy,
Classification accuracy.
08 Results of Training Medium
Provide extensive details of the training process including
visualizations. Make the final model accessible to be downloaded
and used later.
Table 15 Functional Requirements of the Proposed System and Algorithm.
5.5.2. Non-Functional Requirements

5.5.2.1. High Accuracy, Precision, Recall and Intersection Over Union
It is important for the tool to perform really well with results being very useable. Health
informatics tools should have a high accuracy for them to be more reliable. Metrics used
for Segmentation was Intersection Over Union and Dice Coefficient. The F1-Score and
Accuracy is used to measure how well the Image classifier performs. Health informatics
tools should have a high recall, but precision is also important. Therefore, F1-Score was
chosen.
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5.5.2.2. Usability
The usability of the application is very important. The dermatologists should be able to use
the tool with ease. A lot of the complexities involved in the manual screening process are
negated by using an automated approach. Also, the UI of the tool is also required to be very
simple to make it easier for a dermatologist to use it in the screening process.
5.5.2.3. Interpretability
Interpretability of the results is an important aspect. This allows the dermatologists to
understand how and why the predictions made by the tool were made. Being able to
interpret the results allows dermatologists to place their trust on such an automated system
more. Basic Interpretation of the predictions is part of the research.
5.5.2.4. Performance
The performance of the application can be optimized to ensure that the time taken to load
models can be minimized by carrying out certain operations. The predictions need to be
obtained as quick as possible. The optimization of the optimization algorithm is important
such that the algorithm provides quick results.
NFR # Requirement and Description Priority

01 Accuracy of the predictions. High
The accuracy of the predictions made by both the segmentation
and the classification model is very important.
02 An easy to use UI.
To allow for better usability, a very simple UI should be Medium
implemented.
03 Interpretability of predictions. High
The predictions made should be interpretable. Basic interpretation
via visualization should be provided.
04 Performance of application. Medium
The models should be loaded quickly and predictions from the
models should be obtained as quick as possible. The optimization
algorithm should be capable of exploring the search space quickly.
Table 16 Non-Functional Requirements of the Proposed System and Algorithm.
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5.5. Use Case Diagrams
Figure 2 High level use case diagram.
Figure 2 shows a high-level overview of the proposed system. The users of the system,
dermatologists/doctors, may create a new account or access their existing account. Patient
records can be maintained without their personal information. The images uploaded are
patient specific. The uploaded images are preprocessed, segmented, and then classified.
The predictions and visual reasoning for the predictions are saved for each patient.
Use Case Classify Image

Actor(s) Dermatologist, AutoSkreenr
Description
The use case allows the dermatologist to upload an image an obtain predictions on the
image.
Included Use Cases Upload Image, Preprocess Image, Segment
Image, Classify Image, Reason Prediction
Extended Use Cases None
Preconditions
1. Application should be up and running.
2. The dermatologist should be logged in.
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3. The dermatologist should have picked a patient.

Main Flow
1. The dermatologist uploads an image.
2. The image is preprocessed, applying all the preprocessing steps.
3. The segmentation model is loaded.
4. The image mask is generated using the segmentation model.
5. The mask is applied to the uploaded image.
6. The classification model is loaded.
7. The mask applied processed image is classified using the classification model.
8. Reasoning for the obtained prediction is obtained and visualized.
Alternate Flow
None
Exception
1. At Step 1 if Image upload fails, error message is displayed and the execution
ceases.
2. At step 2 if the Image preprocessing fails, error message is displayed and
execution ceases.
3. At step 3 if the segmentation model is unavailable, error message is displayed
and execution ceases.
4. At step 3 if the segmentation fails, error message is displayed and execution
ceases.
5. At step 5 if classification model is unavailable, error message is displayed and
stops.
6. At step 6 if prediction reasoning fails, error message is displayed and execution
stops.
Postconditions
The images (uploaded, preprocessed, mask, segmented and reasoning visualized) are
saved to file storage and the predictions are saved to database.
Table 17 Use case for description for Classify Image.
Use Case Description for Process Image has been added to Appendix G.
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Chapter 6: Design
This chapter discusses the design decisions that was made in developing the proposed
system. The important diagrams that provides an idea of the application have been
explored. The decisions made in the diagrams have also been discussed in this chapter.
6.2. Design Goals

The design goals were chosen to ensure that the application performs as expected. The
following design goals were taken into consideration. Table 18 lists all the design goals.
Goal Description
Correctness It is important for the system to be able to predict the skin disease in
the image very accurately. The system should therefore have a high
accuracy for the system to be usable.
Performance The performance of the tool is very important. The time taken to
produce one result should be as little as possible as the tool will
potentially be used in labs to aid dermatologists in carrying out the
screening process at a faster pace.
Reusability The code should be written in a reusable manner such that based on
newer requirements, the application can be easily modified and
extended. The components in the application should be usable.
Adaptability The application should have the ability to adapt to any new changes
made to the core models such as the segmentation and classification
model.
Table 18 Design Goal intended to achieve via this research.
6.2. High Level System Architecture

For the purpose of this research, a multi-tier architecture has been chosen. A multi-tier
architecture is a client-server architecture in which the application layer, logic layer and
data layer are all physically separated. The post common form of n-tier architecture that is
used is the three-tier architecture (Manuel and AlGhamdi, 2003). The proposed system
follows a three-tier architecture.
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The components of the application are separated to allow for modularity, maintainability,
and extensibility. The contribution of the research mainly lies in the logic tier in a specific
module.
Figure 3 High Level Architecture diagram of the proposed system.
6.3. Class Diagram

The class diagram describes the important classes that will be present as part of the
AutoSkreenr tool to aid the functionalities present in the tool. Previously, decision was
made to use the Object-Oriented Design methodology to design the system. Therefore, a
class diagram was drawn to identify all the classes in the system and their relationship. The
class diagram is shown in Figure 4.
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Figure 4 Class Diagram for the proposed solution.
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6.4. Sequence Diagram
Figure 5 Sequence Diagram for Classify Image Use Case
Figure 5 shows the Sequence diagram for the Classify Image Use Case where an image is
input by the dermatologist and is classified into one of the skin cancers that the
AutoSkreenr tool is capable of classifying. The sequence begins with the dermatologist
uploading a dermoscopic image. The file is validated to ensure that it is in the correct
format and it is then preprocessed, segmented and then classification is carried out using
the image. Based on the predictions obtained, reasonings for the predictions are
determined. The predictions and the reasoning for the prediction are then visualized to the
dermatologist to make better and informed decisions.
Sequence diagram for the Preprocess Image Use Case can be found in Appendix H. An
image is uploaded, resized, enhanced by carrying out enhancement techniques such as
contrast enhancement and removal of artefacts in the image such as hair and ruler. Upon
completion of preprocessing the images are saved to be accessed later when required.
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6.5. Activity Diagram

Activity diagram shows all of the activities that occur to complete the core functionality in
the proposed system. It is a graphical representation of workflows of stepwise activities
and actions. Figure 6 shows the Activity diagram of the proposed system.
Figure 6 Activity diagram of the proposed system.
The above activity diagram beings with the dermatologist logging into the system to begin
the classification on dermoscopic images. The system uses the already trained models to
carry out tasks such as segmentation and classification. These models need to be loaded
onto the system to successfully complete the respective tasks. After the predictions are
obtained on the image fed by the dermatologist and reasonings have been produced for
prediction and visualized on the front-end.
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6.6. Flowcharts
The two most important algorithms explored in this research are the Genetic Algorithm
and Whale Optimization Algorithm. The algorithms are used for architecture search. The
flowcharts below show the theoretical implementation as a pseudocode.
6.6.1. Genetic Algorithm
Figure 7 Vanilla Genetic Algorithm
Figure 7 represents a Flowchart of the Genetic Algorithm used in this research. Genetic
Algorithm (GA) belongs to a class of algorithms known as Evolutionary Algorithms (EA).
They are a heuristic algorithm that follows the concept of evolution and therefore is a nature
inspired algorithm. The algorithm has to important phases to it that aids in finding the
optimum parameters that are optimized. The two important phases are crossover and
mutation where mutation is the random change in the parameter values. Therefore, the
algorithm is known a random-based classical evolutionary algorithm.
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6.6.2. Coyote Optimization Algorithm (COA)
Figure 8 Coyote Optimization Algorithm
Figure 8 represents a Flowchart of the Coyote Optimization Algorithm (COA) used in this
research. It is a meta-heuristic algorithm inspired social organization and adaptation to
environment of Coyotes.
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6.7. E.R. Diagram
Figure 9 ER Diagram for the Web Application Database
The ER Diagram, Figure 9, is used to describe the tables in the application. The Web
Application stores some data about the patient, the images uploaded, and all the predictions
made by the application are also stored in the database. This was decided to allow for the
dermatologists to be able to retrieve all the predictions that were made previously. The
application also allows the dermatologists to annotate the anatomic site for each image.
This can be useful for a data collection process. Also, the dermatologist is allowed to mark
if a prediction is valid for not allowing for data collection for future researches.

The design goals that should be achieved through the system design approaches have been
discussed. High-level and low-level designs have both been discussed. All the different
low-level diagrams such as the class, sequence, activity, and ER diagram have been
discussed in the chapter. The next chapter focuses on the implementation of AutoSkreenr.
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Chapter 7: Implementation
This chapter discusses the implementation of the proposed system for automatic skin
cancer screening. The different decisions that was in terms of the different parts of the
implementation are described in this chapter. The code snippets of the important parts of
the system have been presented along with the explanation.
7.2. Selection of Tools

The tools and technologies required to successfully complete the project should be chosen
intelligently to suit the requirements of the project. The end product of the research is a
web application that can be used by dermatologists to make predictions on dermoscopic
images.
7.2.1. Libraries
Deep Learning – Tensorflow, Keras, Segmentation Models.
Preprocessing – Scikit-Image, OpenCV
Augmentation – Augmentor
Other libraries – Pandas, Numpy, Scikit-Learn, Matplotlib
7.2.2. Dataset
The dataset chosen is the ISIC (International Skin Imaging Collaboration) 2019.
ISIC 2018 – Semantic Segmentation

Real Images 2,594
Augmented Images 2,500
Total Images 5,094
ISIC 2019 – Image Classification
Real Images 25,331
Augmented Images 58,200
Total Images 83,531
Types of Skin Lesions Real Images Augmented Images
Melanoma 4,522 6,000
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Melanocytic Nevus 12,875 0

Basal Cell Carcinoma 3,323 7,000
Actinic Keratosis 867 9,000
Benign Keratosis 2,624 8,000
Dermatofibroma 239 9,500
Vascular Lesion 253 9,500
Squamous Cell Carcinoma 628 9,200
Total 25,231 58,200
Table 19 ISIC 2018 and 2019 Dataset Description
7.3. Optimization Algorithm

Hyperparameter Optimization allows to optimize the parameters of an algorithm in hopes
of improving the accuracy of an algorithm. GA and COA are explored in this section.
7.3.1. Hyperparameters Optimized

Table 20 lists the hyperparameters that were chosen for optimization and their ranges.
Hyperparameter Values/Range
Number of Convolutional 1 – 2
Layers
Number of Dense Layers 1–5
Number of Convolution 32 – 256
Filters (Each Conv Layer)
Size of Convolution Filter 1 – 8
(Each Conv Layer)
Activation Function (Each Sigmoid, Tanh, Relu, Swish
Conv Layer)
Max Pooling Layer (After a 1 (True) or (0) False
Conv Layer)
Pool Size (Each Max 2 (Not Tuned)
Pooling Layer)
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Number of Neurons (Each 32 – 256

Dense Layer)
Activation Function (Each Sigmoid, Softmax, Relu, Swish
Dense Layer)
Batch Normalization (After 1 (True) or (0) False
a Dense Layer)
Optimizer SGD, Adam, Adagrad, Adadelta
Learning Rate 0.1,0.01,0.001,0.0005,0.0001,0.00005,0.00001,0.000001
Table 20 Hyperparameters to Tune the Architecture.
7.3.3. Fitness Evaluation

Parameters are randomly sampled initially. It is important to calculate the fitness of the
parameters to determine the best and least performing parameters. The metric used to
evaluate the fitness of the parameters is the accuracy on the test dataset. Each network
trained using chosen parameters was tested on the MNIST dataset. 48,000 Images were
used for training and 12,000 images for validation. An additional 10,000 images were used
for testing. The dataset consists of 28*28 grayscale images and 10 classes (0-9).
7.3.4. Genetic Algorithm (GA)

One of the algorithms chosen for Hyperparameter Optimization is the GA. GA mimics the
theory of evolution by Charles Darwin. Consists of five phases in the optimization process.
7.3.4.1. Hyperparameter Encoding

A direct encoding technique has been used in this research. The hyperparameters are
represented in binary format. The hyperparameters are treated as blocks. The block
representation has been illustrated in Figure 10.
Figure 10 Convolution Dense Block Representation
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Visual Representation of GA Encoding can be found in Appendix I. Each parameter is

represented in the form of several bits. The sum of the bits + 1 will result in the value of
that specific parameter. For parameters such as Optimizer, the sum is the sum of the bits
and this represents the index of an array which contains the values. Each wide rectangle is
treated as a single block (Conv Block, Dense Block, Optimizer and Learning Rate).
7.3.4.2. Population Initialization

Initially the population is sampled randomly within the given search space.
7.3.4.3. Fitness Evaluation

The fitness of each individual is evaluated using a fitness function. The fitness is measured
using the F1-Score metric chosen for evaluation. The probability of an individual being
selected for the next generation is based on the fitness of each individual.
Some of the design choices made for the algorithm are as follows:
1. Selection: Tournament Selection to choose the parents for crossover.

2. Crossover: Single-point Crossover between two randomly chosen solutions.
3. Mutation: Random Mutation of individual hyperparameters.
4. Elitism: A percentage of the population is chosen based on their fitness. Ex:- 20%
of the population is chosen. This should include the best performing solutions only.
5. Variable Population: This concept is considerably new to Hyperparameter
Optimization using GA. To the fixed population size n at each generation, an
additional k randomly sampled solutions from the search space are added. The size
of the population at each generation will be k+n. For the next generation only n
samples will be chosen and again k new randomly sampled solutions will be added.
Figure 11 Single-Point Crossover
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Figure 11 shows Single Point crossover technique where two parents cross at the crossover
point to produce two offspring by splitting the parents into two at one point.
7.3.4.4. Results
Table 21 presents the list of values for the parameters of the Genetic Algorithm that was
used to tune the parameters of the model that was built on the MNIST dataset.
Parameter Value
Population Size 10
Number of Generations 10
Population Variance 2
Elite Percent 20%
Competitiveness 40%
Mutation Probability 20%
Table 21 Parameters that manipulated the Genetic Algorithm optimization.
Results of hyperparameter tuning is shown in Table 22. 5 different experiments were

carried out to identify the optimal hyperparameters. The results of the algorithm were
consistent across all experiments with an accuracy over 90%.
Experiment Number Highest Fitness Value

1 94.1100001335144
2 97.2800016403198
3 96.2100028991699
4 97.4399983882904
5 95.9832218536285
Table 22 Results of carrying on the hyperparameter tuning on the MNIST dataset.
7.3.5. Coyote Optimization Algorithm (COA)

Coyote Optimization Algorithm is also a bio-inspired algorithm meta-heuristic algorithm.
The algorithm mimics the social organization of coyotes and its adaptation to the
environment. The algorithm unlike other similar algorithm balances the exploration and
exploitation.
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7.3.5.1. Hyperparameter Encoding

A simpler encoding method was used for COA. The following figure represents the
hyperparameter encoding method used for COA. The numbers are directly encoded into an
array. The implementation of COA is such that all Convolutional Layers have the same
properties as the very first layer and all Dense Layers have the same properties as well.
This needs to be further improved to allow for variation in each layer. The encoding
technique for COA can be found in Appendix J.
7.3.5.2. Fitness Evaluation

The fitness function used to evaluate the COA solutions is to build the CNN model
proposed by the algorithm and measure the F1-Score for the produced model.
7.3.5.3. Results
Table 23 presents the list of values for the parameters for the COA that was used to tune
parameters of the model that was built on the MNIST dataset.
Parameter Value
Number of Packs 3
Size of Pack 5
Number of Evaluations 10
Number of Experiments 1
Table 23 Parameters that manipulated the Coyote Optimization Algorithm.
Results of hyperparameter tuning is shown in Table 24. 5 different experiments were

carried out to identify the optimal hyperparameters. The results of the algorithm were
consistent across all experiments with an accuracy over 80%.
Experiment Number Highest Fitness Value

1 93.5107008388144
2 87.8542097431358
3 92.1957593758937
4 79.7589187483714
5 80.8382783931563
Table 24 Results of carrying on the hyperparameter tuning on the MNIST dataset.
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Based on the results of the two Optimization Algorithms, GA and COA, on the MNIST
dataset, GA was chosen to carry out hyperparameter optimization to build the classifier for
skin cancer classification. The choice was made based on the highest value produced and
the consistency of the results produced by the algorithm.
7.3. Model Building

Models have been built for both Segmentation and classification. For segmentation, the
below mentioned preprocessing steps were carried out to build the model. Also, whenever
an image is fed to segment, the image should follow the below explored preprocessing
steps.
For classification, two experiments were carried out to compare the effectiveness of
preprocessing. Experiment 1 involves all the preprocessing steps for the classification
dataset and Segmentation was applied. Augmentation was also used. Experiment 2 does
not involve all the preprocessing steps and only image scaling was performed for the
classification dataset and Segmentation was applied. Augmented was also used.
7.3.1. Preprocessing
Images are preprocessed both during the model building phase and when an image is
uploaded to the app. Experiment 1 involves all of the below mentioned preprocessing step
while Experiment 1 only involves Image Scaling.
7.3.1.1. Image Scaling

Images are scaled down as full-res images require more computational power to train
models with. Also, the dataset contains images of various sizes and therefore it is important
to streamline the size of the image. The images were resized to 256*256 from its initial
size - box resolution.
7.3.1.2. Contrast Enhancement

Contrast Enhancement allows to accentuate the border between the skin and a lesion
allowing to distinguish between them very easily. This improves both classification and
segmentation. Contrast Limited Adaptive Histogram Equalization (CLAHE) is a widely
used Non-Linear Contrast Enhancement in medical imaging problems. This was also used
in this research.
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Figure 12 Original Image of Skin Lesion Figure 13 Contrast Enhancement of Image
7.3.1.3. Color Space Transformation

When the images are loaded, they are in the RGB Color Space which represents more
colors. Therefore, the color space is transformed to LAB color space as it has less colors
represented making all the preceding tasks easier. Contrast Enhancement is carried out in
this color space and the image is reverted back to the RGB color space towards the end.
7.3.1.4. Artifact Removal

Artefacts in the images in both the classification and segmentation datasets were removed.
Morphological closing was performed on the image using the OpenCV python library. A
mask of the image was generated first which was then used to identify the hair artifacts on
the image. Inpainting was used to paint the areas containing hair.
Figure 14 Original Image - Not Preprocessed

Figure 15 Preprocessed Image - Post Artifact Removal
7.3.2. Augmentation
Both ISIC 2018 and 2019 datasets were augmented as seen in Table 19. Augmentation
applied on the ISIC 2019 dataset was to address the class imbalances. Traditional
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Augmentation techniques were applied using the Augmentor library for Python. The
following Augmentation techniques were applied: Rotation, Flipping, Random Zoom,
Gaussian Distortion and Random Distortion, Random Brightness, Contrast and Color.
Figure below shows all the preprocessing steps involved in preprocessing an image.
Figure 16 Preprocessing of a Single Image Function
7.3.3. Semantic Segmentation

Semantic Segmentation was used to segment the images, extracting the Region of Interest
(ROI) from an image. The ROI in a skin cancer image is the lesion in the image.
Segmenting allows the classifier to focus on the cancer and could possibly improve the
classification accuracy. All the images used for Semantic segmentation were preprocessed
to ensure that the lesion/cancer and the surrounding skin are properly distinguishable for
the model.
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7.3.3.1. UNet Architecture

The chosen U-Net architecture is illustrated in Figure 23. The architecture contains two
paths: encoder and decoder. The encoder is the feature extractor which captures the context
of the image. This path consists of Convolutional layers. The decoder is the expanding path
which generates the binary mask for the image and consists of the Transposing
Convolutional Layers. As the backbone of the architecture, EfficientNetB3 was used. The
python library, efficientnet was used to implement the segmentation network. The
architecture used in the research resembles the architecture shown in the diagram but has
variations due to the EfficientNetB3 backbone that was used. Transfer Learning was used
to train the segmentation network with weights transferred from the ImageNet dataset.
Figure 17 UNet Architecture described
Parameter Value
Epochs 60
Batch Size 8
Validation Split 0.2
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Optimizer Adam
Learning Rate 0.001 (Default)
Figure 18 Hyperparameters of the UNet - EfficientNetB3 Model
7.3.3.2. Metrics
Dice Coefficient and Jaccard Index/Intersection Over Union (IoU) are commonly used
metrics for evaluation of segmentation models. Therefore, these metrics were chosen for
this research.
7.3.3.3. Implementation
The segmentation_models library was used. The library provides a UNet implementation
using Keras with Tensorflow as the backend. The library allows to pick the feature
extractor and as mentioned earlier, the EfficientNetB3 backbone was chosen.
Figure 19 UNet Model Define with EfficientNetB3 Feature Extractor
Figure 20 UNet Model Compile with Optimizer, Loss Function and Metrics
Figure 21 UNet Model Training with Callback to save weights if any improvement
The dataset for Segmentation was split using the Holdout method. The dataset was split
into train, test and validation using the train_test_split() method provided by the Scikit
Learn library. The splitting are as follows: Train – 70%, Validation – 20%, and Hold-
Out – 10%. The training and validation set contains augmented data. Segmentation model
was used to create masks for the images in the ISIC 2019 dataset. The masks were then
applied on those images.
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Figure 22 Semantic Segmentation Results – ISIC 2019
7.3.3.4. Segment Classification Dataset

The classification dataset was then segmented using the trained segmentation model. It is
important to have the classification dataset preprocessed before this step. The augmented
and original data was all fed to the segmentation model to predict the mask for each of the
image. The mask was then improvised/smoothened/enhanced using the algorithm in
Figure 23 and applied on the image and saved back so that it can be used for training the
model.
Figure 23 Enhance the Mask and Apply on original image.
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Figure 24 Preprocessed Figure 25 Generated Figure 26 Mask applied Figure 27 Visual

Image – ISIC 2019 Mask – ISIC 2019 on preprocessed image. Reasoning – ISIC 2019
7.3.4. Classification
Classification was carried out as two experiments with different steps explored.
Experiment 1 explores the use of segmentation and preprocessing whereas Experiment 2
explores not using the two steps. Both experiments involve hyperparameter optimization.
Steps Experiment 1 Experiment 2

Preprocessing Yes No (only resize and
normalization).
Augmentation Yes Yes
Segmentation Yes Yes
Hyperparameter Tuning Yes Yes
Table 25 Summary of steps involved in Experiment 1 and 2.
7.3.4.1. Training Approach

Transfer Learning approach was used to train the CNN. Further fine-tuning was also
carried out. This was decided based on the research findings. The dataset was split into
train and test where the model was trained on the train dataset and validated and tested on
the test dataset.
7.3.4.2. CNN Architectures

SOTA architectures were chosen for the purpose of this research. Two pretrained models
were used: VGG-16 and DenseNet101.
Architecture Accuracy Precision Recall F1-Score

DenseNet101 Training Results
56.59% 70.34% 41.6% 50.96%
Test Results
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56.77% 64.63% 50.30% 56.43%

VGG16 Training Results
50.43% 58.11% 43.14% 48.93%
Test Results
59.99% 66.88% 54.42% 59.88%
Table 26 Performance of all the models tried out.
The performance on the Train and Test set was measured and used to identify the best
model. The architectures were trained for 5 epochs and evaluated on the test set using the
F1-Score. VGG16 was chosen as it had a high F1-Score on the Hold-Out set.
7.3.4.3. Hyperparameter Optimization

Hyperparameter Optimization was carried out to improve the accuracy. Hyperparameter
optimization was applied on top of the pretrained models. Parameters optimized:
Hyperparameter Values/Range
Activation Function Tanh, softmax, sigmoid, relu
Optimizer SGD, Adam, Adagrad, Adadelta
Learning Rate 0.1,0.01,0.001,0.0005,0.0001,0.00005,0.00001,0.000001
Number of Layers (Dense) 1 to 3
Number of Neurons Per 32 - 256
Layer
Table 27 Hyperparameters optimized and the search space.
Hyperparameter tuning was performed on top of the pretrained models to add further dense
layers to improve classification. The optimizer and learning rate were also optimized. GA
parameters:
Population Size 5
Population Variance 2
Number of Generations 5
Fitness Metric F1 Score
Elite Percentage 0.2
Mutation Probability 0.2
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Competitiveness 0.4
Epochs 1
Batch Size 8
Table 28 Parameters and Values of Genetic Algorithm
Parameter Value
Number of Dense Layers 2
Number of Neurons for Each Layer 64, 8 (Output Layer)
Batch Normalization for Each Layer Yes, No
Activation Function of Each Layer ReLU, ReLU, Softmax
Optimizer SGD
Learning Rate 0.00005
F1-Score 55.63%
Table 29 Values obtain for parameters upon hyperparameter tuning completion.
Table 24 shows the list of hyperparameters obtained as the best set of hyperparameters to
train the model. VGG16 was then trained for 30 Epochs with a Batch Size of 32.
7.4. Web Application

The web application allows a dermatologist to create and maintain records of multiple
patients and also obtain predictions for the dermoscopic images.
7.4.1. Add New Patient

The dermatologist may add as many patients as required into the application.
Table 30 Web App code to add a new patient to the database.
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7.4.2. View Patient

Each patient can be viewed individually. Images uploaded for each patient and the
predictions obtained for each of the Image uploaded can be viewed with anatomic site
annotated.
Table 31 Web App code to view a single patient with all the predictions.
7.4.3. Obtain Prediction

Dermatologist uploads a dermoscopic image which is processed, segmented, and then
predictions are made on it. Also required to input the anatomic site of the lesion for
annotation purposes. Screenshot of code added in Appendix K.
7.4.4. Validate Prediction

The prediction is validated manually by the dermatologist. The dermatologist may mark
the prediction as valid or invalid once the prediction has been confirmed via further tests.
Table 32 Web App code to validate a prediction made via the application.

The implementation of the prototype has been discussed in this chapter. The technology
choices such as the programming language and library choices have been provided in this
chapter. The implementation of the core functionalities has been discussed next. Finally,
the problems faced during the implementation were discussed.
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Chapter 8. Testing
Testing is carried out to verify if the application works in the intended manner and to
identify any bugs in the application. This chapter focuses on testing all the functional and
non-functional requirements of the implementation. All the implemented algorithms and
functionalities have been tested to ensure that they perform as intended to accomplish the
requirements successfully.
8.2. Objectives & Goals

The implemented software and algorithms are tested to ensure that they perform as
intended to accomplish the required tasks successfully. The main objectives for testing the
Automated Skin Cancer Screening Tool, AutoSkreenr are:
1. To validate and verify the functional and non-functional requirements of the

Automated Skin Cancer Screening Tool.
2. To validate and verify that the optimization algorithms function as they are intended
to.
3. To identify defects in the implemented application and algorithms to minimize the
repercussions of the identified defects.
4. To further improve the functionalities of the implemented application and
algorithms based on the test results.
8.3. Testing Criteria

Multiple testing approaches were carried out to thoroughly test the implemented
application to identify all defects and to ensure that all the requirements were met.
1. Functional Requirement Testing

a. Black Box Testing
b. White Box Testing
c. Integration Testing
2. Non-Functional Requirement Testing
3. Benchmarking
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8.3.1. Black Box Testing

Component Test Case Expected Real Output Status
Output
Upload Image Image uploaded to the Image Saved. Image Saved. Pass
application should be saved.
Preprocessing Input image should be Preprocessed Preprocessed Pass
preprocessed. Image. Image.
Augmentation Given the dataset, Augmented Augmented Pass
traditional augmentation images Images
should be applied to generated and generated and
generate synthetic images. saved. saved.
Segmentation Predict the mask and apply Predicted Predicted Pass
on the image and save both. mask applied mask applied
on the image. on the image.
Optimization Given a parameter list with Parameters Parameters Pass
boundaries, search for the with the with the
optimal parameters and evaluation evaluation
present evaluation results. results. results.
Classification Given the segmented image, Highest Highest Pass
the classifier should predict probability probability
the class of the image and disease and disease and
present it. Probability for Probability
each disease. for each
disease.
Reasoning Given the image and Area of the Area of the Pass
classifier, generate visual image that image that
reasoning. corresponds to corresponds
the prediction. to the
prediction.
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Patient Create Provide details of the patient Patient added Patient added Pass
and create a new patient and to the db and to the db and
add to the application. shown in the shown in the
list of patients. list of patients.
Patient View List all patients created by All patients All patients Pass
the logged in user. created by the created by the
user are listed. user are listed.
Single Patient List all images uploaded All images All images Pass
View with the predictions for each uploaded for uploaded for
image. patient and patient and
predictions predictions
made. made.
Validate Confirm if the prediction The prediction The Pass
Prediction made by the tool is valid or validity prediction
not and save to database. updated in validity
database. updated in
database.
Information Provide the user with Information Information Pass
information related to the related to related to
training process. model model
building building
displayed. displayed.
Table 33 Black Box Test Cases, Expected and Actual Outputs and the status of each test case.
8.3.2. White Box Testing

Component Test Case Expected Actual Output Status
Output
Preprocess Input image should be Resized, Resized, Pass
Image resized to 256*256, Contrast Contrast
converted to LAB Color Enhanced, Enhanced,
Space, Contrast Artefact Artefact
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Enhanced and artefacts Removed Removed

removed. Image. Image.
Image Normalizing image - Array of pixel Array of pixel Pass
Normalization convert the range of values in range values in range
values from 0 to 255 to 0 0 to 1. 0 to 1.
to 1.
Obtain Mask Segmentation model Prediction – Prediction – Pass
predicts on the Array of Pixel Array of Pixel
preprocessed image. values. Mask. values. Mask.
Save Array of Pixel values of Array of pixel Array of pixel Pass
Prediction as the mask is saved as an values saved as values saved as
Image image. an image. an image.
Apply Mask Load mask generated for Image with Image with Pass
actual image and apply on mask applied. mask applied.
the image.
Classify Feed segmented image to Array of Array of Pass
classifier model and probability probability
obtain probabilities values for each values for each
predicted. of the classes. of the classes.
Final Highest probability class Highest Highest Pass
Prediction is chosen as the final probability Probability
prediction. class returned. class returned.
Reasoning Given the classifier and Regions of Regions of Pass
preprocessed image, image that image that
generate visual reasoning corresponds to corresponds to
for the image. the prediction the prediction
visible. visible.
Save Image Image and anatomic Data saved in Data saved in Pass
and Anatomic location of the image database and database and
Location. input. Image and data files. files.
saved in database.
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Save new Details of patients input Input details Input details Pass
patient. and saved to the database. saved to the saved to the
database. database.
List all List of all patients added All the patients All the patients Pass
patients. by user displayed when added by the added by the
View all patients is user are listed. user are listed.
clicked.
Single Patient Patient details and Patient details Patient details Pass
View. predictions made on and all and all
patient displayed when predictions for predictions for
the patient id is clicked patient patient
on. displayed. displayed.
Prediction as User clicks on the Valid Prediction is set Prediction is set Pass
Valid. button to approve a to valid. to valid.
prediction.
Prediction as User clicks on the invalid Prediction is set Prediction is set Pass
Invalid. button to disapprove a to invalid. to invalid.
prediction.
Obtain Clicking on info retrieves Implementation Implementation Pass
Information. all details about the details details
implementation. displayed. displayed.
Table 34 White Box Test Cases, Expected and Actual Outputs and the status of each test case.
8.3.3. Integration Testing

AutoSkreenr is composed of multiple modules that function together to accomplish a task.
Integration Testing was carried out to ensure that all the individual modules work together
as intended and successfully achieve the main objective.
Module Input Expected Actual Status

Output Output
Preprocessing Upload Image Preprocessed Preprocessed. Pass
Image.
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Augmentation Directory of Images Augmented Augmented Pass

Images via Images via
random random
augmenting augmenting
techniques. techniques.
Segmentation Preprocessed Image Image with Image with Pass
segmentation segmentation
applied. applied.
Classification Preprocessed and Predicted Predicted Pass
Segmented Image Probabilities Probabilities
Web Upload Image Predicted Predicted Pass
Application Probabilities Probabilities
with with
Reasoning Reasoning.
Patient Patient Details Successfully Successfully Pass
Management Created Created
Patient. Patent.
8.4. Non-Functional Requirement Testing

Non-Functional Requirement testing was carried out using statistical methods. Suitable
metrics were used to measure the performance of the models. The following is the list of
metrics used to measure the performance of the built models.
1. Segmentation – Intersection Over Union, Dice Coefficient & Accuracy.

2. Classification – Categorical Accuracy, Precision, Recall and F1-Score.
The metric definitions can be found in Appendix L.
8.4.1. Segmentation
The performance of the segmentation model was measured using the IoU and Dice
Coefficient.
Metric Train Validation Hold-Out

Intersection Over Union 82.65% 79.42% 85.95%
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Dice Coefficient 90.44% 88.30% 91.68%

Figure 28 Statistical test results for the Segmentation Model.
Figure 29 shows a mask image obtained from the segmentation model on the ISIC 2018
dataset and the Ground Truth. Figure 30 shows a mask image predicted for an image in
the ISIC 2019 dataset and its enhanced version – sharpening.
Figure 29 Segmentation model result on an image from Figure 30 Segmentation model result on an image from
ISIC 2018 Dataset. ISIC 2019 Dataset.
The performance of the classifier was measured using the F1-Score and Accuracy.
Experiment Metric Train Test

1 Accuracy 94.93% 76.61%
Precision 96.53% 80.19%
Recall 93.05% 73.35%
F1-Score 94.73% 76.56%
2 Accuracy 95.98% 85.99%
Precision 96.86% 88.05%
Recall 94.72% 84.18%
F1-Score 95.76% 86.04%
Figure 31 Statistical test results for Classification Model.
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Experiment 1 (With Preprocessing & Segmentation)

Train vs Test Accuracy, Loss, Recall ad F1-Score graphs were plot for Experiment 1
model as it seemed to exhibit overfitting. It is quite evident from the plots that the model
is indeed overfitting. This is noticeable from the fluctuations in the test curve.
Figure 32 Model Accuracy - Train vs Validation Figure 33 Model Loss - Train vs Validation
Figure 35 Model Recall - Train vs Validation

Figure 34 Model F1-Score - Train vs Validation
Overfitting was experienced with the Experiment 1 model where heavy preprocessing was
carried out. Therefore, the Train vs Test accuracy, loss and f1-score graphs were compared
to confirm this. The extreme fluctuations in the graphs indicate that the models are indeed
being overfitted.
Figure 36 Model Evaluation - Train Data
Figure 37 Model Evaluation - Test Data
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In figures 36 and 37, he first value is the Loss. The second the accuracy. The third is the
Recall. The fourth is the precision and the fifth is the F1-Score.
8.5. Benchmarking
The performance of the Segmentation and Classification Model on the hold-out set was
compared with some of the existing researches identified in the Literature of this research.
8.5.1. Segmentation
Work compared using the Jaccard Index/Intersection Over Union (IoU). The following
table presents the comparison.
Study IoU/Jaccard Index

Proposed Approach – ISIC 2018 (60 85.65%
Epochs)
Mishra and Daescu, 2017 – ISIC 2017 84.2%
Al-masni et al., 2018 – ISIC 2017 84.79%
Zahangir Alom, Aspiras, M. Taha and K. 88.83%
Asari, 2019 – ISIC 2018 (250 Epochs)
The results show that the proposed approach shows a significant improvement in terms of
performance due to the use of a larger dataset and the SOTA architecture for ImageNet
classification, EfficientNet. More epochs could potentially improve the accuracy further to
match it up with the other best accuracies in the same dataset as the approaches involve the
model being trained for over 250 epochs.
The metric used for comparison is the Categorical Accuracy. The following table presents
the comparison.
Study Accuracy
Proposed Approach (Experiment 2) 85.99%
Eddine Guissous, 2019 (ISIC 2019) 91%
Romero-Lopez et al., 2017 (ISIC 2018) 81.33%
Being trained for only 30 epochs, the results on the ISIC 2019 dataset is good but needs
further improvement as it is not as good as the other researcher’s works.
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8.6. Chapter Conclusion

A summary of the testing carried out on both the Segmentation and Classification model
has been presented in this section. The results have been compared with the work carried
about by other researches in the past.
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Chapter 9. Evaluation
This chapter focuses on what the technical experts and domain experts think about the
various aspects of the implemented system such as the architecture, functionalities,
usability, and performance.
9.2. Evaluation Criteria

The identified evaluation criteria are listed in Table. The selection was carried out with the
intention of covering all major phases that was performed as part of the research project.
Criteria Purpose
Overall Concept and Project Idea To get comments and insights from technical and
domain experts.
Scope and Depth of the Project The scope and depth of the project should be
evaluated by technical experts with knowledge in
Deep Learning.
System Design and Architecture Evaluate if the system design and architectures are
valid and upto latest standards.
Accuracy of the Implementation Evaluate how well the application is performing.
User Friendliness of the Interfaces. The usability of the application based on the user
interfaces provided is evaluated by the domain
experts, dermatologists.
Further Enhancements. Identify what potential improvements can be made
to improve the application further.
Usefulness of Visual Reasoning If the provided visual reasoning is usable.
Usability of GUI User-friendliness of the GUI was evaluated by the
domain experts, dermatologists.
Usability and Opinions The usability of the application in skin cancer
screening and the domain expert opinion.
Figure 38 Evalaution Criteria to evalaute the project.
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9.3. Selection of Evaluators

The evaluation requires both Domain and Technical experts. The Domain Experts are
dermatologists with experience and knowledge in Skin Cancer Screening while the
Technical Experts are required to have knowledge in domains such as Computer Vision,
Classification, Segmentation, CNNs and Hyperparameter Optimization.
9.4. Evaluation Methodology and Approach

A mix-mode approach was used for the evaluation. Quantitative approaches have been
used to test the application and Qualitative approach has been used to evaluate the project.
Questionnaire with open-ended questions was distributed.
9.5. Evaluation of Survey Findings

The responses obtained from distributing questionnaires have been evaluated in this
section. The responses are categorized into each of the identified Criteria.
The Technical and Domain Evaluation forms can be found in Appendix J. The Emails sent
to evaluators to get feedback can be found in Appendix K.
9.5.1. Overall Concept and Project Idea

Evaluator Feedback
Dr. Thushani Dabrera Good concept for a general or family practioner.
Doctor
Dr Dantha Hewage Good Concept
Dermatologist
Dr. Asoka Kamaladasa With the present context where people are more inclined to
Consultant Dermatologist
go for a video consultation of their skin diseases, this would
be very much helpful.
Mrs. Chamodi Adikaram This is an innovative project to reduce the gap between
MSc in Computer Science
specialised in Data Science, deep learning and biomedical science. Author has
Analytics and Engineering at
University of Moratuwa
identified an existing problem and has tried to solve it using
novel techniques such as transfer learning and hyper-
parameter optimisation in the domain of image processing.
Deep learning is often regarded as models with low
interpretability. But by applying model interpretation
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techniques such as LIME, author has been able to go

beyond the classification and give reasons for the
classification, which in my opinion will be truly useful for
the medical persons to make informative decisions.
Mr. Hansa Perera Overall concept will be much valuable for both the patient
Associate Architect – Data
Science and doctors. Considering the current situation of social
distancing this will be ideal to minimize the unwanted
exposure for both patient and the medical officer.
Table 35 Feedback on the overall concept and project idea.
9.5.1.1. Summary
Positive feedback was received in terms of the Project Concept. Technical Experts have
considered the exploration a positive of the project along with the visual reasoning
provided. The domain expert also considers the project to be good, but the users should be
reconsidered as it can be used for remote screening.
9.5.2. Scope and Depth of the Project

Evaluator Feedback
Mr. Hansa Perera For an undergraduate project the scope and depth seems to
Science be above the level even though it is successfully executed.
Mrs. Chamodi Adikaram In my opinion, the selected scope and various experiments
specialised in Data Science, tried out in this research is well above the expected level
for an undergraduate research. Even though author has
selected only CNN for this image classification research, it
shows that he has tried out various preprocessing
techniques, augmentation and optimisation methods on top
of the CNN model he has chosen. Adapting architectures
that have given good performance in previous studies, also
shows that the author has conduct a good analysis of
previous literature.
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9.5.2.1. Summary
The Technical Expert(s) considered that the scope and depth of the project is more than
enough. The exploration of different architectures to carry out the segmentation and
classification was welcome.
9.5.3. System Design and Architecture

Evaluator Feedback
Mr. Hansa Perera For an undergraduate level architecture and system designs
Science are acceptable. As a suggestion, better to follow C4
designing method.
Mrs. Chamodi Adikaram By using the 3-tier architecture, the system has been able
specialised in Data Science, to be modularised which will be useful for future
improvements and implementation on various platforms.
As the business logic layer consists the core of this
research, this architecture gives it the liberty to be plugged
in to any platform without major changes to this
component.
9.5.3.1. Summary
The use of the chosen architecture to separate the different sections of the applications was
considered a positive as it allows for easier maintainability of the application with a
suggestion explore a new type of designing methodology known as the CV4 method.
9.5.4. Accuracy of the Implementation

Evaluator Feedback
Mr. Hansa Perera Accuracy of the models are acceptable and above
Science average for an undergraduate level.
Mrs. Chamodi Adikaram Without merely presenting the results, the fact that author
specialised in Data Science, has compared the significance of his research by comparing
its accuracy values against the accuracy values of baseline
models selected from the previous studies, has contributed
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to the quality of this research. Even though the

segmentation model has been able to outperform previous
research, the classification model accuracy has failed to do
so. It has reached a satisfactory Precision score, but in my
opinion in a biomedical research problem of this nature it
is important to identify the perfect balance between both
recall and precision as their importance can vary depending
on the problem at hand.
9.5.4.1. Summary
The performance of Segmentation was applauded. But the failure to improve the
classification accuracy as much was criticized due to the unsatisfactory recall achieved.
9.5.5. Further Enhancements & Feedback

Evaluator Feedback
Mr. Hansa Perera The method can be extended to identification of any skin
Science malignancy. Also, the same concept can be applied to
blood picture evaluation in Hematology and Pathology
which is highly human intensive and time consuming.
But easily adopt the same concept. For commercial
purposes better to come up with a lightweight mobile app
with camera requirements.
Mrs. Chamodi Adikaram I would suggest working on further improving the recall of
specialised in Data Science, the classification model. I'd propose to try out other suitable
optimisation algorithms on the same dataset that was used
for this research as an optimisation algorithm that works
for one dataset might not work for another. More complex
augmentation methods such as GAN-Based Augmentation,
can be tried out to improve the dataset and reduce the class
imbalance problem.
Dr. Asoka Kamaladasa Advantages of this system for both Doctor and patients
Consultant Dermatologist are, it’s not required to see the patients physically to do
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the initial screening, its saves lot of time and money for
the patient. And doctor will be able to provide initial
diagnosis without physically seeing the patient. High
patient compliance. Disadvantages are wrong diagnosis
can happen due to image quality and competence of
person who takes the picture. High quality images are
very important. And 3D images would be more helpful
for a proper diagnosis. If these images are combined with
the images coming from Dermoscope, diagnosis can be
more accurate.
Dr. Dantha Hewage The patient’s whole body has to be examined in order to
Dermatologist conclude a disease, not just the part with the lesion.
Dr. Thushani Dabrera Good initiative. However, the target audience/recipient
Doctor should be a family/general practitioner.
9.5.5.1. Summary
Overall, a positive feedback with suggestions to explore the possible areas in which the
application can be used. Suggestions to use better augmentation techniques such as GANs
and more suitable optimization algorithm was given. Should reconsider target audience.
9.5.6. Usefulness of the Visual Reasoning

One a scale from to 5, Dr Dantha Hewage considered it to be very useful (5) while Dr.
Thushani Dabrera and Dr. Asoka Kamalada considered it to be moderately useful (4).
9.5.6.1. Summary
It can be concluded that although the visual reasoning was not the center of the research, it
is still considered useful especially, when the practitioner lacks expertise.
9.5.7. Usability of the GUI

Feedback for this was received from Dr. Dantha Hewage and Dr. Thushani Dabrera. The
rating received was 4 on a scale from 1 to 5 where 5 is considered the best. Dr. Asoka
Kamaladasa gave a rating of 5.
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9.5.7.1. Summary
It can be deduced that the application is very usable and therefore, usability has been
successfully achieved.
9.5.8. Usability of the tool in the Screening Process and Opinion on the system
Evaluator Feedback
Dr. Asoka Kamaladasa This could be helpfull in initial screening of skin cancers
Consultant Dermatologist
Dr. Dantha Hewage Could be useful.
Dermatologist
Dr. Thushani Dabrera If it is intended for a consultant dermatologist who is an
Doctor expert in the diagnosis of skin conditions and can
differentiate and diagnose skin cancer at a glance- not
very useful for them. It will be very useful for a general
of family practitioner/OPD doctor.
9.6 Self Evaluation

Self-evaluation of the identified evaluation criteria has been discussed in this section. An
evaluation of the project as a whole has also been provided in this section.
Criteria Self-Evaluation
Overall Concept and Idea The idea of the research was to identify the
effectiveness of the chosen preprocessing steps for
classification and also the effectiveness of
hyperparameter optimization. This has opened newer
paths for future researches. Also, the findings of the
two experiments carried out can also be extended in
future researchers.
Scope and Depth of the Project The initial project scope was defined based on the
project timeline. A combination of several approaches
was required to be tested within the period of time
provided for this project and the resources that was
accessible by the author. Therefore, the scope had to
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be limited to the time and resource availability. The

depth was satisfactorily explored under this scope.
System Design and The use of 3-tier architecture allowed for modularity
Architecture and maintainability in the system and conforms to the
industry standards as the designing and selection of
architecture was carried out based on that. All of the
components that was initially planned to develop and
implement were all implemented.
Accuracy of the These requirements were achieved but can be
Implementation improved further to achieve a much better accuracy,
especially for classification.
Usefulness of Visual The visual reasoning provided is considered useful, but
Reasoning more research needs to be carried out to improve the
reasoning as its current state it is very minimal.
Usability of the GUI A user-friendly GUI was developed for ease of use for
dermatologists as the process shouldn’t be complicated
by a confusing GUI.
Usability of the tool in the The tool can be used in the screening process.
Screening Process Currently it only supports dermoscopy images.
Support from handheld camera images can be added.
Further Enhancements One of the limitations in the project is the lack of
computational resources such as GPU as the training
of the models in the application was a resource
intensive task.
Another limitation is the lack of data in some of the
classes in the dataset. Although this was addressed via
traditional augmentation techniques, more complex
augmentation techniques may also be applied.
Furthermore, collecting real data can improve the
system more rather than augmenting data. Adding
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more diverse data can help generalize the application

for more population.
Figure 39 Self Evaluation of the Project
9.7. Completion Status of Functional Requirements

Priorities – High, Medium, and Low
Completion Status – Implemented or Not Implemented
Requirement Priority Completion Status
Upload Image High Implemented
Preprocess Image High Implemented
Segment Image High Implemented
Classify Image High Implemented
Reason the Prediction High Implemented
Create and Manage Patients Medium Implemented
Provide Technical Low Implemented
Information.
Results of Training Medium Not Implemented
Figure 40 Completion Status of the Functional Requirements of the Project

This chapter discusses the Evaluation Criteria that was chosen to evaluate the project. The
choice of evaluators to evaluate the project have also been discussed to evaluate the project
thoroughly. A choice was made to get the project evaluated by both Domain and Technical
Experts. The Technical Evaluator was chosen to evaluate the different stages of the project
while the Domain Evaluator was chosen to evaluate the concept, the usability and the
outcome of the project. A summary of the evaluation provided by the evaluators have been
provided. Positive feedback was received in most of the aspects of the implemented
solution although one drawback that was identified is the accuracy of the classification as
it should be further improved due to the domain, medical domain. A self-evaluation was
performed concluding the evaluation of the project.
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Chapter 10. Conclusion

The Conclusion of this project is discussed in this chapter. The project aims and objectives
are considered for the completion of the project. How existing skills and content from the
provided courses was utilized, the new skills developed, problems faced, and limitations
of this research will also be discussed in this chapter. The chapter is concluded with the
contribution of this project and concluding remarks.
10.2. Achievement of Aims and Objectives

10.2.1. Aim of this Project
The aim of this research is to design, develop & evaluate a system which should be capable
of carrying out skin cancer screening automatically using dermoscopic images.
The aim of this research was successfully achieved within the given period of time to an
extent as a GA was implemented to design and train CNN architectures automatically. Both
experiments were conducted to compare and identify which experiment performs best. It
was realized that the use of heavy preprocessing does not improve the accuracy but rather
adversely affects the performance of the classification.
10.2.2. Completion of Objectives

Objective Status Evidence
Explore and identify the different image datasets Complete Chapter 2,
available on Skin Lesions/Cancer. Chapter 7
Analyse the different image pre-processing Complete Chapter 2,
techniques that can be applied. Chapter 7
Analyse the different data augmentation techniques Complete Chapter 2,
can be applied. Chapter 7
Analyse the different optimization algorithms that Complete Chapter 2,
exist to build the network architecture to carry out the Chapter 7
disease classification.
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Complete Chapter 7
To compare the use of preprocessing with not using
preprocessing to build a classification model.
Design and develop an interface that can be used Complete Chapter 6,

alongside the screening process to perform the skin Chapter 7
cancer classification.
Analyse the different techniques existing to interpret Complete Chapter 2,
deep learning models to provide reasonings for Chapter 7
prediction.
Table 36 Objectives Completeness
10.3. Utilization of Knowledge from Course Modules

Module Utilization
Software Development Principles I & II Fundamental programming principle
knowledge was gained via this module. A
lot of the basics was covered in this
module. All preceding knowledge were
gained on top of the knowledge gained
from this module.
Object Oriented Programming Object Oriented knowledge was gained via
this module. OOP knowledge was used in
developing the application.
Client-Server Architecture Helped in deciding the architecture for
developing the application. N-tier
architecture was chosen based on the
knowledge gained in this module.
Software Develop Group Project The module introduced Software
Development Projects. Project initiation to
project completion was taught in this
module.
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Database Systems The database knowledge gained from this

module was used to design and use the
database with the application.
Figure 41 Utilizing knowledge from the degree.
10.4. Use of Existing Skills

Skills related to the research project was acquired prior and throughout the degree
programme. These acquired skills helped towards the successful completion of the project.
• The author gained knowledge related to Data Science and Machine Learning during
the Placement Year as the author interned as a Data Scientist, gaining hands-on
experience on Data Science and Machine Learning projects.
• During the placement year, knowledge regarding the Python programming
language was acquired. The knowledge in Python vastly helped in initiating the
project as the knowledge allowed to start work on the project much sooner.
10.5. Learning Outcomes

• Knowledge regarding Machine Learning was acquired during the placement year
but not a lot of knowledge was gained related to Deep Learning. Self-learning had
to be performed to gain knowledge regarding Deep Learning.
• Knowledge regarding hyperparameter optimization was absent and not taught as
part of the BSc program. Therefore, self-learning had to be carried out to acquire
knowledge regarding this area.
• Research skills were developed as part of the project. Research project differs vastly
from an application project and requires more effort and an entirely different
workflow. A lot of research had to be performed to make appropriate decisions and
to gather the required knowledge.
• Problem solving and critical thinking skills were developed and is one of the most
important learning outcome of this project. Formal documentation skills were also
developed as the project required extensive documentation of the work being
carried out.
108
10.6. Problems and Challenges Faced

Problem Description
Lack of Knowledge The author’s lack of knowledge in the area
of Neural Network Architectures and
Hyperparameter Optimization posed a big
challenge as it was highly important for the
successful completion of the project.
Resource Requirements The available resources was not enough in
the beginning and therefore a Virtual
machine was used to address the lack of
resources. Tasks such as Hyperparameter
Optimization of CNNs had to be toned
down by reducing the types of layers and
depth of the architectures searched due to
the resource constraints.
Training was also carried out for a
relatively less number of epochs.
Scope Analysis Although the scope was set and defined,
the skin cancer screening research is vast
and there are a variety of researches that are
being carried out.
Time Constraint Although the initially thought of project
timeline was supposed to fit within the
provided time, due to unavoidable
circumstances, a lot of changes had to be
made resulting in having to work within a
short span of time.
Virus Pandemic The Virus Pandemic affected the
evaluation of the project as meeting people
in person was restricted due to constant
109
curfew impositions. Therefore, receiving

responses for evaluation proved to be very
difficult.
10.7. Research Contribution

1. Genetic Algorithm for Hyperparameter Optimization with Population Variance.
The GA algorithm was used for hyperparameter optimization in this research. The vanilla
GA algorithm was modified to support population variance. This is a concept where in
addition the fixed number of populations, another variable size is attached to the population
where at each generation, completely new solutions are added based on the variable size.
This variable size remains constant throughout all generations. Population variance was
introduced to improve the diversity of the solutions produced by the algorithm.
2. EfficientNetB3 with U-Net Architecture for Dermoscopic Skin Cancer Image

Segmentation.
The application of EfficientNet with the U-Net Architecture has not been explored before
for skin cancer image segmentation. The results from this research shows that the approach
produces promising results. Therefore, further research can be carried out to experiment
with wider EfficientNet architectures such as EfficientNetB7.
3. A Critical Analysis of Computer Aided Approaches for Skin Cancer Screening
This is a review paper published by the author. An analysis of all the different Computer
Aided Approaches that has been carried out by different researchers till date and how they
compare with each other. The limitations of the compared systems have also been
identified and listed.
10.8. Limitations
1. The lack of variation in the dataset used for both segmentation and classification.
It is important to introduce variations such as ethnicity and color. Such variations
can allow the dataset to generalize more towards the general public.
110
2. Reasonings provided by the application is not self-explainable and this needs to be

improved and only then the dermatologist will be able to make use of the provided
explanations.
10.9. Future Enhancements

1. Performing a complete architecture search/hyperparameter optimization on CNNs
to find the most suitable architecture for the problem in hand. Introducing more
types of layers that can give the Optimization algorithm to search for more complex
architectures should be worked on.
2. Using more complex augmentation techniques such as the use of Generative
Adversarial Networks (GANs) for data augmentation should be explored as this
approach could generate more realistic synthetic data and potentially improve the
segmentation and classification accuracy.
10.10 Concluding Remarks

This is the concluding chapter of this thesis where the completion of the aims and
objectives of the project are discussed. How the knowledge gained from the modules that
the author has taken up has also been explored. The new skills that the author has gathered
via carrying out the research and the problems faced during the research have also been
discussed. The limitations of the research and future enhancements that can possibly be
explored by other researchers have also been stated.
111
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Appendices
Appendix A – Conceptual Graph
121
Appendix B – Time Management

Task Start Date End Date Duration
Project Initiation 01/09/2019 20/10/2019 49 Days
Literature Review 06/10/2019 15/04/2019 192 Days
Requirement 14/11/2019 31/12/2019 47 Days
Gathering
Designing the 31/12/2019 30/01/2020 30 Days
System
Selecting Tools and 10/01/2020 15/01/2020 5 Days
Technologies
Developing the 15/01/2020 10/04/2020 87 Days
System
Testing 01/03/2020 10/04/2020 40 Days
Evaluation 10/04/2020 20/04/2020 10 Days
Documentation 31/12/2019 25/04/2020 116 Days
122
Appendix C – Work Breakdown Structure
123
Appendix D – Gantt Chart
124
Appendix E – Onion Diagram
125
Appendix F – SRS Questionnaire
126
Appendix G – Use Case - Process Image

Use Case Preprocess Image
Actor(s) Dermatologist, AutoSkreenr
Description
The use case allows the AutoSkreenr to preprocess an uploaded image.
Included Use Cases None
Extended Use Cases None
Preconditions
1. Application should be up and running.
2. The dermatologist should be logged in.
3. The dermatologist should have picked a patient.
Main Flow
1. The image is uploaded.
2. The image is resized.
3. The image is enhanced.
4. Artefacts in image are removed.
5. The preprocessed image is then saved.
Alternate Flow
None
Exception
1. At step 1 if the uploaded image fails validation, the user is shown an error
message and execution ceases.
2. At any step if the process fails, an error message is displayed and the execution
ceases.
Postconditions
The images preprocessed image is saved.
The next steps in the prediction pipeline in the AutoSkreenr tool are carried out.
127
Appendix H – Sequence Diagram
128
Appendix I – GA Hyperparameter Encoding
Appendix J – COA Hyperparameter Encoding
129
Appendix K – Prediction Function Web App
130
Appendix L – Metric Definitions

Metric Purpose Formula/Representation
Accuracy Used to measure Accuracy = Number of
performance of Correct Predictions / Total
classification and Number of Predictions
segmentation model.
Intersection Over Union Jaccard Coefficient. Used
to evaluate the accuracy of
the segmentation model.
Figure 42 The equation to calculate

Intersection Over Union
Dice Coefficient Finds the similarity Dice score=2*Number of True
between of two data Positives / (2*Number of True

Positives + Number of False
samples. Used with Image
Positives + Number of False
Segmentation performance
Negatives)
measure. Penalized False
Positives.
Precision Positive Predictive Value Precision=True Positives /
(PPV). Measures the (True Positives + False

Positives)
proportion identified by the
model as relevant is
actually relevant.
Classification.
Recall Sensitivty. Measures the Recall=True Positives / (True
proportion of the data Positives + False Negatives)
samples that are actually

relevant but not if it has also
been identified relevant.
Classification.
131
F1-Score Combines both precision F1Score=2*((Precision*Recall)

and recall, bringing a / (Precision+Recall))
balance. Harmonic mean of

precision and recall.
Classification.
Appendix M – Evaluation Forms

Domain Evaluator
132
Technical Evaluator
133
Appendix N – Evaluation Emails

Feedback from Mr. Hansa Perera
Feedback from Mrs. Chamodi Adikaram
Feed from Mrs. Dantha Hewage
Feedback from Dr. Thushani Dabrera
134
Feedback from Dr. Asoka Kamaladasa
135
Appendix O – Published Review Paper
136
137
138
139
140

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Informatics Institute of Technology

Mr. Minoj Selvarasa

Mr. Achala Chathuranga Aponso

Submitted in partial fulfillment of the requirements for the

Full Name of the Student: Minoj Selvarasa

IIT Registration ID: 2016131

UoW Registration ID: w1654542

Deep Learning, CNN, Hyperparameter Tuning, Genetic Algorithm, Coyote Optimization

I would like to extend my gratitude to the management of Informatics Institute of

Conference: International Conference on Image Processing and Robotics, 2020

Venue: Negombo, Sri Lanka

Publication: IEEE Xplore

2.4.3. Machine Learning in Skin Cancer Screening ................................................. 28

5.2. Stakeholder Analysis ............................................................................................. 52

7.3.5. Coyote Optimization Algorithm (COA) ......................................................... 75

9.5.1. Overall Concept and Project Idea ................................................................... 98

Appendix G – Use Case - Process Image ................................................................... 127

A person suspected to have a benign or malignant skin lesion undergoes a screening

1.2. Problem Statement

1.3. Research Question

1.4. Research Aim

1.5. Research Motivation

1.6. Research Objectives

1. To explore and identify the different image datasets available on Skin

2. To analyse the different image pre-processing techniques that can be applied.

1.7. Related Work

1.8. Project Scope

In Scope Out of Scope

Finding a dataset to be used for Including variation in the dataset by

Identifying robust preprocessing steps and Complex architecture components such as

Identifying image augmentation steps and

Identifying suitable algorithms for

Choosing the hyperparameters for

Carry out experiments to compare the

Providing reasons for the prediction based

Table 1 In Scope and Out of Scope

1.9. Rich Picture

Figure 1 Rich Picture

1.10. Resource Requirements

1.10.1. Software Requirements

1.10.2. Hardware Requirements

1.10.3. Data Requirements

1.11. Chapter Summary

Chapter 2: Literature Review

2.2. Conceptual Graph

The Conceptual Graph has been added to Appendix A.

2.3. Domain Justification

2.4. Literature Review of the Domain

2.4.1.1. Unaided Visual Inspection

2.4.1.2. Aided Visual Inspection

2.4.2. Computer Aided Skin Cancer Screening

2.4.3. Machine Learning in Skin Cancer Screening

Researches have been carried out to explore the effectiveness of ML in classifying

2.4.4. Deep Learning in Skin Cancer Screening

Ravichandran, 2016). Classification of segmented dermoscopic images using ANN has

Study Methodology Limitations

Learning and training from • Using a larger dataset

2.4.5. Preprocessing of Skin Cancer Images

2.4.6. Segmentation of Skin Cancer Images

A Gradient and Feature Adaptive Contour model is proposed by Sreelatha, Subramanyam

applying any artefact removal technique (Majtner, Lidayova, Yildirim-Yayilgan and

Study Methodology Limitation

Jafari et al., 2016 CNN architecture for both • Smaller dataset.

2.5. Algorithmic Analysis