Theses - Department of Computer Engineering
Faculty of Engineering
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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, ... -
Parallel streaming graph partitioning utilizing multilevel framework
(Bilkent University, 2018-08)Graph partitioning is widely used for e cient parallelization of a variety of applications. Streaming graph partitioning is a one pass partitioning solution provided to overcome high computation costs of o ine graph ... -
Spatio-temporal gene discovery for autism spectrum disorder
(Bilkent University, 2018-08)Whole Exome Sequencing (WES) studies for Autism Spectrum Disorder (ASD) could identify only around six dozen risk genes to date, because the genetic architecture of the disorder is highly complex. To speed the gene ... -
Relevance feedback and sparsity handling methods for temporal data
(Bilkent University, 2018-08)Data with temporal ordering arises in many natural and digital processes with an increasing importance and immense number of applications. This study provides solutions to data mining problems in analyzing time series ... -
Privacy-preserving computation and robust watermarking techniques for healthcare data
(Bilkent University, 2018-08)Health and genomic data is sensitive in terms of carrying private information about individuals. One can infer inherited/genetic disorders, their occurrence probabilities, information about race, and kinship by analyzing ... -
Spadis: selecting predictive and diverse SNPS in GWAS
(Bilkent University, 2018-08)Phenotypic heritability of complex traits and diseases is seldom explained by individual genetic variants identi ed in genome-wide association studies (GWAS). Many methods have been developed to select a subset of variant ... -
Improvements on pathwaymapper: a collaborative pathway curation tool
(Bilkent University, 2018-07)Information visualization focuses on visually representing abstract data to amplify human cognition. Graph visualization is one of the most common types in the eld of information visualization because of its capabilities ... -
Methods and tools for synchronized visualization of evolving networks
(Bilkent University, 2018-07)Graph visualization is a powerful tool to convey and analyze relational information in the form of networks such as biological networks, social networks, and computer networks. Abundant research has been conducted on the ... -
Fine-grained object recognition in remote sensing imagery
(Bilkent University, 2018-06)Fine-grained object recognition aims to determine the type of an object in domains with a large number of sub-categories. The steadily increase in spatial and spectral resolution entailing new details in remote sensing ... -
High throughput udp-based peer-to-peer secure data transfer
(Bilkent University, 2018-06)High throughput sequencing (HTS) platforms have been developed in recent years. These technologies enable researchers to answer a wide range of biological questions by obtaining whole or targeted segments of genomes of ...
