Doktora Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/5800
Browse
Search Results
Doctoral Thesis Gen İfade Miktarı Verisi Analizi için Yinelemeli Öbek Eliminasyon Yöntemlerinin İyileştirilmesi(2024) Kuzudişli, Cihan; Güngör, BurcuYeni teknolojilerle üretilen biyolojik verilerin giderek artan boyutluluğunun neden olduğu hesaplama ve yorumlama güçlükleri önemli bir zorluk oluşturmaktadır. Özellik seçimi (FS) yöntemleri boyutu azaltmayı amaçlar ve özellik gruplaması, özellikler arasında güçlü korelasyonları tespit etmeyi ve ilgisiz özellikleri belirlemeyi amaçlayan FS teknikleri için bir temel olarak ortaya çıkmıştır. Bu tezde, gözetimli bir bağlamda özellik gruplandırmasını kullanan yöntemler geliştirilmiştir. Başlangıçta farklı kümeleme algoritmalarının SVM-RCE üzerindeki etkilerini test ettik ve K-means ile en iyi performansı gözlemledik. Geliştirilen ilk yöntem olan Öbek İçi Özellik Eleme ile Yinelemeli Öbek Eleme (RCE-IFE) yönteminde, her öbek azaltma adımında hem öbek hem de öbek içi eleme yinelemeli olarak gerçekleştirilir. Deneysel bulgularımız, RCE-IFE'nin güçlü bir sınıflandırıcı performansı sağladığını ve özellik ilgisini ve tutarlılığını korurken özellik boyutunu önemli ölçüde azalttığını göstermektedir. İkinci geliştirilen Gruplama – Puanlama – Model (G-S-M) tabanlı çalışma olan G-S-M_Rep'de, hastalık gruplarını oluşturmak için ön bilgileri kullanıyoruz ve her grubu temsil edecek en iyi özellikleri seçiyoruz. Bu temsili özellikler model tarafından kümülatif bir şekilde öğrenilir. Sonuçlar G-S-M_Rep'in az sayıda özellikle tatmin edici bir model performansına ulaştığını göstermektedir. Sonuç olarak, bu tez özellik gruplandırmaya dayalı yöntemleri sunmakta ve özellik azaltma yeteneğini, sınıflandırma performansını, özellik alaka düzeyini ve özellik tutarlılığını iyileştirmeye odaklanmaktadır.Doctoral Thesis Çoklu Robot Sistemleri için Lokalizasyon Algoritması Tasarımı ve Gerçekleştirilmesi(2024) Kabore, Kader Monhamady; Güler, SametÇok robotlu sistemler (MRS), tek bir robot için son derece zorlayıcı olan karmaşık görevleri gerçekleştirebilir. Örneğin, iş birliğiyle taşıma, alan kapsama ve arama-kurtarma operasyonları gibi uygulamalarda, MRS en iyi seçenek olabilir. MRS, görevleri daha basit komutlara bölerek bireysel robotlara atar. Bu yapı, ölçeklenebilirlik ve tek bir hata noktasına karşı dayanıklılık gibi önemli avantajlar sağlayan merkezi olmayan yaklaşımlara ilgiyi artırmıştır. MRS'deki formasyon kontrolü, özellikle GPS'in bulunmadığı ve dış altyapının olmadığı ortamlarda güçlü robot konumlandırmasına dayanır. Dış ortamlarda GPS mutlak konumlandırma sağlayabilir ancak kapalı alanlar veya tüneller gibi ortamlarda sürü robotları için yetersiz kalabilir. Hareket yakalama sistemleri gibi kapalı alan konumlandırma çözümleri, yüksek maliyetli olup ek altyapı kurulum prosedürleri gerektirir. Bu sınırlamalar, sürü robotikleri uygulamaları için uygun, dayanıklı ve dahili konumlandırma sistemlerine olan ihtiyacı vurgulamaktadır. Bu çalışma, tamamen dahili yeteneklere dayanan, dış altyapıya bağımlılığı ortadan kaldıran yeni bir merkezi olmayan, işaretleyicisiz konumlandırma çerçevesi sunmaktadır. MRS için bir konumlandırma çözümü bulmak amacıyla, yöntemimiz, derin öğrenme ile güçlendirilmiş iş birliği temelli konumlandırma algoritmalarını formasyon kontrol mekanizmalarıyla birleştirmektedir. Önerilen çerçevenin etkinliğini doğrulamak için kapsamlı simülasyonlar ve gerçek dünya deneyleri gerçekleştirilmiştir. Sistem ölçeklenebilirliği, farklı ekip boyutlarına uyum sağlayarak test edilmiştir ve uygulamalardaki etkinliği gösterilmiştir. Bu çalışma ayrıca yer robotları için açık kaynaklı bir veri seti sunarak MRS alanında daha fazla araştırmayı teşvik etmektedir.Doctoral Thesis Hastalık Tahmini ve Biyobelirteçlerin Tespiti için Makine Öğrenim Modellerinin Tasarımı ve Geliştirilmesi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Temiz, Mustafa; Güngör, Burcu; Yousef, MalikIn medical science, the prediction of diseases and the identification of biomarkers play an important role in the diagnosis and treatment of various health conditions. The recent proliferation of data mining techniques has accelerated the development of disease prediction systems. In particular, machine learning methods are an effective way to analyze medical data and identify patterns to predict the likelihood of the disease development. Machine learning methods also help to identify biomarkers. Recently, the increasing incidence and mortality rates of inflammatory bowel disease, colorectal cancer and type 2 diabetes have drawn researchers' attention to these research areas. The aim of this thesis is to reduce the number of features and improve the prediction performance of machine learning based on complex biological datasets with a large number of disease-related features, as well as to identify potential biomarkers. In this thesis, three different studies are presented. The first study predicts eleven different cancer subgroups using miRNA data and biological domain knowledge and identifies potential biomarkers for these diseases. The second study predicts three different diseases using metagenomic data and biological domain knowledge and identifies potential biomarkers. The third study uses metagenomic data related to colorectal cancer to conduct global and population-based comprehensive experiments with traditional feature selection methods to identify potential biomarkers. This thesis presents a promising avenue for early disease detection, facilitating expedited treatment protocols, improving human survival rates, and potentially alleviating economic burdens within these critical research domains.Doctoral Thesis Makine Öğrenmesi Tabanlı Ağ Anomali Tespiti(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Hacılar, Hilal; Güngör, Burcu; Güngör, Vehbi ÇağrıIntelligent technologies have led to a significant rise in internet users and applications. However, this rise in internet usage has also brought serious security challenges. Organizations rely on Network Intrusion Detection systems (NIDS) to protect sensitive data from unauthorized access and theft. To enhance the capabilities of IDS, Machine Learning (ML) and Deep Learning (DL) techniques have been increasingly integrated into these systems. In this context, anomaly-based network intrusion detection surpasses other detection mechanisms significantly in several instances. These systems analyze network traffic to detect suspicious activities, such as attempted breaches or cyberattacks. However, existing studies lack a thorough assessment of class imbalances, feature selection and extraction methods, hyperparameter optimization, and classification performance for different types of network intrusions: wired, wireless, and Software Defined Networking (SDN). Additionally, existing methods may achieve high accuracy; they may suffer from high training times, low detection rate (DR), and computational complexity. By combining metaheuristics and neural networks, it is possible to solve complex optimization problems that are challenging to solve using conventional methods. To address these challenges, this thesis study first evaluates different network intrusion datasets, such as wired, wireless, and SDN, together, considering class imbalance, feature selection, and hyperparameter optimization tasks. Secondly, it proposes a novel hybrid approach combining Deep Autoencoder (DAE) and Artificial Neural Network (ANN) models trained by a parallel Artificial Bee Colony (ABC) algorithm with Bayesian hyperparameter optimization.Doctoral Thesis Merkezi Olmayan Elektronik Sağlık Kaydı Yönetim Sistemi ve Makine Öğrenmesi Yöntemleri ile Hastalık Tahmini(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Dedetürk, Beyhan Adanur; Güngör, BurcuElectronic health records (EHRs) are vital to the advancement of healthcare and can help detect and prevent diseases early. However, EHR sharing faces challenges such as managing large data volumes, ensuring data privacy, security, and interoperability. This thesis aims to develop and analyze a blockchain-based EHR sharing system for disease prediction mechanism integration using SysML. The AguHyper platform, built by merging the InterPlanetary File System (IPFS) with Hyperledger Fabric, ensures the immutability of health records by storing hash values in the blockchain and encrypted records in IPFS. The system architecture and implementation configurations, including CouchDB and the Raft consensus mechanism, are thoroughly examined. The study also presents a novel hybrid approach called CSA-DE-LR, which integrates Differential Evolution (DE) and Clonal Selection Algorithm (CSA) with Logistic Regression (LR) to improve LR weights for precise categorization of cardiovascular diseases. The integration of the AguHyper with the CSA-DE-LR is explained in detail. At the end of our performance evaluations, we concluded that the AguHyper model has the potential to speed up the process of collecting and sharing data, and it offers an efficient platform for the participants.Doctoral Thesis Derin Öğrenme Tabanlı Kompozit Malzemelerin Ultrasonik Tomografi Görüntülerinden Kusurların Tespiti ve Sınıflandırılması(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Gülşen, Abdulkadir; Güngör, Burcu; Kolukısa, BurakThis thesis introduces novel methodologies for enhancing defect classification and characterization in advanced composite materials by leveraging state-of-the-art machine learning (ML), deep learning (DL), and federated learning (FL) techniques within ultrasonic and acoustic emission (AE) inspection environments. First, a new ultrasonic dataset (UNDT), comprising 1,150 images from 60 distinct composite materials, is introduced. Applying transfer learning methods to both the UNDT and a publicly available dataset demonstrates the efficacy of advanced neural architectures—such as DenseNet121 and VGG19—achieving accuracy rates up to 98.8% and 98.6%, respectively. Next, the scope is extended to AE-based health monitoring by introducing an ensemble feature selection methodology to identify features strongly correlated with damage modes. By selecting amplitude and peak frequency for labeling and subsequently applying unsupervised clustering, the analysis confirms that both traditional AE features (e.g., counts and energy) and less commonly employed features (e.g., partial powers) correlate with distinct defect types. Finally, a novel FL framework is introduced to address the scarcity of publicly available, real-world ultrasonic datasets. This decentralized approach preserves data privacy while maintaining performance levels comparable to centralized methods, ensuring scalability and confidentiality in diverse data environments. Overall, these contributions significantly advance the field of NDT, offering robust defect classification and characterization. In doing so, the findings not only improve the accuracy and reliability of material integrity assessments but also lay a durable foundation for more secure, collaborative, and efficient NDT systems.Doctoral Thesis Nesnelerin İnterneti Tabanlı Araç Tipi Sınıflandırma ve Ağ Anomalisi Tespiti için Makine Öğrenmesi Yaklaşımları(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Kolukısa, Burak; Güngör, Vehbi ÇağrıThis thesis presents innovative approaches in the realms of Intelligent Transportation Systems (ITS) and Network Intrusion Detection Systems (NIDS) within the Internet of Things (IoT). Leveraging IoT technologies, a low-cost, battery-operated 3-D magnetic sensor has been developed for ITS to enable the classification of vehicle categories. The research presents machine learning and deep learning models that are improved by using oversampling, feature selection and extraction methods, hyperparameter optimization, and converting signals into 2-D images. New methods have been proposed for vehicle type classification to boost classification performance and achieve an accuracy of up to 92.92%. Additionally, the increasing reliance on IoT devices for such applications introduces significant cybersecurity risks. To mitigate these vulnerabilities, a novel logistic regression model trained with a parallel artificial bee colony (LR-ABC) algorithm has been proposed for network anomaly detection. This model incorporates hyperparameter optimization to enhance detection capabilities, showcasing superior performance on popular benchmark NIDS datasets with accuracies of 88.25% and 90.11%. Overall, this research contributes to the advancement of IoT and IoT cybersecurity by offering robust, scalable, and efficient solutions. These innovations not only enhance vehicle type classification and network security in the IoT era but also pave the way for future IoT infrastructure development in an increasingly connected digital landscape.Doctoral Thesis Genetik ve Enfeksiyon Hastalıklarının Tespiti için Makine Öğrenmesi Yöntemleri(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Işık, Yunus Emre; Aydın, ZaferCompletion of the whole human genome in the 2003 has led to various advances in many fields, particularly in biology, genetics, health sciences, treatment, and pharmacology. In the following years, spread of faster and cheaper sequencing technologies has enabled us to extract and analyze genetic profiles of individuals digitally. Consequently, individual-specific forecasting and personalized treatment and precision medicine-, what once seemed like science fiction, have become more and more real. In both approaches, one of the crucial steps is identifying the presence of diseases using individual-specific genetic data. This thesis aims to comprehensively and comparatively evaluate the predictive performance of machine learning methods for Behçet's disease and respiratory infections. Additionally, feature selection methods were employed to identify the genetic factors (such as SNPs and genes) associated with disease presence for both diseases. Furthermore, the usability of selected features depending on biological pathway-driven active subnetworks listed in the literature was analyzed for the prediction of Behçet's disease. For the respiratory infection prediction problem, on the other hand, the prediction performance of features calculated by single-sample gene set enrichment analysis (ssGSEA) was evaluated using different machine learning methods. As the data types used in both experiments were different (genome-wide association studies data, gene expression profiles), the performance of machine learning approaches on different data types was also observed. It is hoped that the findings of both experiments will contribute to future machine learning based disease prediction studies.Doctoral Thesis Trafik Yoğunluğu Tahmini için Derin Öğrenme Modelleri(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2024) Çini, Nevin; Aydın, ZaferIn the last 50 years, with the growth of cities and increase in the number of vehicles and mobility, traffic has become troublesome. As a result, traffic flow prediction started to attract attention as an important research area. However, despite the extensive literature, traffic flow prediction still remains as an open research problem, specifically for long- term traffic flow prediction. Compared to the models developed for short-term traffic flow prediction, the number of models developed for long-term traffic flow prediction is very few. Based on this shortcoming, in this study, we focus on long-term traffic flow prediction and propose a novel deep ensemble model (DEM). In order to build this ensemble model, first, we developed a convolutional neural network (CNN), a long short term memory (LSTM) network, and a gated recurrent unit (GRU) network as deep learning models, which formed the base learners. In the next step, we combine the output of these models according to their individual forecasting success. We use another deep learning model to determine the success of the individual models. Our proposed model is a flexible ensemble prediction model that can be updated based on traffic data. To evaluate the performance of the proposed model, we use a publicly available dataset. Numerical results show that our proposed model performs better than individual deep learning models (i.e., LSTM, CNN, GRU), selected traditional machine learning models (i.e., linear regression (LR), decision tree regression (DTR), k-nearest-neighbors regression (KNNR) and other ensemble models such as random-forest-regression(RFR).