Doktora Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/5800
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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 Histopatoloji Görüntülerinden Bilgisayar Destekli Kanser Tespiti(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2023) Taşdemir, Sena Büşra Yengeç; Yılmaz, Bülent; Aydın, ZaferDetecting colon adenomatous polyps early is crucial for reducing colon cancer risk. This thesis investigated various deep learning approaches for computer-aided diagnosis of colon polyps on histopathology images using deep learning. The thesis addressed key challenges in polyp classification, including differentiating adenomatous polyps from non-adenomatous tissues and multi-class classification of polyp types. Initially, a histopathology image dataset is collected and refined from Kayseri City Hospital. The first study used stain normalization algorithms and an ensemble framework for binary classification, achieving 95% accuracy on the custom dataset and 91.1% and 90% on UnitoPatho and EBHI datasets, respectively. The second study implemented a tailored version of the supervised contrastive learning model for multi-class classification, outperforming state-of-the-art deep learning models with accuracies of 87.1% on custom dataset and 70.3% on UnitoPatho dataset. The third study proposed a self-supervised contrastive learning approach for utilizing all data in cases of limited labeled images. This approach achieved better performance than transfer learning with ImageNet pre-trained models. In conclusion, this PhD thesis investigated deep learning approaches for computer-aided diagnosis of colon polyps on histopathology images, demonstrating high accuracy in binary and multi-class classification, outperforming state-of-the-art models. These findings contribute to improving colon polyp classification accuracy and efficiency, ultimately facilitating the early detection and prevention of colon cancer.Doctoral Thesis Protein Yapı Tahmini için Derin Öğrenme Modellerinin Geliştirilmesi(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Görmez, Yasin; Aydın, ZaferThe three-dimensional structure of a protein provides important clues about the function of that protein. Although there have been many studies on protein structure prediction, the problem has still not been solved completely. As it is very difficult to predict the three-dimensional structure of a protein directly, predictions of structural properties of proteins such as secondary structure, solvent accessibility, and torsion angles are carried out first, which are later used as inputs to more elaborate structure estimation tasks. In this thesis, novel deep learning models have been developed by using convolutional neural networks (CNN), graph convolutional networks (GCN) and long-short-term memory (LSTM) recurrent neural networks to predict secondary structure, solvent accessibility and torsion angles of proteins. A rich feature set formed by using PSI-BLAST, HHBlits, physicochemical properties, structural profile matrices, AA index values, and graphs representing the relationship between amino acids were used as inputs to the models. In the first study, a deep learning model was developed by using CNN and GCN layers for secondary structure prediction. In the second study, LSTM layers were added to the first model, which was extended to make solvent accessibility and torsion angle predictions as well using the multi-task learning approach. In both studies, graphs were generated using neighborhood relations between amino acids. In the last study, a novel U-net-based model was designed for secondary structure prediction using CNN, GCN, and LSTM layers. The graph matrices used as input to GCN layers were obtained by using protein contact map prediction. All models were trained, optimized and tested on benchmark data sets. Improvements were obtained in accuracy as compared to the state-of-the-artDoctoral Thesis Zamansal Bilgiden Faydalanarak Videodan Orman Yangınlarının Erken Tespiti(Abdullah Gül Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Taş, Merve; Taşdemir, Kasım; Aydın, ZaferForest fires are considered as the major threats to lives, properties and to the integrity of the ecosystem around the world. In most cases, the fire damage can be reduced, when the initial signs of the fire are detected in a timely manner. Since smoke is considered as the first visual sign of fire, detection of smoke is vital. Hence, a successfully designed smoke detection system is essentially critical in the early detection of smoke for outdoor environments. The existing smoke detection methods suffer from high false alarm rates and cannot accurately detect smoke in hazy environments. To address these problems, this thesis is focused on smoke detection model at an early stage that utilizes deep learning (DL) based techniques for outdoor locations. This work contributes mainly to four aspects of smoke detection: (1) new datasets preparation for three smoke detection tasks classification, detection-segmentation, and video classification, (2) utilizing transfer learning to detect the smoke on the relatively small dataset, (3) image dehazing process that includes removing the haze from the dataset images to enhance the system performance, (4) designing a novel hybrid video classification model by combining the two DL based video classification structures. This work will be a resourceful reference for researchers working in the fields of forest fire or smoke detection studies at an early stage. The experiments, research findings, and enhanced performance of the smoke detection system provide a source of information about smoke detection. Current studies can be utilized to further improve the design of efficient and reliable fire safety models. Keywords: Deep Learning, Spatio-Temporal Information, Forest Fire Early Detection, Smoke Detection, Image Dehazing