Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/5799
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Master Thesis İnsan Bağırsak Mikrobiyotasından Hastalık Biyobelirteçlerinin Tespiti için Makine Öğrenmesi Temelli Sistem Geliştirilmesi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Koçak, Ayşegül; Güngör, Burcu; Yousef, MalikThe human gut microbiota consists of a diverse ecosystem of organisms, encompasses billions of species. Recently developed next-generation sequencing methods have enabled researchers to examine the microbiota in greater detail, leading to new insights into its functions and dysfunctions. This study aims to identify metagenomic biomarkers (Microorganism-Enzyme Pairs) for colorectal cancer (CRC). The tool that we used allows for the analysis of microorganisms and enzymes within the gut microbiota. It achieves this by initially clustering enzymes based on their correlations with species and subsequently utilizing these clustering results to evaluate the ability of groups to differentiate between patient and healthy cohorts. By integrating species and enzymes, it is possible to identify pathogen microorganisms and enzyme clusters, that have the potential to distinguish cases (individuals with CRC) from controls (healthy individuals). The identified enzyme clusters and associated species could potentially act as biomarkers for colorectal cancer (CRC), enabling early diagnosis and more effective treatment. This approach holds promise for further exploration of the gut microbiota and its importance in human health and illness. Keywords: Bioinformatics, Machine Learning, Colorectal Cancer DiagnosisMaster Thesis Tree-net: Biyomedikal Görüntü Segmentasyonu için Tree-net: Darboğaz Özellik Süpervizyonu Kullanılan Yapay Sinir Ağı Modeli(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Demirci, Orhan; Yılmaz, BülentIn this thesis, we introduce Tree-NET, a novel approach for medical image segmentation utilizing bottleneck feature supervision. This method enhances traditional segmentation algorithms by keeping supervision between bottleneck features of the network. The primary goal is to improve the model's ability to learn discriminative and robust features while simultaneously reducing computational costs. Bottleneck feature supervision involves compressing the input and label data using Autoencoders and then supervising the bottleneck features with a segmentation network named 'Bridge-Net,' which can be any segmentation model of choice. We applied Tree-NET to two critical medical image segmentation tasks: skin lesion segmentation and polyp segmentation. Our experiments demonstrate significant improvements in segmentation accuracy and efficiency. For instance, the U-NET backboned Tree-NET uses only 154.43 MB for executing and storing the model, which is almost 3.5 times smaller than the original U-Net while having a close number of trainable parameters. In skin lesion segmentation, Tree-NET achieved dice, Intersection-over-Union (IoU), and accuracy scores of 0.893, 0.751, and 0.977 respectively. For polyp segmentation, the scores were 0.856, 0.795, and 0.923 for dice, IoU, and accuracy respectively. Compared to traditional segmentation models, the empirical results show that Tree-NET achieves higher accuracy with reduced training time and computational cost, thus representing a significant advancement in medical image analysis by providing more reliable and efficient tools for clinical applications.Master Thesis RNA Etkileşimlerinin İn Silico Analizi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Orhan, Mehmet Emin; Demirci, Müşerref Duygu SaçarMany supervised machine learning models have been developed for the classification and identification of non-coding RNA (ncRNA) sequences. These models play a significant role in the diagnosis and treatment of various diseases. During such analyses, positive learning datasets typically consist of known ncRNA examples, some of which may even be confirmed with strong experimental evidence. However, there is no database of validated negative sequences for ncRNA classes or standardized methodologies for generating high quality negative samples. To overcome this challenge, a new method for generating negative data called the NeRNA (Negative RNA) method has been developed in this study. NeRNA generates negative sequences using known ncRNA sequences and their octal representations, similar with frame shift mutations found in biology but without base deletions or insertions. In this thesis, the NeRNA method was tested separately with four different ncRNA datasets, including microRNA (miRNA), transfer RNA (tRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). Additionally, a species-specific case study was conducted to demonstrate and compare the performance of the study's miRNA predictions. The results of 1000-fold cross-validation on machine learning algorithms such as Decision Trees, Naive Bayes, Random Forest classifiers, and deep learning algorithms like Multilayer Perceptrons, Convolutional Neural Networks, and Simple Feedforward Neural Networks showed that models developed using datasets generated by NeRNA exhibited significantly high prediction performance. NeRNA has been published as an easy-to-use, updatable, and modifiable KNIME workflow, along with example datasets and required extensions that can be downloaded and utilized. NeRNA is designed specifically as a powerful tool for RNA sequence data analysis.Master Thesis Meme Kanseri Histopatoloji Görüntülerinde Evrişimsel Sinir Ağları Kullanarak Tümör Tespiti(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Şahbaz, Zeki; Aksebzeci, Bekir HakanBreast cancer is one of the most common cancer types among women worldwide. Early detection significantly increases the chances of survival and effective treatment, making advancements in diagnostic methodologies crucial. This study aims to improve the detection of tumor cells in breast cancer histopathology images using deep learning and image processing techniques. Significant modifications have been made to the hyperparameters, including the tumor bounding box size, batch size, optimization algorithms, learning rate, and weight decay. These changes focus on determining the best parameters of the Faster R-CNN model. A comprehensive analysis of different parameters was conducted using the Breast Cancer Histopathological Annotation and Diagnosis (BreCaHAD) dataset. The analysis identified the best settings for model performance, shows by improvements in precision, recall, and F-score. Our research contributes to the field of medical image analysis by identifying critical factors that affect the accuracy of tumor detection, contributing to the development of more accurate diagnostic tools.Master Thesis Makine Öğrenimi Algoritmalarını Kullanarak Ağ Trafiğini Analiz Etme ve Ağ Tehditlerini Tespit Etme(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Küçükkoç, Abdurrahman; Aydın, ZaferAs information technologies progress, the possibilities of access to information increase and therefore it becomes difficult to ensure the security of information. Today, with the use of information systems in all areas of life, network threats have also increased. The increase in individual access to and use of the internet has also brought network threats. In addition, the latest developments in information technologies, developing global communication networks, the internet of things aiming to connect all objects with networks, cloud technologies, the spread of mobile internet and the renewal of devices have brought network threats and uncertainties. Network threats increase the security vulnerabilities in the information and communication systems of individuals and organisations day by day. This situation causes systems to malfunction, economic damage and cyber security to be jeopardised. In order to contribute to individuals, institutions and organisations, our thesis aims to protect information systems against network threats, to ensure data confidentiality, integrity and accessibility, to detect network threats in advance and to take measures against these threats. We believe that by analysing heterogeneous network traffic, which includes most network attacks on the Internet, and using machine learning algorithms, we will reach a result close to reality in the detection of network threats. In line with this result, we will be able to take precautions against network threats in information systems and structuresMaster Thesis Koroner Arter Hastalığının Makine Öğrenimi Yaklaşımları ile Teşhisi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Halıcı, İkram; Güngör, Vehbi ÇağrıThe World Health Organization states that Coronary Artery Disease (CAD) ranks as a primary cause of recorded fatalities. CAD occurs as a result of the blockage of coronary artery vessels, which are located on the surface of the heart and supply the blood that the heart needs. Diagnosing the disease using traditional methods is challenging and requires costly tests. In recent years, the use of machine learning-based methods has increased as an alternative diagnostic approach. However, existing studies in the literature suffer from low detection rates and long training times. Therefore, there is still a need for reliable and low-cost diagnostic methods. In this thesis, a new model, CSA-PSO-ANN, is proposed for the diagnosis of coronary artery disease. The aim is to reduce the training time of the machine learning model and achieve a higher accuracy in diagnosing the disease. Experiments have been conducted on two publicly available datasets. Parallelization, feature selection, and hyperparameter optimization have been performed to shorten the model's training time. The performance of the model has been compared with well-known machine-learning algorithms and previous studies. The experiments showed that the proposed model effectively diagnoses the disease and outperforms other methods in terms of accuracy and F1 score performance metrics.Master Thesis Derin Öğrenme Yöntemleri Kullanarak Dermatoskopik Görüntülerden Otomatik Cilt Kanseri Tespiti ve Sınıflandırılması(Abdullah Gül Üniversitesi / Fen Bilimleri Enstitüsü, 2023) Kalaycı, Serdar; Yılmaz, BülentEarly detection of skin cancer is crucial for successful treatment and improved patient outcomes. The most prevalent form of cancer is skin cancer and if left undetected, it can spread and become more difficult to treat. A dangerous and frequently fatal type of skin cancer is melanoma. Regular skin examinations and self-examinations can help identify suspicious moles or lesions, which can then be evaluated by a dermatologist. In addition, advances in technology and artificial intelligence have enabled the development of tools for automated skin cancer screening, providing a convenient and efficient means of early detection. This can lead to more efficient diagnosis, reduced healthcare costs and improved patient care. By evaluating skin lesions from images, deep learning techniques have shown considerable potential in increasing the precision of melanoma detection. By using large datasets and complex neural networks, deep learning algorithms can effectively distinguish between benign and malignant skin lesions with high accuracy. Ensemble of CNN models helps improve the performance and reliability of the classification task. By combining the predictions of multiple CNN models lead to more accurate and robust predictions. In this thesis, for melanoma classification problem, many different data augmentations techniques applied and different convolutional neural networks architectures evaluated, applied vignetting effect filter and hair noise in accordance with the dataset and results of ensemble of the best CNN models are promising. This thesis attempts to produce a reliable model for the classification of melanoma by conducting experiments on two combined publically accessible data sets, ISIC 2019 and ISIC 2020. On the testing sets in our studies, the proposed solution attained 95.75% AUC.Master Thesis Bilgisayar Algoritmalarının GPU ile Hızlandırılması(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Yalçın, Salih; Alkan, Gülay YalçınTravelling Salesman Problem (TSP) is one of the significant problems in computer science which tries to find the shortest path for a salesman who needs to visit a set of cities and it involves in many computing problems such as networks, genome analysis, logistic etc. Using parallel executing paradigms, especially GPUs, is appealing in order to reduce the problem-solving time of TSP. One of the main issues in GPUs is to have limited GPU memory which would not be enough for the entire data. Therefore, transferring data from host device would reduce the performance in execution time. In this study, we present a methodology for compressing data to represent cities in the TSP so that we include more cities in GPU memory. We implement our methodology in Iterated Local Search (ILS) algorithm with 2-opt and show that our implementation presents 29% performance improvement compared to the state-of-the-art GPU implementation.Master Thesis Erken Orman Yangını Tespiti için Otonom Heterojen Çoklu Robot Sistemi Tasarımı(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Serin, Ömer Faruk; Güler, SametThe usage of autonomous multi-robot systems for human life-endangering applications is emerging. Early wildfire detection and firefighting are two example applications. In this study, a heterogenous multi-robot system is proposed for both fire detection and response. The system employs an unmanned aerial vehicle for beyond-visual line-of-sight observations and an unmanned ground robot for fire extinguisher carrying. The proposed method uses ultrawideband (UWB) communication and ranging modules for the relative localization of robots during their movements. A specially trained YOLOv7 object detection model is used for robustly detecting forest fires and smoke while a modified version of the Vector Field Histogram Plus (VFH+) algorithm on the ground robot is used for obstacle avoidance while navigating. The structural design of the system requires no odometry or mapping of the environment hence improving the applicability of the system while decreasing system complexity. Additionally, the proposed UWB localization system is shown to be robust in long-lasting operations unlike many odometry-based approaches which accumulate errors with time. Moreover, localization of the UAV is realized with only three independent UWB-based range measurements and the altitude information of the UAV. The system is tested both in a realistic simulation environment and in real experimental setups with multiple runs. Results showed that the proposed system is improvable for better detection and practical to implement even in a dense forest environment without the need for GPS sensors, odometer data, or magnetometer.Master Thesis Kanser Alt Tipi Tanımlama Problemi için Bir Etiket Yayma Yaklaşımı Geliştirme(Tubitak Scientific & Technological Research Council Turkey, 2022) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, Mustafa; Güner, Pınar; Güngör, Burcu; Coşkun, MustafaKanser terimi, anormal hücrelerin kontrolden çıkıp diğer dokuları istila ettiği hastalıkları tanımlamak için kullanılır. Çok sayıda kanser türü vardır ve birçok kanser türü, farklı klinik ve biyolojik etkileri olan çeşitli alt tiplere sahiptir. Bu farklılıklar, kanserin farklı alt tiplerinin tedavisi için farklı yöntemlerin izlenmesi gerektiğini göstermektedir. Kişiselleştirilmiş tıbbın geliştirilmesine yardımcı olabileceğinden, kanser alt tiplerini keşfetmek biyoinformatikte önemli bir problemdir. Kanserin alt tipinin bilinmesi, tedavi basamaklarının ve öngörünün belirlenmesinde faydalıdır. Hesaplamalı biyoinformatik yöntemler, farklı kanser alt tiplerinin ortak moleküler patolojisini ortaya çıkararak hedeflenen tedavileri tasarlamak için kanser analizi yapmaya yardımcı olur. Şimdiye kadar, kanser alt tiplerini keşfetmek veya kanseri bilgilendirici alt tiplere ayırmak için çeşitli hesaplamalı yöntemler önerildi. Ancak, mevcut çalışmalar verilerin seyrekliğini dikkate almamakta ve kötü koşullu (tersi alınamayan) çözümle sonuçlanmaktadır. Bu eksikliği gidermek için, bu tezde, uygulamalı sayısal cebir tekniklerini kullanarak kanseri alt tiplerine ayırmak için alternatif bir denetimsiz hesaplama yöntemi öneriyoruz. Daha detaylı olarak, bu etiket yayma tabanlı yaklaşımı kolon, baş ve boyun, rahim, mesane ve meme tümörlerinin somatik mutasyon profillerini sınıflandırmak için uyguladık. Sonra, yöntemimizin performansını temel yöntemlerle karşılaştırarak değerlendirdik. Kapsamlı deneyler, yaklaşımımızın, modern denetimsiz ve denetimli yaklaşımlardan büyük ölçüde daha iyi performans göstererek tümör sınıflandırma görevlerini yüksek oranda yerine getirdiğini kanıtlamaktadır.