Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Development of a Machine Learning Platform for Analysis of Mitochondrial Features in Live-Cell Images(01. Izmir Institute of Technology, 2022) Tarkan, Yalçın; Tuğlular, Tuğkan; Tuğlular, TuğkanIt is a laborious and error-prone manual process to mark the organelles in 2D and 3D images of living cells and identify the behavioral feedback to stimulations under measured conditions. This manual process can be simplified by being largely automated with machine learning techniques. We created a machine learning-based software platform named MitoML, which extracts sub-cellular structures, specifically mitochondria, and helps to identify the effects of external factors or changes under natural conditions. We investigate appropriate machine learning techniques for these objectives. Image processing and segmentation techniques with neural networks, enable researchers to carry out experiments with much better accuracy and a larger scale by automatically segmenting and counting the mitochondria, calculate the energy potentials based on region brightness. This way, analysis of mitochondria feedback in healthy and cancer cells under various conditions, such as nanomedicine and different treatment therapies, can be performed using MitoML. As a result of our work, we proposed a cascaded neural network architecture that can identify and count mitochondria, quantify its energy levels in fluorescence and other microscopy images, fast and at a standard reliable accuracy. Our test results outperformed the classical image processing algorithms provided in segmentation tools and software for medical image segmentation which was taken as a base line. Achieved accuracy rates 93.4% and %89.6 according to Dice and IoU metrics respectively are also better than any other related work encountered during the research. The proposed method can be improved to cover other sub-cellular structures relieving the researchers from non-standardized and laborious manual work which is prone to human error.Master Thesis Application of Graph Neural Networks on Software Modeling(01. Izmir Institute of Technology, 2020) Leblebici, Onur Yusuf; Tuğlular, Tuğkan; Belli, FevziDeficiencies and inconsistencies introduced during the modeling of software systems can cause undesirable consequences that may result in high costs and negatively affect the quality of all developments made using these models. Therefore, creating better models will help the software engineers to build better software systems that meet expectations. One of the software modelling methods used for analysis of graphical user interfaces is Event Sequence Graphs (ESG). The goal of this thesis is to propose a method that predicts missing or forgotten links between events defined in an ESG via Graph Neural Networks (GNN). A five-step process consisting of the following steps is proposed: (i) data collection from ESG model, (ii) dataset transformation, (iii) GNN model training, (iv) validation of trained model and (v) testing the model on unseen data. Three performance metrics, namely cross entropy loss, area under curve and accuracy, were used to measure the performance of the GNN models. Examining the results of the experiments performed on different datasets and different variations of GNN, shows that even with relatively small datasets prepared from ESG models, predicts missing or forgotten links between events defined in an ESG can be achieved.