Theses - Department of Computer Engineering
Faculty of Engineering
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Deep feature representations and multi-instance multi-label learning of whole slide breast histopathology images
(Bilkent University, 2019-03)The examination of a tissue sample has traditionally involved a pathologist investigating the case under a microscope. Whole slide imaging technology has recently been utilized for the digitization of biopsy slides, ... -
Matrix factorization with stochastic gradient descent for recommender systems
(Bilkent University, 2019-02)Matrix factorization is an efficient technique used for disclosing latent features of real-world data. It finds its application in areas such as text mining, image analysis, social network and more recently and popularly ... -
Reducing processor-memory performance gap and improving network-on-chip throughput
(Bilkent University, 2019-02)Performance of computing systems has tremendously improved over last few decades primarily due to decreasing transistor size and increasing clock rate. Billions of transistors placed on a single chip and switching at ... -
Efficient querying of SBGN maps stored in a graph database
(Bilkent University, 2019-02)Graph visualization is an important research area that endeavors to make graphs more understandable and easier to analyze. In various domains, graph visualization techniques and standards are developed to effectively ... -
Graph embeddings on protein interaction networks
(Bilkent University, 2019-02)Protein-protein interaction (PPI) networks represent the possible set of interactions among proteins and thereby the genes that code for them. By integrating isolated signals on single genes such as mutations or differential ... -
Graph/hypergraph partitioning models for simultaneous load balancing on computation and data
(Bilkent University, 2019-01)In the literature, several successful partitioning models and methods have been proposed and used for computational load balancing of irregularly sparse applications on distributed-memory architectures. However, the ... -
Automatic determination of navigable areas, pedestrian detection, and augmentation of virtual agents in real crowd videos
(Bilkent University, 2018-12)Crowd simulations imitate the behavior of crowds and individual agents in the crowd with personality and appearance, which determines the overall model of a multi-agent system. In such studies, the models are often ... -
Rule based segmentation of colon glands
(Bilkent University, 2018-09)Colon adenocarcinoma, which accounts for more than 90 percent of all colorectal cancers, originates from epithelial cells that form colon glands. Thus, for its diagnosis and grading, it is important to examine the ... -
Recognition of occupational therapy exercises for cerebral palsy
(Bilkent University, 2018-09)Depth camera-based virtual rehabilitation systems are gaining traction in occupational therapy for approaching patients with cerebral palsy. When developing such a system, a domain speci c exercise recognition method is ... -
Algorithms for structural variation discovery using multiple sequence signatures
(Bilkent University, 2018-09)Genomic variations including single nucleotide polymorphisms (SNPs), small INDELs and structural variations (SVs) are known to have significant phenotypic effects on individuals. Among them, SVs, that alter more than 50 ... -
Accelerating the understanding of life's code through better algorithms and hardware design
(Bilkent University, 2018-08)Our understanding of human genomes today is affected by the ability of modern computing technology to quickly and accurately determine an individual's entire genome. Over the past decade, high throughput sequencing (HTS) ... -
Fog supported wireless sensor networks for forest fire detection
(Bilkent University, 2018-09)Fog computing is a new paradigm that aims to extend the concept of cloud computing to the edge of the network, providing the end users network with extra storage and processing power. One big contribution of Fog computing ... -
Characterization of large structural variation using linked-reads
(Bilkent University, 2018-09)Many algorithms aimed at characterizing genomic structural variation (SV) have been developed since the inception of high-throughput sequencing. However, the full spectrum of SVs in the human genome is not yet assessed. ... -
Automated cell analysis in microscopy images
(Bilkent University, 2018-09)High-throughput microscopy systems have become popular recently, which facilitate to acquire boundless microscopy images without requiring human intervention. However, the analysis of such amount of images using conventional ... -
A producer-centric caching strategy for named data networking
(Bilkent University, 2018-09)With growing number of users and content on Internet, the existing Internet architecture needs to evolve to be more efficient to find and carry content, and Named Data Networking (NDN) is a new Internet architecture ... -
Privacy protection for spatial trajectories against brute-force attacks
(Bilkent University, 2018-08)The prevalence of Global Positioning System (GPS) equipped mobile devices and wireless communication technologies have resulted in widespread development of location-based services (LBS). As some typical examples of LBS, ... -
Quantifying and protecting genomic privacy
(Bilkent University, 2018-08)Today, genome sequencing is more accessible and affordable than ever. It is also possible for individuals to share their genomic data with service providers or on public websites. Although genomic data has significant ... -
Deep learning based cell segmentation in histopathological images
(Bilkent University, 2018-08)In digital pathology, cell imaging systems allow us to comprehend histopathological events at the cellular level. The first step in these systems is generally cell segmentation, which substantially affects the subsequent ... -
Graph problems in call models and switching networks
(Bilkent University, 2018-08)In the first part of this dissertation, we focus on graph problems that arise in call models. Such models are used to study the combinatorial properties of certain types of calls that include unicast, multicast, and ... -
Deepkinzero: zero-shot learning for predicting kinase phosphorylation sites
(Bilkent University, 2018-08)Protein kinases are a large family of enzymes that catalyze the phosphorylation of other proteins. By acting as molecular switches for protein activity, the phosphorylation events regulate intracellular signal transduction, ...
