Theses - Department of Computer Engineering
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OpenCL-based efficient HLS implementation of iterative graph algorithms on FPGA
(Bilkent University, 2021-01)The emergence of CPU-FPGA hybrid architectures creates a demand for high abstraction programming tools such as High-Level Synthesis (HLS). HLS handles most of the FPGA development tasks automatically, thus freeing up ... -
Self-supervised representation learning with graph neural networks for region of interest analysis in breast histopathology
(Bilkent University, 2021-01)Deep learning has made a major contribution to histopathology image analysis with representation learning outperforming hand-crafted features. However, two notable challenges remain. The first is the lack of large ... -
Weakly supervised approaches for image classification in remote sensing and medical image analysis
(Bilkent University, 2021-01)Weakly supervised learning (WSL) aims to utilize data with imprecise or noisy annotations to solve various learning problems. We study WSL approaches in two different domains: remote sensing and medical image analysis. For ... -
Text mining analysis of translation, social communication and literary writing for Turkish
(Bilkent University, 2021-01)Text mining is an important research area considering the increase in text generation and the need for analysis. Text mining in Turkish is still not a wellinvested research area, compared to the other languages. In this ... -
Accelerating pagerank with a heterogeneous two phase CPU-FPGA algorithm
(Bilkent University, 2021-01)PageRank is a network analysis algorithm that is used to measure the importance of each vertex in a graph. Fundamentally it is a Sparse Matrix-Vector multiplication problem and suffers from the same bottlenecks, such as ... -
Bounding volume hierarchy-tetrahedralization hybrid acceleration structure for ray tracing
(Bilkent University, 2020-12)The computational cost of the ray-tracing method is directly proportional to the number of ray-surface intersection tests. The naive ray-tracing algorithm requires O(N) computational cost for the ray-surface intersection ... -
On the tradeoff between privacy and utility in genomic studies: differential privacy under dependent tuples
(Bilkent University, 2020-11)The rapid progress in genome sequencing and the decrease in the sequencing costs have led to the high availability of genomic data. Studying these data can greatly help answer the key questions about disease associations ... -
Deep learning for digital pathology
(Bilkent University, 2020-11)Histopathological examination is today’s gold standard for cancer diagnosis and grading. However, this task is time consuming and prone to errors as it requires detailed visual inspection and interpretation of a ... -
Multitask learning of gene risk for autism spectrum disorder and intellectual disability
(Bilkent University, 2020-11)Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) are comorbid neurodevelopmental disorders with complex genetic architectures. Despite largescale sequencing studies only a fraction of the risk genes were ... -
Predicting informative spatio-temporal neurodevelopmental windows and gene risk for autism spectrum disorder
(Bilkent University, 2020-11)Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder with a strong genetic basis. Due to its intricate nature, only a fraction of the risk genes were identified despite the effort spent on large-scale ... -
Unsupervised concept drift detection using sliding windows: two contributions
(Bilkent University, 2020-10)Data stream mining has become an important research area over the past decade due to the increasing amount of data available today. Sources from various domains generate limitless volume of data in temporal order. Such ... -
A compound graph layout algorithm with support for ports
(Bilkent University, 2020-11)Information visualization is a eld of study that aims to represent abstract data in an aesthetically pleasing and easy to comprehend visual manner. Various approaches and standards have been created to reinforce the ... -
Scratch-pad memory based custom processor design for graph applications
(Bilkent University, 2020-09)As more and more domains have started to process ever-growing graphs, the importance of graph analytics applications became more apparent. However, general-purpose processors are challenged to deal with the large memory ... -
Custom hardware optimizations for reliable and high performance computer architectures
(Bilkent University, 2020-09)In recent years, we have witnessed a huge wave of innovations, such as in Artificial Intelligence (AI) and Internet-of-Things (IoT). In this trend, software tools are constantly and increasingly demanding more processing ... -
Doubletdetector: a method to detect doublet cells in open chromatin regions
(Bilkent University, 2020-09)Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a simple and effective technique in genomic studies that shows the chromatin accessibility of the genome. The open regions of the genome play an ... -
Predicting carbon spectrum in heteronuclear single quantum coherence spectroscopy for online feedback during surgery
(Bilkent University, 2020-09)1H High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) is a reliable technology used for detecting metabolites in solid tissues. Fast response time enables guiding surgeons in real time, for ... -
Towards a taxonomy of code review smells
(Bilkent University, 2020-10)Code review is a crucial step of the software development life cycle in order to detect possible problems in source code before merging the changeset to the codebase. Although there is no consensus on a formally defined ... -
Parallel stochastic gradient descent on multicore architectures
(Bilkent University, 2020-09)The focus of the thesis is efficient parallelization of the Stochastic Gradient Descent (SGD) algorithm for matrix completion problems on multicore architectures. Asynchronous methods and block-based methods utilizing 2D ... -
Server and wireless network resource allocation strategies in heterogeneous cloud data centers
(Bilkent University, 2020-09)Resource allocation is one of the most important challenges in operating a data center. We investigate allocation of two main types of resources: servers and network links. Server resource allocation problem is the ... -
GateKeeper-GPU: accelerated pre-alignment filtering in short read mapping
(Bilkent University, 2020-09)Recent advances in high throughput sequencing (HTS) facilitate fast production of short DNA fragments (reads) in numerous amounts. Although the production is becoming inexpensive everyday, processing the present data for ...
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