Graduate School of Informatics

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Recent Submissions

Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge
Ali, Sharib; et. al. (2024-12-01)
Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, appearance, and location makes the detection of polyps challenging. Moreover, colonoscopy surveillance and removal of p...
Efficient primer design for genotype and subtype detection of highly divergent viruses in large scale genome datasets
Demiralay, Burak; Acar, Aybar Can; Department of Medical Informatics (2024-3-11)
Identification of microorganisms is a crucial step in diagnostics, pathogen screening, biomedical research, evolutionary studies, agriculture, and biological threat assessment. While progress has been made in studying larg...
FPGA-friendly compact and efficient AES-like 8 × 8 S-box
Malal, Ahmet; Tezcan, Cihangir (2024-03-01)
One of the main layers in the Advanced Encryption Standard (AES) is the substitution layer, where an 8 × 8 S-Box is used 16 times. The substitution layer provides confusion and makes the algorithm resistant to cryptanalysi...
An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data
Shojaei, Mona; Mohammadvand, Navid; DOĞAN, TUNCA; Alkan, Can; Çetin Atalay, Rengül; Acar, Aybar Can (2024-02-01)
Non-silent single nucleotide genetic variants, like nonsense changes and insertion-deletion variants, that affect protein function and length substantially are prevalent and are frequently misclassified. The low sensitivit...
Abnormally low sensorimotor α band nonlinearity serves as an effective EEG biomarker of Parkinson’s disease
Özkurt, Tolga Esat (2024-02-01)
Biomarkers obtained from the neurophysiological signals of patients with Parkinson’s disease (PD) have objective value in assessing their motor condition for effective diagnosis, monitoring, and clinical intervention. Prom...
BioNet-XR: Biological Network Visualization Framework for Virtual Reality and Mixed Reality Environments
Şenderin, Büşra; Tunçbağ, Nurcan; Sürer, Elif (2024-02-01)
Protein-protein interaction networks (PPIN) enable the study of cellular processes in organisms. Visualizing PPINs in extended reality (XR), including virtual reality (VR) and mixed reality (MR), is crucial for exploring s...
Spatiotemporal signal space separation for regions of interest: Application for extracting neuromagnetic responses evoked by deep brain stimulation
Oswal, Ashwini; Abdi-Sargezeh, Bahman; Sharma, Abhinav; Özkurt, Tolga Esat; Taulu, Samu; Sarangmat, Nagaraja; Green, Alexander L.; Litvak, Vladimir (2024-02-01)
Magnetoencephalography (MEG) recordings are often contaminated by interference that can exceed the amplitude of physiological brain activity by several orders of magnitude. Furthermore, the activity of interference sources...
PathFinder - An Intelligent Algorithm for MCDC Test-Path Generation
Şimşekoğlu, İsmail; Koçyiğit, Altan; Department of Software Management (2024-1-31)
Introducing Pathfinder, an innovative automated tool designed for generating comprehensive test cases in the realm of C language source codes. The primary objective is to fulfill Modified Condition/Decision Coverage (MC/DC...
Smart Contract Vulnerabilities
Özgen, Mustafa Uğur; Tezcan, Cihangir; Department of Cybersecurity (2024-1-26)
Various industries, particularly financial technologies, are adopting blockchain to create decentralized applications through smart contracts due to its popularity and features such as immutability, pseudo-anonymity, trans...
Analyzing decision making behaviour under risk and uncertainty with the help of computational cognitive modeling and neuroscience perspectives
Bulur, Hatice Gonca; Çakır, Murat Perit; Department of Cognitive Science (2024-1-26)
This study aims to understand individuals' decision making behaviour under risk and uncertainty by bringing insights from computational cognitive modeling and neuroscience perspectives. More specifically, it investigates c...
A GENERIC BLOCKCHAIN PROCESS REFERENCE MODEL FOR SOFTWARE DEVELOPMENT IN SAFETY CRITICAL DOMAINS
Baysal, Merve Vildan; Özcan Top, Özden; Betin Can, Aysu; Department of Information Systems (2024-1-26)
In recent years, blockchain technology has garnered significant interest and shown promises in various safety critical domains such as health, automotive, and energy. In safety critical domains, any failure or malfunction ...
Predicting Alzheimer's Disease Stage Transformations 12 Months in Advance using 3D Convolutional LSTM based on 3D Magnetic Resonance Images
Erdemir, Elifnur; Aydın Son, Yeşim; Department of Medical Informatics (2024-1-25)
This study evaluates the ability to predict the transition from the healthy cognitive stage to the Alzheimer's stage using a 3D LSTM model. The model was trained on a data set created from MR images taken at different time...
Process, Technology and Human Aspects of a Security Operations Center
Erdıvan, Cem; Acar, Aybar Can; Department of Cybersecurity (2024-1-24)
This report presents the high level aspects of any security operations center and tries to define a baseline for SOC processes, technologies to be used and roles to be assigned for an effective and efficient service. This ...
Prediction of Covid-19 risk of a person by analyzing computed tomography images using convolutional neural networks
Topçu, Kaan; Acar, Aybar Can; Department of Information Systems (2024-1-24)
In this thesis, 4 main research questions are answered to evaluate the performance of convolutional neural networks (CNN) in predicting Covid-19 risk by using computed tomography (CT) images. The CT images by Yang et al., ...
CROSS-DISCIPLINARITY IN COGNITIVE SCIENCE: A DOCUMENT SIMILARITY ANALYSIS
Alaşehir, Oğuzhan; Çakır, Murat Perit; Acartürk, Cengiz; Department of Information Systems (2024-1-22)
Systematic quantification of cross-disciplinarity necessitates bibliometric and spatial analysis, socio-institutional aspects, or text-based techniques. Especially, with the advancement in bibliometric methods, a variety o...
Uncovering Hidden Connections and Functional Modules via pyPARAGON: a Hybrid Approach for Network Contextualization
ARICI, Muslum Kaan; Acar, Aybar Can; Tunçbağ, Nurcan; Department of Bioinformatics (2024-1-22)
State-of-the-art omics technologies provide molecular insights into various biological contexts, such as disease states, patients, and drug perturbations. Network inference and reconstruction methods utilize several omics ...
A REFERENCE ARCHITECTURE FOR SIMULATION-BASED DIGITAL TWINS
Kandaz, Murat; Koçyiğit, Altan; Department of Software Management (2024-1-21)
Digital twins can be based on data, physics, rules, behaviors, and geometry models/features. Together with the conventional data-based approach that has been used for decades, other models that are generally based on engin...
Investigating Emotions over the Monetary Outcomes of Wheel-Spin Game using Bayesian Models
Arıcı, İrem; Yet, Barbaros; Department of Cognitive Sciences (2024-1-19)
This study investigates the relationship between emotions and outcomes of wheel-spin game with monetary reward. The inference of emotions by a probabilistic programming language account for both the overall emotional respo...
IDENTIFYING TECHNICAL DEBT AND TOOLS FOR TECHNICAL DEBT MANAGEMENT IN SOFTWARE DEVELOPMENT
Muratdağı, Tolga; Koçyiğit, Altan; Department of Software Management (2024-1-19)
This term project explores the concept of technical debt in software development, as initially articulated by Ward Cunningham in 1992. Technical debt is a multifaceted compromise that involves finding a balance between spe...
A Review of Cyber Security Maturity Assessment Models for OT Systems
Özkaya, Kamil Olcay; Tezcan, Cihangir; Department of Cybersecurity (2024-1-19)
Cyber security holds significant importance in today's interconnected and digitized industrial landscape. Devices ranging from printers to thermostats, washing machines, and cars are produced in a way that allows them to c...
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