Computer Engineering / Bilgisayar Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/10
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Conference Object Enhancing genomic data sharing with blockchain-enabled dynamic consent in beacon V2(Springernature, 2024) Binokay, Leman; Celik, Hamit Mervan; Gurdal, Gultekin; Ayav, Tolga; Tuglular, Tugkan; Oktay, Yavuz; Karakulah, GokhanArticle Citation - WoS: 9Citation - Scopus: 13Microservice-Based Projects in Agile World: a Structured Interview(Elsevier, 2024) Unlu, Huseyin; Kennouche, Dhia Eddine; Soylu, Gorkem Kiling; Demirors, OnurContext: During the last decade, Microservice-based software architecture (MSSA) has been a preferred design paradigm for a growing number of companies. MSSA, specifically in the form of reactive systems, has substantial differences from the more conventional design paradigms, such as object-oriented analysis and design. Therefore, adaptation demands software organizations to transform their culture. However, there is a lack of research studies that explore common practices utilized by software companies that implement MSSAs.Objective: In this study, our goal is to get an insight into how practices such as an agile methodology, software analysis, design, test, size measurement, and effort estimation are performed in software projects which embrace the Microservice-based software architecture paradigm. Together with the identification of practices utilized for the MSSA paradigm, we aim to determine the challenges organizations face to adopt microservice-based software architectures.Method: We performed a structured interview with participants coming from 20 different organizations over different roles, domains, and countries to collect information on their views, experience, and the challenges faced.Results: Our results reveal that organizations find agile development compatible with microservices. In general, they continue to use traditional object-oriented modeling notations for analysis and design in an abstract way. They continue to use the same subjective size measurement and effort estimation approaches that they were using previously in traditional architectures. However, they face unique challenges in developing microservices.Conclusion: Although organizations face challenges, practitioners continue to use familiar techniques that they have been using for traditional architectures. The results provide a snapshot of the software industry that utilizes microservices.Article Citation - WoS: 1Citation - Scopus: 1How Software Practitioners Perceive Work-Related Barriers and Benefits Based on Their Educational Backgrounds: Insights From a Survey Study(IEEE, 2023) Ünlü, Hüseyin; Yürüm, Ozan Raşit; Özcan Top, Özden; Demirörs, OnurSurvey results show that software practitioners from nonsoftware-related backgrounds face more barriers, have fewer benefits, and feel less satisfied in their work life. However, these differences reduce with more than 10 years of experience and involvement in software-related graduate programs, certificates, and mentorship.Article Citation - Scopus: 1An Interestingness Measure for Knowledge Bases(Elsevier, 2023) Oğuz, Damla; Soygazi, FatihAssociation rule mining and logical rule mining both aim to discover interesting relationships in data or knowledge. In association rule mining, relationships are identified based on the occurrence of items in a dataset, while in logical rule mining, relationships are determined based on logical relationships between atoms in a knowledge base. Association rule mining has been widely studied in transactional databases, mainly for market basket analysis. Confidence has become the most widely used interesting measure to assess the strength of a rule. Many other interestingness measures have been proposed since confidence can be insufficient to filter negatively associated relationships. Recently, logical rule mining has become an important area of research, as new facts can be inferred by applying discovered logical rules. They can be used for reasoning, identifying potential errors in knowledge bases, and to better understand data. However, there are currently only a few measures for logical rule mining. Furthermore, current measures do not consider relations that can have several objects, called quasi-functions, which can dramatically alter the interestingness of the rule. In this paper, we focus on effectively assessing the strength of logical rules. We propose a new interestingness measure that takes into account two categories of relations, functions and quasi-functions, to assess the degree of certainty of logical rules. We compare our proposed measure with a widely used measure on both synthetic test data and real knowledge bases. We show that it is more effective in indicating rule quality, making it an appropriate interestingness measure for logical rule evaluation. & COPY; 2023 Karabuk University. Publishing services by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Article Citation - WoS: 3Citation - Scopus: 4Scalable Rfid Authentication Protocol Based on Physically Unclonable Functions(Elsevier, 2023) Kurt, Işıl; Alagöz, Fatih; Akgün, MeteRadio Frequency Identification (RFID) technology is commonly used for tracking and identifying objects. However, this technology poses serious security and privacy concerns for individuals carrying the tags. To address these issues, various security protocols have been proposed. Unfortunately, many of these solutions suffer from scalability problems, requiring the back-end server to work linearly in the number of tags for a single tag identification. Some protocols offer O(1) or O(log n) identification complexity but are still susceptible to serious attacks. Few protocols consider attacks on the reader-side. Our proposed RFID authentication protocol eliminates the need for a search in the back-end and leverages Physically Unclonable Functions (PUFs) to securely store tag secrets, making it resistant to tag corruption attacks. It provides constant-time identification without sacrificing privacy and offers log2 n times better identification performance than the state-of-the-art protocol. It ensures destructive privacy for tag holders in the event of reader corruption without any conditions. Furthermore, it enables offline readers to maintain destructive privacy in case of corruption.Article Citation - WoS: 3Citation - Scopus: 6An Exploratory Case Study Using Events as a Software Size Measure(Springer, 2023) Hacaloğlu, Tuna; Demirörs, OnurSoftware Size Measurement is a critical task in Software Development Life Cycle (SDLC). It is the primary input for effort estimation models and an important measure for project control and process improvement. There exist various size measurement methods whose successes have already been proven for traditional software architectures and application domains. Being one of them, functional size measurement (FSM) attracts specific attention due to its applicability at the early phases of SDLC. Although FSM methods were successful on the data-base centric, transaction oriented stand-alone applications, in contemporary software development projects, Agile methods are highly used, and a centralized database and a relational approach are not used as before while the requirements suffer from a lack of detail. Today's software is frequently service based, highly distributed, message-driven, scalable and has unprecedented levels of availability. In the new era, event-driven architectures are appearing as one of the emerging approaches where the 'event' concept largely replaces the 'data' concept. Considering the important place of events in contemporary architectures, we focused on approaching the software size measurement problem from the event-driven perspective. This situation guided us to explore how useful event as a size measure in comparison to data-movement based methods. The findings of our study indicates that events can be promising for measurement and should be investigated further in detail to be formalized for creating a measurement model thereby providing a replicable approach.Article Citation - WoS: 41Citation - Scopus: 50Bim-Carem: Assessing the Bim Capabilities of Design, Construction and Facilities Management Processes in the Construction Industry(Elsevier, 2023) Gökçen, Yılmaz; Akçamete, Aslı; Demirörs, OnurBIM adoption has accelerated worldwide since it is an important enabling technology for digitalisation in the construction industry. Adopting BIM requires transforming the traditional building life cycle stages (planning, design, construction and facilities management) into BIM-integrated project deliveries. Assessing the BIM ca- pabilities of these stages helps organisations to identify gaps in their BIM uses and improve them. There is a lack of a comprehensive model in the literature for assessing the BIM capabilities of individual building life cycle stages and their processes. Existing assessment models focus on assessing the BIM maturity of construction projects and organisations which do not inform the required BIM improvements for individual stages and their processes. Hence, we iteratively developed the Building Information Modelling (BIM) Capability Assessment REference Model (BIM-CAREM) and demonstrated its usability through multiple explanatory case studies per- formed with two international design and engineering companies and two general contractors in Turkey. We assessed the BIM capabilities of design, construction and facility management processes of various buildings i.e. residential, stadiums, hospitals and airports. The results showed that the BIM capability levels of design, con- struction and facility management processes vary within and across the companies.Article Citation - WoS: 4Citation - Scopus: 4Integrative Biological Network Analysis To Identify Shared Genes in Metabolic Disorders(Institute of Electrical and Electronics Engineers, 2022) Tenekeci, Samet; Işık, ZerrinIdentification of common molecular mechanisms in interrelated diseases is essential for better prognoses and targeted therapies. However, complexity of metabolic pathways makes it difficult to discover common disease genes underlying metabolic disorders; and it requires more sophisticated bioinformatics models that combine different types of biological data and computational methods. Accordingly, we built an integrative network analysis model to identify shared disease genes in metabolic syndrome (MS), type 2 diabetes (T2D), and coronary artery disease (CAD). We constructed weighted gene co-expression networks by combining gene expression, protein-protein interaction, and gene ontology data from multiple sources. For 90 different configurations of disease networks, we detected the significant modules by using MCL, SPICi, and Linkcomm graph clustering algorithms. We also performed a comparative evaluation on disease modules to determine the best method providing the highest biological validity. By overlapping the disease modules, we identified 22 shared genes for MS-CAD and T2D-CAD. Moreover, 19 out of these genes were directly or indirectly associated with relevant diseases in the previous medical studies. This study does not only demonstrate the performance of different biological data sources and computational methods in disease-gene discovery, but also offers potential insights into common genetic mechanisms of the metabolic disorders.Article Citation - WoS: 6Citation - Scopus: 6Cauchy-Rician Model for Backscattering in Urban Sar Images(Institute of Electrical and Electronics Engineers, 2022) Karakuş, Oktay; Kuruoğlu, Ercan Engin; Achim, Alin; Altınkaya, Mustafa AzizThis letter presents a new statistical model for urban scene synthetic aperture radar (SAR) images by combining the Cauchy distribution, which is heavy tailed, with the Rician backscattering. The literature spans various well-known models most of which are derived under the assumption that the scene consists of multitudes of random reflectors. This idea specifically fails for urban scenes since they accommodate a heterogeneous collection of strong scatterers such as buildings, cars, and wall corners. Moreover, when it comes to analyzing their statistical behavior, due to these strong reflectors, urban scenes include a high number of high amplitude samples, which implies that urban scenes are mostly heavy-tailed. The proposed Cauchy-Rician model contributes to the literature by leveraging nonzero location (Rician) heavy-tailed (Cauchy) signal components. In the experimental analysis, the Cauchy-Rician model is investigated in comparison to state-of-the-art statistical models that include $\mathcal {G}_{0}$ , generalized gamma, and the lognormal distribution. The numerical analysis demonstrates the superior performance and flexibility of the proposed distribution for modeling urban scenes.Article Citation - WoS: 6Citation - Scopus: 10Efficient Privacy-Preserving Whole-Genome Variant Queries(Oxford University Press, 2022) Akgün, Mete; Pfeifer, Nico; Kohlbacher, OliverMotivation: Diagnosis and treatment decisions on genomic data have become widespread as the cost of genome sequencing decreases gradually. In this context, disease-gene association studies are of great importance. However, genomic data are very sensitive when compared to other data types and contains information about individuals and their relatives. Many studies have shown that this information can be obtained from the query-response pairs on genomic databases. In this work, we propose a method that uses secure multi-party computation to query genomic databases in a privacy-protected manner. The proposed solution privately outsources genomic data from arbitrarily many sources to the two non-colluding proxies and allows genomic databases to be safely stored in semi-honest cloud environments. It provides data privacy, query privacy and output privacy by using XOR-based sharing and unlike previous solutions, it allows queries to run efficiently on hundreds of thousands of genomic data. Results: We measure the performance of our solution with parameters similar to real-world applications. It is possible to query a genomic database with 3 000 000 variants with five genomic query predicates under 400 ms. Querying 1 048 576 genomes, each containing 1 000 000 variants, for the presence of five different query variants can be achieved approximately in 6 min with a small amount of dedicated hardware and connectivity. These execution times are in the right range to enable real-world applications in medical research and healthcare. Unlike previous studies, it is possible to query multiple databases with response times fast enough for practical application. To the best of our knowledge, this is the first solution that provides this performance for querying large-scale genomic data.