In this study, we presented a regression model, which was applied on cytotoxic bioactivity data obtained from HCC cells (from CanSyL dataset). Our objective was to predict off-target effects as potential new targets by regularizing the regression space based on the kinome tree topology. Our model was tested on the CanSyL dataset by applying LOOCV and achieved promising predictions. Then we scaled up our approach to the public datasets (CCLE and GDSC). Some kinase inhibitors were identified as outliers based on their individual RMSE. This difference suggests that outlier inhibitors are more specific inhibitors while non-outlier inhibitors are mostly multi-kinase inhibitors.

Date: 06.09.2019 / 10:00 Place: A-108

In the first part of this thesis, a BIM based architectural visualization and design tool is developed for VR, MR and PC environments. BIM provides detailed information and tools to professionals so that they can develop and manage buildings and infrastructures efficiently. In the second part of this thesis, two tutorial-like serious games, based on VR and MR environments, are developed to improve the users’ overall experience and to ease the user interactions in virtual environments. The developed tool and the serious games were tested by architects and game developers, and were evaluated from presence, usability, and technology acceptance perspectives.

Date: 29.08.2019 / 16:00 Place: A-212

Features extracted from speech are widely used for problems such as biometric speaker identification, but the use of speech data raises concerns about privacy. We propose a method for speech and posture classification using only breath data. The acoustical information was extracted from breath instances using the Hilbert-Huang transform and fed into our CNN-LSTM network for classification. We also created our publicly available dataset, BreathBase, which contains more than 4600 breath instances of 20 participants in 5 different postures with 4 different microphones. Using this data, 56% speaker classification and 96% posture classification accuracy is obtained.

Date: 02.09.2019 / 11:00 Place: A-212

Accumulation of genomic alterations can lead to tumorigenesis. One of the deadliest brain tumor type, Glioblastoma is well-known for its genomic heterogeneity which makes the disease as incurable. In this thesis, we aimed to decrease the heterogeneity among Glioblastoma patients from The Cancer Genome Atlas (TCGA), classify the patients and propose therapeutic hypothesis for patient groups by using patient mutation profiles. We therefore implemented a systems level approach using three dimensional (3D) spatial organization of the mutations (mutation patches), organization of mutated proteins in patient specific protein interaction networks, and drug responses of the GBM cell lines.

Date: 28.08.2019 / 11:00 Place: A-212

There is a high demand for realistic computer aided imagery by many applicatiion areas such as games and movies. Due to the complicated characteristics of certain natural phenomena such as fire, smoke or mist, it is difficult to realistically mimic these effects. There are various approximation methods to visually synthesize lifelike 3D artifacts. The use of flow fields to guide the motion of particles creates a random but natural-looking effect. The aim of this study is to use flow fields to generate realistic 3D visual effects.

Date: 06.09.2019 / 11:00 Place: A-212

In this thesis, we investigated the suitability and adaptability of the lightweight cryptographic algorithms on IoT devices, and compare their implementations with those of standard algorithms. We realized our implementations on the Arduino Uno platform, which is widely used in several embedded applications and preferred as a target development platform for its low price-performance ratio. We mainly focused on block ciphers and hash functions, which are the fundamental components of many cryptographic protocols. Among these protocols, Internet Protocol Security (IPSec) suite and DTLS are perhaps from the most well-known and commonly used ones. With our study, we plan to provide results that may be guidelines for existing and future lightweight implementations of IPSec, DTLS and other security protocols on IoT devices.

Date: 26.07.2019 / 13:00 Place: A-212

In this thesis, we aim to analyze NGS data of three different domestic horse families to detect de novo mutations that occur within one generation. We found a higher number of true positives in highly covered data, while a lower number of true positives in the low covered data, showing the importance of sequencing coverage to detect true de novo mutations. In addition, to make estimations on the demographic history of the families we made PSMC and ROH analysis. Results of these analyses were coherent with previous studies. All in all, we had an idea for the minimum coverage threshold and quality of whole-genome sequencing data, to determine de novo mutations and to estimate population demography.

Date: 29.07.2019 / 11:00 Place: A-212

Neolithic transition which has started approximately 10,000 year ago in west Eurasia and created a major shifts in human life. In many studies, strong selection signals on the genes related to changes in life-style were determined. With the advent of archeogenomics studies, those adaptations have also been supported using ancient DNA. Here, polygenic adaptations in Anatolia were investigated by comparing Neolithic (n=36) and modern-day (n=16) genome sequences for 40 polygenic traits potentially associated with diet, immunity and other related complex traits using pairwise F_ST and population branch statistics (PBS) method which provides a genome-wide selection analysis including a distant population.

Date: 29.07.2019 Place: A-212

The work reported in thesis investigates direction-of-arrival estimation methods for sound sources and proposes novel method called HiGRID and its extensions with DPD test and EB-MUSIC. Proposed methods are based on spherical harmonic decomposition and rigid spherical microphone arrays enables trivial calculation of spherical harmonic decomposition of sound fields. Evaluation of proposed methods are presented in terms of direction-of-arrival estimation errors.

Date: 26.07.2019 Place: A-212

Artificial reverberators provide a computationally viable alternative to full-scale room acoustics simulation methods for games and extended reality applications. Scattering delay network (SDN) is a relatively recent artificial reverberator that allows direct parametric control over the geometry of a simulated rectangular enclosure. We propose a new model called coupled volume scattering delay networks (CV-SDN) which extends the classic SDN structure for enclosures coupled via an aperture. The extension allows independent control of acoustical properties of volumes and the size of the connecting aperture. The utility of the proposed method is demonstrated by the energy decay curves obtained from impulse responses.

Date: 26.07.2019 Place: A-212