Takan, Savaş
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Takan, S
Takan, S.
Takan, Savas
Takan, S.
Takan, Savas
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03.04. Department of Computer Engineering
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| Journal | Count |
|---|---|
| 12th Turkish National Software Engineering Symposium, UYMS 2018 | 1 |
| 28th International Conference on Architecture of Computing Systems, ARCS 2015 | 1 |
| 7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012 | 1 |
| Advanced Materials Research | 1 |
| CEUR Workshop Proceedings | 1 |
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Doctoral Thesis Fourier Analysis Based Testing of Finite State Machines(Izmir Institute of Technology, 2019) Takan, Savaş; Takan, Savaş; Ayav, Tolga; Ayav, TolgaFinite state machine (FSM) is a widely used modeling technique for circuit and software testing. FSM testing is a well-studied topic in the literature and there are several test case generation methods such as W, Wp, UIO, UIOv, DS, HSI and H. Despite the existing methods, there is still a need for alternative techniques with better performance in terms of test suite size, fault detection ratio and test generation time. In this thesis, two new test case generation methods, F and Fw have been proposed. The proposed test generation methods are based on Fourier analysis of Boolean functions. Fourier transformations have been studied extensively in mathematics, computer science and engineering. The proposed F method only tests outputs whereas Fw method also tests the next state with the outputs. In this context, the proposed methods are compared with UIO andWmethods in terms of characteristic, cost, fault detection ratio and effectiveness. The evaluation data are analyzed using T-Test and Hedges’ g. Results show that F and Fw methods outperform the existing methods in terms of the fault detection ratio per test.Master Thesis A common representation, standardization, analysis for de novo sequencing results(Izmir Institute of Technology, 2012) Takan, Savaş; Aytaç, İsmail SıtkıProteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics proteins can be identified or sequenced by either database search or de novo sequencing. Both methods have certain advantages and drawbacks but in the long run we envision de novo sequencing to become the predominant tool. Currently, there is no a general solution to store and share de novo sequencing results which diminishes the usefulness of these results. Hence, they need to be integrated and further analyzed and cannot be used directly as evidence for peptide identification and protein sequencing at present. In order to make improvements the field of de novo sequencing a standard is vitally important. In an attempt to overcome the standardization problem, the de novo markup language (DNML) and De Novo MS Ontology (DNMSO) are developed. These standards provide many-to-many relationships between spectra and predictions, exchange and merging functions, showing all results, PTMs, compact, no using proprietary formats. Next, a programming interface is developed since it is thought that the missing of proper APIs as another obstacle, introducing a needlessly high learning curve for developers. It is standard, compact, modular, easily extensible and also have read, write, create, convert, supports current standards facilities. In order to allow the experimental proteomics community to analyze data stored in the DNMSO standard, Graphical User Interface is developed , DNMSO Analyzer, to provide some facilities such as reading of various spectra file formats, reading, viewing, summarizing of DNMSO, and several conversions from existing de novo results to DNMSO in DNMSO Analyzer.Article Citation - WoS: 1Citation - Scopus: 1Dnmso; an Ontology for Representing De Novo Sequencing Results From Tandem-Ms Data(PeerJ Inc., 2020) Takan, Savaş; Allmer, JensFor the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and, as such, drives proteomics. MS/MS spectra need to be assigned a peptide sequence for which two strategies exist. Either database search or de novo sequencing can be employed to establish peptide spectrum matches. For database search, mzIdentML is the current community standard for data representation. There is no community standard for representing de novo sequencing results, but we previously proposed the de novo markup language (DNML). At the moment, each de novo sequencing solution uses different data representation, complicating downstream data integration, which is crucial since ensemble predictions may be more useful than predictions of a single tool. We here propose the de novo MS Ontology (DNMSO), which can, for example, provide many-to-many mappings between spectra and peptide predictions. Additionally, an application programming interface (API) that supports any file operation necessary for de novo sequencing from spectra input to reading, writing, creating, of the DNMSO format, as well as conversion from many other file formats, has been implemented. This API removes all overhead from the production of de novo sequencing tools and allows developers to concentrate on algorithm development completely. We make the API and formal descriptions of the format freely available at https://github.com/savastakan/dnmso.Article Citation - WoS: 2Citation - Scopus: 1Mutant Selection by Using Fourier Expansion(Türkiye Klinikleri Journal of Medical Sciences, 2020) Takan, Savaş; Ayav, TolgaMutation analysis is a widely used technique to evaluate the effectiveness of test cases in both hardware and software testing. The original model is mutated systematically under certain fault assumptions and test cases are checked against the mutants created to see whether the test cases can detect the faults or not. Mutation analysis is usually a computationally intensive task, particularly in finite state machine (FSM) testing due to a possibly huge amount of mutants. Random selection could be a practical reduction method under the assumption that each mutant is identical in terms of the probability of occurrence of its associating fault. The present study proposes a mutant selection method based on Fourier analysis of Boolean functions. Fourier helps to identify the most effective transitions on the output so that the mutants related to those transitions can be selected. Such mutants are considered more important since they are more likely to be killed. To evaluate the method, test cases are generated by the well-known W method, which has the capability of detecting every potential fault. The original and reduced sets of mutants are compared with respect to their importance values. Evaluations show that the mutants selected by the proposed technique are more effective, which reduces the cost of mutation analysis without sacrificing the performance of the mutation analysis.Conference Object Model Checker-Based Delay Fault Testing of Sequential Circuits(Springer Verlag, 2015) Takan, Savaş; Güler, Berkin; Ayav, TolgaThis paper applies model checker-based testing, a well-known method from software engineering, to the delay fault testing of synchronous sequential logic circuits. We first model the circuit as timed automata to reveal its timing characteristics. The model is repeatedly mutated by injecting the delay faults under a certain fault assumption and all the mutant models are checked against the given properties by exploiting a model checker. Counterexamples returned from the model checker form the basis of test input sequences. Finally, the test suite minimization is defined as an integer programming problem.Conference Object Sonlu Durum Makinelerinin Fourier Analizi Tabanlı Sınanması(CEUR Workshop Proceedings, 2018) Takan, Savaş; Ayav, TolgaSonlu durum makinesi (FSM), devre ve yazılım testlerinde yaygın kullanıma sahip bir modelleme tekniğidir. FSM'lerin testi için literatürde çeşitli yöntemler bulunmakla birlikte, modellerin büyümesi sonucu test kümesinin büyüklüğü, hata yakalama oranı ve test üretim süresi gibi konularda yüksek başarıma sahip alternatif test yöntemlerine ihtiyaç bulunmaktadır. Bu çalışma ikili fonksiyonların Fourier analizine dayanan yeni bir test oluşturma yöntemi önermektedir. İlk sonuçlar, fonksiyonun frekans bileşenlerinden yararlanarak oluşturulan test takımının daha yüksek bir performansa sahip olduğunu göstermektedir. Önerilen yöntem, karakteristiği, maliyeti ve hata yakalama oranı üzerinden literatürden seçilen iki yöntemle karşılaştırılmıştır.Conference Object Developing Applications On-Board of Robots With Becerik(Trans Tech Publications, 2012) Kumova, Bora İsmail; Takan, SavaşRobot applications are mostly first developed on a computer and thereafter loaded onto the robot. However, in many situations, developing applications directly on the robot may be more effective. For instance, children who have not learned using a computer yet and who develop their robot applications while playing. Or for instance in the robots' operating environment, where there is no computer available. In this contribution we present the properties of the software tool becerik, for developing applications on-board a robot and for running them in multi-tasking mode concurrently. Furthermore, we introduce the programming language of the applications that has the same name becerik, which consists of only 6 commands. © (2012) Trans Tech Publications, Switzerland.Article Citation - WoS: 1Creation of Mutants by Using Centrality Criteria in Social Network Analysis(PeerJ Inc., 2020) Takan, SavaşMutation testing is a method widely used to evaluate the effectiveness of the test suite in hardware and software tests or to design new software tests. In mutation testing, the original model is systematically mutated using certain error assumptions. Mutation testing is based on well-defined mutation operators that imitate typical programming errors or which form highly successful test suites. The success of test suites is determined by the rate of killing mutants created through mutation operators. Because of the high number of mutants in mutation testing, the calculation cost increases in the testing of finite state machines (FSM). Under the assumption that each mutant is of equal value, random selection can be a practical method of mutant reduction. However, in this study, it was assumed that each mutant did not have an equal value. Starting from this point of view, a new mutant reduction method was proposed by using the centrality criteria in social network analysis. It was assumed that the central regions selected within this frame were the regions from where test cases pass the most. To evaluate the proposed method, besides the feature of detecting all failures related to the model, the widely-used W method was chosen. Random and proposed mutant reduction methods were compared with respect to their success by using test suites. As a result of the evaluations, it was discovered that mutants selected via the proposed reduction technique revealed a higher performance. Furthermore, it was observed that the proposed method reduced the cost of mutation testing.Conference Object Citation - Scopus: 1De Novo Markup Language, a Standard To Represent De Novo Sequencing Results From Ms/Ms Data(Institute of Electrical and Electronics Engineers Inc., 2012) Takan, Savaş; Allmer, JensProteomics is the study of the proteins that can be derived from a genome. For the identification and sequencing of proteins, mass spectrometry has become the tool of choice. Within mass spectrometry-based proteomics, proteins can be identified or sequenced by either database search or de novo sequencing. Both methods have certain advantages and drawbacks but in the long run we envision de novo sequencing to become the predominant tool. Currently, de novo sequencing results are stored in arbitrary file formats, depending on the developers of the algorithms. We identified this as a large and unnecessary obstacle while integrating results from multiple de novo sequencing algorithms. Therefore, we designed a standard file format for the representation of de novo sequencing results. We further developed an application programming interface since we identified the lack of proper APIs as another obstacle, introducing a needlessly high learning curve for developers. © 2012 IEEE.Conference Object Sayısal Devrelerin Model Kontrol Tabanlı Testi(CEUR-WS, 2015) Takan, SavaşBu tezin amacı yazılım mühendisliği alanında yaygınca kullanılan bir test yöntemi olan model doğrulama tabanlı test yönteminin, devrelerin gecikme hata testinin denetlenmesi işlemine uygulamaktır. Devre gecikme hatası devrelerin istenilen zamanda istenilen işlevin yerine getirilmemesinden kaynaklanmaktadır. Bu metodolojide, öncelikle devre bir zamanlı otomata olarak modellenir ve böylece devrenin zamansal karakteristikleri ortaya çıkarılır. Ardından model sürekli olarak belirli varsayımlar çerçevesinde gecikme hataları oluşması için mutasyona uğratılır ve tüm mutant modeller verilen niteliklere göre model doğrulayıcı tarafından kontrol edilir. Test giriş dizisi, model doğrulayıcı tarafından geri döndürülen karşıt örneklerden oluşur. Aşağıda metodolojinin kısa özeti verilmiştir.