Mühendislik ve Doğa Bilimleri Fakültesi

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Citation Count: 5
(3+3+2) Warped-Like Product Manifolds With Spin(7) Holonomy
(Elsevier Science Bv, 2011) Uğuz, Selman; Bilge, Ayşe Hümeyra
We consider a generalization of eight-dimensional multiply warped product manifolds as a special warped product by allowing the fiber metric to be non-block diagonal. We define this special warped product as a (3 + 3 + 2) warped-like manifold of the form M = F x B. where the base B is a two-dimensional Riemannian manifold and the fibre F is of the form F = F-1 x F-2 where the F-i(i = 1 2) are Riemannian 3-manifolds. We prove that the connection on M is completely determined by the requirement that the Bonan 4-form given in the work of Yasui and Ootsuka [Y. Yasui and T. Ootsuka Spin(7) holonomy manifold and superconnection Class. Quantum Gravity 18(2001)807-816] be closed. Assuming that the F-i are complete connected and simply connected it follows that they are isometric to S-3 with constant curvature k > 0 and the Yasui-Ootsuka solution is unique in the class of (3 + 3 + 2) warped-like product metrics admitting a specific Spin(7) structure. Crown Copyright (C) 2011 Published by Elsevier B.V. All rights reserved.
Citation Count: 11
Accurate Refinement of Docked Protein Complexes Using Evolutionary Information and Deep Learning
(Imperıal College Press, 2016) Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work we introduced AccuRefiner a machine learning based tool for refining protein-protein complexes. Given a docked complex the refinement tool produces a small set of refined versions of the input complex with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 angstrom error margin on average by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.
Citation Count: 4
Agent-Based Optimization To Estimate Nash Equilibrium in Power Markets
(Taylor & Francis Inc, 2013) Yücekaya, Ahmet; Valenzuela, Jorge
In most deregulated power markets firms bid daily into a day-ahead power market. The auction mechanism supply and demand determine the equilibrium at each hour. In this environment firms aim to maximize their revenues by carefully determining their bids. This requires the development of effective computational methods that help them estimate their competitors' behaviors under incomplete information. In this article an agent-based method that uses particle swarm optimization is described to simulate the behavior of market participants. Particle swarm optimization is used in the bidding process and an agent-based model is applied to find a Nash equilibrium. Different stopping conditions are used to determine the equilibrium. Experimental results are presented for two power systems.
Citation Count: 0
An Alternative Approach To Design Lumped Element Delay Equalizers
(Istanbul Univ Fac Engineering, 2015) Şengül, Metin Y.
In this paper an algorithm has been proposed to design lumped element delay equalizers which is considered as a single block as opposed to the existing methods in literature. Then after obtaining the desired delay performance the designed delay equalizer is divided and realized as cascaded first-order and/or second-order all-pass circuits. An example is given to illustrate the utilization of the proposed algorithm.
Citation Count: 0
Alternative Transducer Power Gain Expression in Broadband Matching Network Designs
(IEEE, 2016) Şengül, Metin Y.
In this paper a reflection coefficient based transducer power gain expression has been derived which is an alternative to the impedance based expression exists in the literature. A broadband double matching problem is solved by using the derived gain expression and the obtained performance has been compared with the performance obtained via the existing expression.
Citation Count: 1
An Analysis for the Use of Compressed Sensing Method in Microwave Imaging
(IEEE, 2017) Yiğit, Enes; Tekbaş, Mustafa; Ünal, İlhami; Erdoğan, Sercan; Çalışkan, Cafer
One of the most important problems encountered in microwave imaging methods is intensive data processing traffic that occurs when high resolution and real time tracking is desired. Radar signals can be recovered without loss of data with a randomly selected subset of the measurement data by compression sensing (CS) method which has been popular in recent years. For this reason, in this study, the use and capabilities of the CS method were investigated for tracking moving human, and the target information was correctly determined for the data obtained much below the Nyquist sampling criterion. In this study, it was revealed that the CS method can be developed for target detection and tracking
Citation Count: 3
Analytic Network Process (anp) for Solar Power Plant Location Problem
(Institute of Industrial Engineers, 2010) Ayağ, Zeki; Samanlıoğlu, Funda
Solar energy is the most readily available source of energy and one of the most important sources of the renewable energy because it is non-polluting and helps in lessening the greenhouse effect. Main problem of establishing a solar power plant is to determine its location. In the presence of many location alternatives and evaluation criteria a multiple-criteria decision making problem arises. In this work the location problem will be solved by using Analytic Network Process (ANP) to figure out the most satisfying alternative. A numerical example is also included to show the proposed methodology in Turkey.
Citation Count: 2
Anomaly Detection İn Walking Trajectory [yürüyüş Yörüngesinde Anormallik Algılama]
(Institute of Electrical and Electronics Engineers Inc., 2018) Öğrenci, Arif Selçuk
Analysis of the walking trajectory and the detection of anomalies in this trajectory provide important benefits in the fields of health and security. In this work two methods to detect anomalies in trajectories are compared. Firstly an unsupervised method is used where the conformance among trajectories are taken into consideration. Trajectories that deviate from others are qualified as anomalies. Secondly the points in the trajectories are considered as a time series. Artifical neural networks performing supervised learning based on the backpropagation algorithm are used. The results are compared and the points to be enhanced are highlighted.
Citation Count: 10
Application of Epidemic Models To Phase Transitions
(Taylor & Francis Ltd, 2012) Bilge, Ayşe Hümeyra; Pekcan, Önder; Gürol, M. V.
The Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) models describe the spread of epidemics in a society. In the typical case, the ratio of the susceptible individuals fall from a value S-0 close to 1 to a final value S-f, while the ratio of recovered individuals rise from 0 to R-f = 1 - S-f. The sharp passage from the level zero to the level R-f allows also the modeling of phase transitions by the number of "recovered" individuals R(t) of the SIR or SEIR model. In this article, we model the sol-gel transition for polyacrylamide-sodium alginate (SA) composite with different concentrations of SA as SIR and SEIR dynamical systems by solving the corresponding differential equations numerically and we show that the phase transitions of "classical" and "percolation" types are represented, respectively, by the SEIR and SIR models.
Citation Count: 1
Ask me: A Question Answering System via Dynamic Memory Networks
(Institute of Electrical and Electronics Engineers Inc., 2019) Yiğit, Gülsüm; Amasyalı, Mehmet Fatih
Most of the natural language processing problems can be reduced into a question answering problem. Dynamic Memory Networks (DMNs) are one of the solution approaches for question answering problems. Based on the analysis of a question answering system built by DMNs described in [1], this study proposes a model named DMN∗ which contains several improvements on its input and attention modules. DMN∗ architecture is distinguished by a multi-layer bidirectional LSTM (Long Short Term Memory) architecture on input module and several changes in computation of attention score in attention module. Experiments are conducted on Facebook bAbi dataset [2]. We also introduce Turkish bAbi dataset, and produce increased vocabulary sized tasks for each dataset. The experiments are performed on English and Turkish datasets and the accuracy performance results are compared by the work described in [1]. Our evaluation shows that the proposed model DMN∗ obtains improved accuracy performance results on various tasks for both Turkish and English.
Citation Count: 13
Bayesian Compressive Sensing for Primary User Detection
(Inst Engineering Technology-IET, 2016) Başaran, Mehmet; Erküçük, Serhat; Cirpan, Hakan Ali
In compressive sensing (CS)-based spectrum sensing literature most studies consider accurate reconstruction of the primary user signal rather than detection of the signal. Furthermore possible absence of the signal is not taken into account while evaluating the spectrum sensing performance. In this study Bayesian CS is studied in detail for primary user detection. In addition to assessing the signal reconstruction performance and comparing it with the conventional basis pursuit approach and the corresponding lower bounds signal detection performance is also considered both analytically and through simulation studies. In the absence of a primary user signal the trade-off between probabilities of detection and false alarm is studied as it is equally important to determine the performance of a CS approach when there is no active primary user. To reduce the computation time and yet achieve a similar detection performance finally the effect of number of iterations is studied for various systems parameters including signal-to-noise-ratio compression ratio mean value of accumulated energy and threshold values. The presented framework in this study is important in the overall implementation of CS-based approaches for primary user detection in practical realisations such as LTE downlink OFDMA as it considers both signal reconstruction and detection.
Citation Count: 3
Bayesian Compressive Sensing for Ultra-Wideband Channel Estimation: Algorithm and Performance Analysis
(Springer, 2015) Özgör, Mehmet; Erküçük, Serhat; Çırpan, Hakan Ali
Due to the sparse structure of ultra-wideband (UWB) channels compressive sensing (CS) is suitable for UWB channel estimation. Among various implementations of CS the inclusion of Bayesian framework has shown potential to improve signal recovery as statistical information related to signal parameters is considered. In this paper we study the channel estimation performance of Bayesian CS (BCS) for various UWB channel models and noise conditions. Specifically we investigate the effects of (i) sparse structure of standardized IEEE 802.15.4a channel models (ii) signal-to-noise ratio (SNR) regions and (iii) number of measurements on the BCS channel estimation performance and compare them to the results of -norm minimization based estimation which is widely used for sparse channel estimation. We also provide a lower bound on mean-square error (MSE) for the biased BCS estimator and compare it with the MSE performance of implemented BCS estimator. Moreover we study the computation efficiencies of BCS and -norm minimization in terms of computation time by making use of the big- notation. The study shows that BCS exhibits superior performance at higher SNR regions for adequate number of measurements and sparser channel models (e.g. CM-1 and CM-2). Based on the results of this study the BCS method or the -norm minimization method can be preferred over the other one for different system implementation conditions.
Citation Count: 5
Biclustering Expression Data Based on Expanding Localized Substructures
(Springer-Verlag Berlin, 2009) Erten, Cesim; Sözdinler, Melih
Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. We provide a method LEB (Localize-and-Extract Biclusters) which reduces the search space into local neighborhoods within the matrix by first localizing correlated structures. The localization procedure takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. Once interesting structures are localized the search space reduces to small neighborhoods and the biclusters are extracted from these localities. We evaluate the effectiveness of our method with extensive experiments both using artificial and real datasets.
Citation Count: 12
Blind Dockings of Benzothiazoles To Multiple Receptor Conformations of Triosephosphate Isomerase From Trypanosoma Cruzi and Human
(Wiley-VCH Verlag GmbH, 2011) Kurkcuoglu, Zeynep; Ural, Gulgun; Akten, Ebru Demet; Doruker, Pemra
We aim to uncover the binding modes of benzothiazoles which have been reported as specific inhibitors of triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) by performing blind dockings on both TcTIM and human TIM (hTIM). Detailed analysis of binding sites and specific interactions are carried out based on ensemble dockings to multiple receptor conformers obtained from molecular dynamics simulations. In TcTIM dimer dockings the inhibitors preferentially bind to the tunnel-shaped cavity formed at the interface of the subunits whereas non-inhibitors mostly choose other sites. In contrast TcTIM monomer binding interface and hTIM dimer interface do not present a specific binding site for the inhibitors. These findings point to the importance of the tunnel and of the dimeric form for inhibition of TcTIM. Specific interactions of the inhibitors and their sulfonate-free derivatives with the receptor residues indicate the significance of sulfonate group for binding affinity and positioning on the TcTIM dimer interface. One of the inhibitors also binds to the active site which may explain its relatively higher inhibition effect on hTIM.
Citation Count: 1
Broadband Matching Via Reflection Function Optimization
(Wiley, 2017) Şengül, Metin Y.
In this paper a practical approach is presented for designing broadband matching networks via reflection function optimization. In the proposed algorithm the input or output reflection function of the matching network is expressed in terms of three real polynomials describing the matching network load and generator reflection coefficients. Next one of the polynomials is optimized to get minimum reflection function values in the passband. Then matching network topology and element values are obtained via the formed input reflection coefficient expression. Two examples are presented to explain the usage of the new approach. Copyright (c) 2016 John Wiley & Sons Ltd.
Citation Count: 2
Broadband Matching Via Unequal Length Cascaded Transmission Lines
(World Scientific Publ Co Pte Ltd, 2017) Şengül, Metin Y.
In this paper a new approach based on the real frequency technique (RFT) has been proposed to solve broadband matching problems using cascaded unequal length transmission lines. At the end of the design process optimum characteristic impedance and delay values of transmission lines are obtained. Two examples are given to illustrate the utilization of the proposed approach.
Citation Count: 4
Broadband Single Matching With Lumped Elements
(Institute of Electrical and Electronics Engineers Inc., 2016) Şengül, Metin Y.
While designing broadband single matching networks for microwave communication systems via commercially available software tools it is necessary for these tools to select the proper matching network topology and element values. But how to make these selections is an unknown problem. But the proposed approach in this paper presents a practical method to generate single matching networks with good initial element values. After completing the design the performance of the designed single matching network is trimmed employing the commercially available computer-aided design (CAD) tools. The approach is explained via the given example which shows that proposed approach provides very good initials for CAD tools. © 2015 Chamber of Electrical Engineers of Turkey.
Citation Count: 3
Busy Tone Based Coexistence Algorithm for Wran and Wlan Systems in Tv White Space
(Inst Engineering Technology-IET, 2018) Karatalay, Onur; Erküçük, Serhat; Baykaş, Tunçer
TV White Space (TVWS) refers to frequency band reserved only for licensed terrestrial TV broadcasting and is opened to unlicensed use under regulatory conditions. While regulations protect licensed systems from interference interference among unlicensed systems is left mainly to manufacturers. Consequently there is a need to develop new coexistence approaches between TVWS networks. Busy tone broadcasting is a coexistence method which can be used by TVWS networks to announce the selected frequency band is occupied. In this paper a busy tone based coexistence algorithm is proposed for IEEE 802.11af and IEEE 802.22 networks and analyzed by considering different client distributions experiencing log-normal shadowing where the exact interfering packet rate and successful packet transmission rate expressions are obtained and validated by simulations for different scenarios. The results show that with the proposed coexistence approach a WLAN can reliably detect the busy tone signal to change its frequency band and can reduce interference to WRAN. Even if there is no available frequency band for the WLAN the WRAN still maintains its enhanced successful packet transmission performance. The deployment of the proposed algorithm is important for successful coexistence between cognitive wireless networks where interference is not regulated such as in TVWS bands.
Citation Count: 1
Busy Tone Based Power Control for Coordination of Iffy 802.11af and 802.22 System
(IEEE, 2017) Ülgen, Oğuz; Erküçük, Serhat; Karatalay, Onur; Baykas, Tuncer
In this paper, a new power control algorithm based on busy tone approach has been proposed for the coordination of IEEE 802.22 and IEEE 802.11af systems in TV white space. Different from the earlier studies, in addition to both 802.11af access point and clients listening to the busy tone, they also adjust their communication power according to the location information and use hopping for communication, if needed Acccordingly, interference caused to 802.22 systems has been reduced while the 802.11af systems are still able to communicate. This study quantifies the 802.11af and 802.22 system performances in terms of interfering packet rate and succesful packet transmission rate for different scenarios considering the communication parameters and channel models adapted for the standards.
Citation Count: 18
Carboxylic Acid Derivatives Display Potential Selectivity for Human Histone Deacetylase 6: Structure-Based Virtual Screening Molecular Docking and Dynamics Simulation Studies
(Elsevier Science, 2018) Uba, Abdullahi Ibrahim; Yelekçi, Kemal
Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of alpha-tubulin making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available providing avenues for structure-based drug design campaign. Here in our continuous effort to identify potentially selective HDAC6 inhibitors structure-based virtual screening of similar to 72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated Delta G < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment displayed potential selectivity for HDAC6 over HDAC7 and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions and the root-mean-square deviation (RMSD) radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity. (C) 2018 Elsevier Ltd. All rights reserved.

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