Bilgisayar Mühendisliği Bölümü

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Citation - WoS: 6
Citation - Scopus: 6
Auction-Based Serious Game for Bug Tracking
(Wiley, 2019) Usfekes, Cagdas; Tuzun, Eray; Yilmaz, Murat; Macit, Yagup; Clarke, Paul
Today, one of the challenges in software engineering is utilising application lifecycle management (ALM) tools effectively in software development. In particular, it is hard for software developers to engage with the work items that are appointed to themselves in these ALM tools. In this study, the authors have focused on bug tracking in ALM where one of the most important metrics is mean time to resolution that is the average time to fix a reported bug. To improve this metric, they developed a serious game application based on an auction-based reward mechanism. The ultimate aim of this approach is to create an incentive structure for software practitioners to find and resolved bugs that are auctioned where participants are encouraged to solve and test more bugs in less time and improve quality of software development in a competitive environment. They conduct hypothesis tests by performing a Monte Carlo simulation. The preliminary results of this research support the idea that using a gamification approach for an issue tracking system enhances the productivity and decreases mean time to resolution.
Citation - WoS: 17
Citation - Scopus: 18
Boron Doped Graphene Nanostructures
(Wiley-v C H verlag Gmbh, 2008) Ozdogan, Cem; Kunstmann, Jens; Fehske, Holger; Quandt, Alexander
We present results from an ab initio study of metallized semiconducting graphene nanostructures. Our model system consists of an alternating chain of quasi-planar B-7 clusters embedded into a semiconducting arm-chair nanoribbon. We observe the appearance of overlapping bands around the Fermi-level, with crystal momenta pointing into the direction of these boron chains. This observation could be a vantage point for the development of graphene nanodevices and integrated nanocircuits, based on existing technologies. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
Citation - WoS: 21
Citation - Scopus: 22
Computerized Detection and Segmentation of Mitochondria on Electron Microscope Images
(Wiley, 2012) Tasel, S. F.; Perkins, G.; Martone, M. E.; Gurcan, M. N.; Mumcuoglu, E. U.; Hassanpour, R.
Mitochondrial function plays an important role in the regulation of cellular life and death, including disease states. Disturbance in mitochondrial function and distribution can be accompanied by significant morphological alterations. Electron microscopy tomography (EMT) is a powerful technique to study the 3D structure of mitochondria, but the automatic detection and segmentation of mitochondria in EMT volumes has been challenging due to the presence of subcellular structures and imaging artifacts. Therefore, the interpretation, measurement and analysis of mitochondrial distribution and features have been time consuming, and development of specialized software tools is very important for high-throughput analyses needed to expedite the myriad studies on cellular events. Typically, mitochondrial EMT volumes are segmented manually using special software tools. Automatic contour extraction on large images with multiple mitochondria and many other subcellular structures is still an unaddressed problem. The purpose of this work is to develop computer algorithms to detect and segment both fully and partially seen mitochondria on electron microscopy images. The detection method relies on mitochondria's approximately elliptical shape and double membrane boundary. Initial detection results are first refined using active contours. Then, our seed point selection method automatically selects reliable seed points along the contour, and segmentation is finalized by automatically incorporating a live-wire graph search algorithm between these seed points. In our evaluations on four images containing multiple mitochondria, 52 ellipses are detected among which 42 are true and 10 are false detections. After false ellipses are eliminated manually, 14 out of 15 fully seen mitochondria and 4 out of 7 partially seen mitochondria are successfully detected. When compared with the segmentation of a trained reader, 91% Dice similarity coefficient was achieved with an average 4.9 nm boundary error.
Citation - WoS: 22
Citation - Scopus: 24
Deep Learning Methods in the Diagnosis of Sacroiliitis From Plain Pelvic Radiographs
(Oxford Univ Press, 2023) Ureten, Kemal; Maras, Yuksel; Duran, Semra; Gok, Kevser
Objectives The aim of this study is to develop a computer-aided diagnosis method to assist physicians in evaluating sacroiliac radiographs. Methods Convolutional neural networks, a deep learning method, were used in this retrospective study. Transfer learning was implemented with pre-trained VGG-16, ResNet-101 and Inception-v3 networks. Normal pelvic radiographs (n = 290) and pelvic radiographs with sacroiliitis (n = 295) were used for the training of networks. Results The training results were evaluated with the criteria of accuracy, sensitivity, specificity and precision calculated from the confusion matrix and AUC (area under the ROC curve) calculated from ROC (receiver operating characteristic) curve. Pre-trained VGG-16 model revealed accuracy, sensitivity, specificity, precision and AUC figures of 89.9%, 90.9%, 88.9%, 88.9% and 0.96 with test images, respectively. These results were 84.3%, 91.9%, 78.8%, 75.6 and 0.92 with pre-trained ResNet-101, and 82.0%, 79.6%, 85.0%, 86.7% and 0.90 with pre-trained inception-v3, respectively. Conclusions Successful results were obtained with all three models in this study where transfer learning was applied with pre-trained VGG-16, ResNet-101 and Inception-v3 networks. This method can assist clinicians in the diagnosis of sacroiliitis, provide them with a second objective interpretation and also reduce the need for advanced imaging methods such as magnetic resonance imaging.
Citation - Scopus: 6
Design Effort Estimation Using Complexity Metrics
(2004) Salman, N.; Salman, Nael; Doǧru, A.; Bilgisayar Mühendisliği
Component-oriented software development is a new trend and is becoming very popular these days. In addition to requiring a different development approach, the new orientation also requires a different metrics approach. A set of metrics for Component Oriented Software Engineering was first introduced in previous research. These metrics set were used to measure the quality of component-oriented software designs. The impact of these metrics on design effort is investigated in this paper. A statistical model is developed based on nine projects that carried out component-oriented software development. Design effort is expressed as a junction of a subset of the complexity metrics.
Citation - WoS: 107
Citation - Scopus: 111
Determination of Complete Melting and Surface Premelting Points of Silver Nanoparticles by Molecular Dynamics Simulation
(Amer Chemical Soc, 2013) Yavuz, M.; Zhou, Y.; Alarifi, H. A.; Atis, M.; Ozdogan, C.; Hu, A.
A molecular dynamics simulation based on the embedded-atom method was conducted at different sizes of single-crystal Ag nanoparticles (NPs) with diameters of 4 to 20 nm to find complete melting and surface premelting points. Unlike the previous theoretical models, our model can predict both complete melting and surface premelting points for a wider size range of NPs. Programmed heating at an equal rate was applied to all sizes of NPs. Melting kinetics showed three different trends that are, respectively, associated with NPs in the size ranges of 4 to 7 rim, 8 to 10 nm, and 12 to 20 nm. NPs in the first range melted at a single temperature without passing through a surface premelting stage. Melting of the second range started by forming a quasi-liquid layer that expanded to the core, followed by the formation of a liquid layer of 1.8 nm thickness that also subsequently expanded to the core with increasing temperature and completed the melting process. For particles in the third range, the 1.8 nm liquid layer was formed once the thickness of the quasi-liquid layer reached S rim. The liquid layer expanded to the core and formed thicker stable liquid layers as the temperature increased toward the complete melting point. The ratio of the quasi-liquid layer thickness to the NP radius showed a linear relationship with temperature.
Citation - WoS: 10
Citation - Scopus: 12
The Diagnosis of Developmental Dysplasia of the Hip From Hip Ultrasonography Images With Deep Learning Methods
(Lippincott Williams & Wilkins, 2023) Ureten, Kemal; Tokdemir, Gul; Tolunay, Tolga; Ciceklidag, Murat; Atik, Osman Sahap; Atalar, Hakan
Background:Hip ultrasonography is very important in the early diagnosis of developmental dysplasia of the hip. The application of deep learning-based medical image analysis to computer-aided diagnosis has the potential to provide decision-making support to clinicians and improve the accuracy and efficiency of various diagnostic and treatment processes. This has encouraged new research and development efforts in computer-aided diagnosis. The aim of this study was to evaluate hip sonograms using computer-assisted deep-learning methods. Methods:The study included 376 sonograms evaluated as normal according to the Graf method, 541 images with dysplasia and 365 images with incorrect probe position. To classify the developmental hip dysplasia ultrasound images, transfer learning was applied with pretrained VGG-16, ResNet-101, MobileNetV2 and GoogLeNet networks. The performances of the networks were evaluated with the performance parameters of accuracy, sensitivity, specificity, precision, F1 score, and AUC (area under the ROC curve). Results:The accuracy, sensitivity, specificity, precision, F1 score, and AUC results obtained by testing the VGG-16, ResNet-101, MobileNetV2, and GoogLeNet models showed performance >80%. With the pretrained VGG-19 model, 93%, 93.5%, 96.7%, 92.3%, 92.6%, and 0.99 accuracy, sensitivity, specificity, precision, F1 score, and AUC results were obtained, respectively. Conclusion:In this study, in addition to the ultrasonography images of dysplastic and healthy hips, images were also included of probe malpositioning, and these images were able to be successfully evaluated with deep learning methods. On the sonograms, which provided criteria appropriate for evaluation, successful differentiation could be made of healthy hips and dysplastic hips.
Citation - WoS: 2
The Effect of Population and Tourism Factors on Covid-19 Cases in Italy: Visual Data Analysis and Forecasting Approach
(Wiley, 2022) Ozyer, Baris; Ozyer, Gulsah Tumuklu; Tokdemir, Gul; Uguz, Sezer; Yaganoglu, Mete
At the beginning of 2020, the new coronavirus disease (Covid-19), a deadly viral illness, is declared as a public health emergency situation by WHO. Consequently, it is accepted as pandemic that affected millions of people worldwide. Italy is one of the most affected countries by Covid-19 disease among the world. In this article, our main goal is to investigate the effect of intensity of Covid-19 cases based on the population size and tourism factors in certain regions of Italy by visual data analysis. The regions of Lombardia, Veneto, Campania, Emilia-Romagna, Piemonte are the top five regions covering 58.50% of the total Covid-19 cases diagnosed in Italy. It has been shown by visual data analysis that population and tourism factors play an important role in the spread of Covid-19 cases in these five regions. In addition, a prediction model was created using Bi-LSTM and ARIMA algorithms to forecast the number of Covid-19 cases occurring in these five regions in order to take early action. We can conclude that these northern regions have been affected mostly by Covid-19 and the distribution of the resident population and tourist flow factors affected the number of Covid-19 cases in Italy.
Citation - WoS: 5
Citation - Scopus: 6
Exploring the Belief Systems of Software Development Professionals
(Taylor & Francis inc, 2015) O'Connor, Rory V.; Yilmaz, Murat
It is commonly accepted that an individual's beliefs and actions are based on his or her assessment and perceptions of the world. In order to determine what practices an individual is likely to follow at any given time, it is necessary to understand the individual's behavioral intention in a given circumstance. From an Information Technology perspective, a software development professional's belief systems are potentially the basis for the adoption and implementation of new and innovative work practices and processes. In this article, we explore the belief systems of software development professionals in order to understand the beliefs underlying intention and practice, and we seek answers about how they adopt or reject new and innovative software development processes and practices. The results point out a strong influence of past experiences, personality types, and repeated behavior on current software development processes and practices in industrial settings.
Citation - WoS: 7
Citation - Scopus: 10
Extending a Sentiment Lexicon With Synonym-Antonym Datasets: Swnettr Plus
(Tubitak Scientific & Technological Research Council Turkey, 2019) Genc, Burkay; Sever, Hayri; Saglam, Fatih
In our previous studies on developing a general-purpose Turkish sentiment lexicon, we constructed SWNetTR-PLUS, a sentiment lexicon of 37K words. In this paper, we show how to use Turkish synonym and antonym word pairs to extend SWNetTR-PLUS by almost 33% to obtain SWNetTR++, a Turkish sentiment lexicon of 49K words. The extension was done by transferring the problem into the graph domain, where nodes are words, and edges are synonym- antonym relations between words, and propagating the existing tone and polarity scores to the newly added words using an algorithm we have developed. We tested the existing and new lexicons using a manually labeled Turkish news media corpus of 500 news texts. The results show that our method yielded a significantly more accurate lexicon than SWNetTR-PLUS, resulting in an accuracy increase from 72.2% to 80.4%. At this level, we have now maximized the accuracy rates of translation-based sentiment analysis approaches, which first translate a Turkish text to English and then do the analysis using English sentiment lexicons.
Citation - WoS: 7
Citation - Scopus: 8
Fragmentation of Water Clusters: Molecular-Dynamics Simulation Study
(Springer-verlag, 2001) Erkoç, S; Kökten, H; Güvenç, Z
The fragmentation of water clusters, [(H2O)(n): n = 2-8], have been investigated by using molecular-dynamics simulation method. In the simulations a polarizable-dissociable potential energy function for water has been used. Particular attention has been paid to investigate the effect of structural properties and cluster size of the fragmentation.
Citation - WoS: 43
Citation - Scopus: 53
Gamification as a Disruptive Factor in Software Process Improvement Initiatives
(Graz Univ Technolgoy, inst information Systems Computer Media-iicm, 2014) Herranz, Eduardo; Yılmaz, Murat; Colomo-Palacios, Ricardo; de Amescua Seco, Antonio; Yilmaz, Murat; Yazılım Mühendisliği
For any Software Process Improvement (SPI) initiative to succeed human factors, in particular, motivation and commitment of the people involved should be kept in mind. In fact, Organizational Change Management (OCM) has been identified as an essential knowledge area for any SPI initiative. However, enough attention is still not given to the human factors and therefore, the high degree of failures in the SPI initiatives is directly linked to a lack of commitment and motivation. Gamification discipline allows us to define mechanisms that drive people's motivation and commitment towards the development of tasks in order to encourage and accelerate the acceptance of an SPI initiative. In this paper, a gamification framework oriented to both organization needs and software practitioners groups involved in an SPI initiative is defined. This framework tries to take advantage of the transverse nature of gamification in order to apply its Critical Success Factors (CSF) to the organizational change management of an SPI. Gamification framework guidelines have been validated by some qualitative methods. Results show some limitations that threaten the reliability of this validation. These require further empirical validation of a software organization.
Citation - WoS: 49
Citation - Scopus: 49
Global Minima of Aln, Aun and Ptn, N≤80, Clusters Described by the Voter-Chen Version of Embedded-Atom Potentials
(Iop Publishing Ltd, 2005) Sebetci, A; Güvenç, ZB
We report the global minima for aluminium, gold and platinum metal clusters modelled by the Voter-Chen version of the embedded-atom model potential containing up to 80 atoms using the basin-hopping Monte Carlo minimization approach. The results show that the global minima of the Al, Au and Pt clusters have structures based on either octahedral, decahedral, icosahedral or a mixture of decahedral and icosahedral packing. The 54-atom icosahedron without a central atom is found to be more stable than the 55-atom complete icosahedron for all of the elements considered in this work. Most of the Al global minima are identified as face-centred cubic structures and many of the An global minima are found to be low symmetric structures, both of which are in agreement with the previous theoretical and experimental Studies. Although many of the Pt global minima are identical with the global minima of the corresponding Au clusters, the most stable sizes of the Pt clusters correspond to the same sizes of the Al clusters.
Citation - WoS: 2
Citation - Scopus: 2
Guest Editorial: Gamification and Persuasive Games for Software Engineering
(inst Engineering Technology-iet, 2019) O'Connor, Rory V.; Colomo-Palacios, Ricardo; Clarke, Paul; Yilmaz, Murat
Citation - WoS: 3
Citation - Scopus: 4
Improving Social Aspects of the Software Development Process: Games, Gamification and Related Approaches
(Graz Univ Technolgoy, inst information Systems Computer Media-iicm, 2016) Yilmaz, Murat; Yılmaz, Murat; O'Connor, Rory V.; Mora, Manuel; Yazılım Mühendisliği
Citation - WoS: 13
Citation - Scopus: 17
Integration of Accessibility Design Patterns With the Software Implementation Process of Iso/Iec 29110
(Wiley, 2019) Sanchez-Gordon, Mary; Yilmaz, Murat; O'Connor, Rory V.; Sanchez-Gordon, Sandra
The Web Content Accessibility Guidelines was developed by World Wide Web Consortium with a goal of providing a single shared standard for web content accessibility that meets the needs of individuals, organizations, and governments. Given that there is a large percentage of very small entities that develop software who also utilize the ISO/IEC software process standard, the purpose of this study is the development of software design patterns for users with visual disabilities. As a result, four accessibility design patterns are defined: Authentication adapter, Blindness adapter, Dichromatic color vision adapter, and Blurry vision adapter. These patterns will help to improve the design of the web applications built using them while being compliant with the ISO/IEC 29110 standard. The use of design patterns also enables the transfer of design experience to programming practices and improves the software documentation. To validate the set of patterns, an online course for Spanish speakers was developed, and the evaluation was carried out using simulators, automated tools, experts, and users. Simulators and automated tools showed no accessibility errors and experts evaluated 10 heuristics principles and did not identify any severity issues. Taken together, our results provide positive evidence that users with visual disabilities could benefit from the proposed features.
Citation - WoS: 23
Citation - Scopus: 28
Interactive Three-Dimensional Virtual Environment To Reduce the Public Speaking Anxiety Levels of Novice Software Engineers
(inst Engineering Technology-iet, 2019) Yilmaz, M.; Gulec, U.; Yilmaz, A. E.; Isler, V.; O'Connor, R. V.; Clarke, P.; Nazligul, M. Denizci
Software engineering is a set of activities that rely not only on the technical tasks but also require abilities focused on social duties such as daily meetings and product introduction presentations. However, engineers may experience elevated levels of anxiety when required to present their work in an unfamiliar environment. More specifically, they may suffer from public speaking anxiety even though they are supposed to be effective in those social tasks as well as in their engineering activities. Fortunately, previous studies suggest that the virtual exposure intervention is an effective strategy to reduce public speaking anxiety. In this study, an interactive three-dimensional virtual environment similar to real classrooms and auditoriums was developed to examine whether this might decrease the anxiety levels of novice software engineers. To compare the traditional and virtual exposure intervention, the sample set was divided equally into two groups including one experimental group and one control group. For 4 weeks, the virtual exposure intervention was conducted in the experimental group, whereas the cognitive behaviour therapy-based psychoeducation was used in the control group. The findings from authors' study illustrate that the virtual exposure intervention may represent an alternative solution to the traditional interventions for software engineers seeking to overcome public presentation anxiety.
Citation - WoS: 7
Citation - Scopus: 10
A Literature Survey: Is It Necessary To Develop a New Software Development Methodology for Virtual Reality Projects
(Graz Univ Technolgoy, inst information Systems Computer Media-iicm, 2017) Güleç, Ulaş; Gulec, Ulas; Yilmaz, Murat; Yılmaz, Murat; Isler, Veysi; Bilgisayar Mühendisliği; Yazılım Mühendisliği
Software development is a complex human endeavour with high failure rates. Although a variety of software development methodologies have been proposed to improve the software development process, there is no universal model for all software development organizations. Virtual reality (VR) is an emerging trend especially for the gaming industry, which should prepare itself for VR development. The goal of this study is to explore potential software development activities and determine whether designing a new software development methodology for VR projects is an important topic for software development organizations working on VR software development. For this purpose, a literature survey has been completed and 71 academic studies have been examined in detail. This study shows that no work is being conducted in the field of developing a new methodology for VR projects. However, the study does show that there are similar endeavours in the field of human computer interaction (HCI), such as game development methodology.
Citation - WoS: 8
Citation - Scopus: 8
Localization of Metallicity and Magnetic Properties of Graphene and of Graphene Nanoribbons Doped With Boron Clusters
(Taylor & Francis Ltd, 2014) Kunstmann, Jens; Quandt, Alexander; Ozdogan, Cem
As a possible way of modifying the intrinsic properties of graphene, we study the doping of graphene by embedded boron clusters with density functional theory. Cluster doping is technologically relevant as the cluster implantation technique can be readily applied to graphene. We find that B-7 clusters embedded into graphene and graphene nanoribbons are structurally stable and locally metallize the system. This is done both by the reduction of the Fermi energy and by the introduction of boron states near the Fermi level. A linear chain of boron clusters forms a metallic "wire" inside the graphene matrix. In a zigzag edge graphene nanoribbon, the cluster-related states tend to hybridize with the edge and bulk states. The magnetism in boron-doped graphene systems is generally very weak. The presence of boron clusters weakens the edge magnetism in zigzag edge graphene nanoribbon, rather than making the system appropriate for spintronics. Thus, the doping of graphene with the cluster implantation technique might be a viable technique to locally metallize graphene without destroying its attractive bulk properties.
Citation - WoS: 3
Observed Effects of Software Processes Change in Three Software Firms: Industrial Exploratory Case Study
(Pamukkale Univ, 2019) Yilmaz, Murat
Software development processes require continuous improvement in line with emerging new technologies and the possibilities it provides. A new generation of software development models based on product demands of software customers with marketable functions aims to increase the intermediate product production speed and thus the number of interim versions. In the light of these needs, software companies need to oversee their development processes to meet their customers' needs. But more importantly, companies are forced to change their processes in line with innovative practices in order not to cut back on the software production line. In this article, the software development methods of the three companies that develop software are examined in detail by the case study method, and the process change activities are systematically detailed. In the light of the information obtained, the experiences of the three firms in the software development methods are questioned and the effects of these acquisitions on the processes are discussed. As a result of the study, it has been observed that the software development success has a significant impact on the well-being of the process, and the software development teams are trying to design their own processes in the light of the gains they acquire.

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