Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Now showing 1 - 5 of 5
  • Master Thesis
    Development of Visual Analysis Interfaces for Large Biological Data and Characterization of Immunomodulatory Noncoding Rna Networks Cancer
    (01. Izmir Institute of Technology, 2023) Kuş, Muhammet Emre; Ekiz, Hüseyin Atakan; Ekiz, Hüseyin Atakan
    These days we are collecting data in higher and higher dimensions, processing it, and developing tools that have strong descriptive and predictive powers. Especially in the field of cancer, the processing of data collected from patients has substantial potential in terms of discovering new biomarkers, developing personalized treatment methods, and better prognosticators. However, there are significant difficulties in utilizing and analyzing high-dimensional data. A good level of coding skills is required to bring the data together and apply different analysis methods. With the visual interfaces created in this study, we offer the opportunity to examine and analyze the high-dimensional data of thousands of cancer patients, which are open to the public through The Cancer Genome Atlas initiative, especially for bench scientists who has no prior coding expertise. The Cancer Genome Explorer, shortly TCGEx, is a robust bioinformatic tool that we developed to facilitate high-throughput cancer data analysis through several sophisticated algorithms. With special features like subset-specific analysis and comparative analysis by using multiple cancer data, TCGEx can contribute to the literature by accelerating the studies, especially in hypothesis-driven research. This study also describes a use-case scenario that demonstrates how hypothesis-driven research can be performed using TCGExplorer for melanoma. In melanoma, elucidating the interactions between the tumor and the immune system at the miRNA level is crucial for developing new therapeutics. In this study, we characterize the properties of potential therapeutic targets that act on tumor and immune cells, which we have identified using various statistical analysis methods including machine learning, dimensionality reduction, and survival modeling using the TCGEx portal.
  • Master Thesis
    Deep Learning Based Real-Time Sequential Facial Expression Analysisusing Geometric Features
    (01. Izmir Institute of Technology, 2023) Köksal, Talha Enes; Gümüş, Abdurrahman
    In this thesis, macro and micro facial expression sequences from various datasets are trained using neural networks to classify them in one of the basic emotions. In macro expression experiments, for each frame of the sequences facial landmarks are extracted using MediaPipe FaceMesh solution and geometric features using both spatial and temporal information based on these landmarks are created. To classify the features, ConvLSTM2D followed by multilayer perceptron blocks are used. In order to achieve real time classification performance, all algorithms are implemented compatible to run on GPU. The proposed method for macro expressions is tested with CK+, Oulu-CASIA VIS, Oulu-CASIA NIR and MMI datasets. In micro expression experiments, apart from geometric features also blendshape features provided by MediaPipe are used. In order to improve classification performance, Phase-Based Video Motion Processing technique is used to magnify subtle facial movements of micro expressions. Experiments are conducted separately on same classification layers that consist of ConvLSTM1D followed by multilayer perceptron blocks. The proposed method for micro expressions is tested with SAMM and CASME II datasets. The datasets utilized in this study were accessed upon signing corresponding license agreements. Each dataset is specifically designated for academic purposes and is made available under these agreements. Only data from subjects who provided consent for their information to be used in publications was included in the thesis. The license agreements for each dataset can be found in the appendices section.
  • Master Thesis
    Recognition of Counterfactual Statements in Turkish
    (01. Izmir Institute of Technology, 2023) Acar, Ali; Tekir, Selma
    Counterfactual statements describe an event that did not happen or cannot happen, and optionally the consequence of this event if it would happen. Counterfactual statements are the building blocks of human thought processes as people constantly reflect upon past happenings and consider their future implications. Counterfactual reasoning is essential for machine intelligence and explainable artificial intelligence studies. Detecting counterfactuals automatically with machine learning algorithms is very crucial for these areas. This thesis presents the development of the first-ever Turkish counterfactual detection dataset. It presents a comprehensive classification baseline and expands the scope of counterfactual detection to include the Turkish language.
  • Master Thesis
    A Mutation-Based Approach To Alleviate the Class Imbalance Problem in Software Defect Prediction
    (01. Izmir Institute of Technology, 2023) Güner, Dinçer; Demirörs, Onur; Demirörs, Onur; Giray, Görkem
    Highly imbalanced training datasets considerably degrade the performance of software defect predictors. Software Defect Prediction (SDP) datasets have a general problem, which is class imbalance. Therefore, a variety of methods have been developed to alleviate Class Imbalance Problem (CIP). However, these classical methods, like data-sampling, balance datasets without connecting any relation with SDP. Over-sampling techniques generate synthetic minor class instances, which generalize a small number of minor class instances and result in less diverse instances, whereas under-sampling techniques eliminate major class instances, resulting in significant information loss. In this study, we present an approach that uses software mutations to balance software repositories. Mutation-based Approach (MBA) injects mutants into defect-free instances, causing them to transform into defective instances. In this way, MBA balances datasets with diverse data produced by mutation operators, and there is no loss on instances as in under-sampling. For recall scores, almost all rebalancing methods outperformed Baseline in Inter-release Defect Prediction (IRDP) scenario but only MBA significantly outperformed Baseline in Cross-project Defect Prediction (CPDP) scenario. The performance increase in recall resulted in the production of more false alarms. We can not generalize that MBA outperforms Baseline and the five over-sampling strategies in terms of AUC scores. In terms of recall values, the MBA performed better in CPDP than IRDP. For both IRDP and CPDP scenarios, there were significant and positive correlations between SMC (the change percentage of software measures) and recall, and SMC and false alarm but there was no significant correlation between SMC and AUC.
  • Master Thesis
    Hierarchical Image Classification With Self-Supervised Vision Transformer Features
    (Izmir Institute of Technology, 2022) Karagüler, Caner; Özuysal, Mustafa
    There are lots of works about image classification and most of them are based on convolutional neural networks (CNN). In image classification, some classes are more difficult to distinguish than others because of non-even visual separability. These difficult classes require domain-specific classifiers but traditional convolutional neural networks are trained as flat N-way classifiers. These flat classifiers can not leverage the hierarchical information of the classes well. To solve this issue, researchers proposed new techniques that embeds class-hierarchy into the convolutional neural networks and most of these techniques exceed existing convolutional neural networks' success rates on large-scale datasets like ImageNet. In this work, we questioned if a hierarchical image classification with self- supervised vision transformer features can exceed hierarchical convolutional neural networks. During this work, we used a hierarchical ETHEC dataset and extract attention features with the help of vision transformers. Using these attention features, we implemented 3 different hierarchical classification approaches and compared the results with CNN alternative of our approaches.