Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - Scopus: 34Machine Learning Methods for Microrna Gene Prediction(Humana Press Inc., 2014) Saçar,M.D.; Allmer,J.MicroRNAs (miRNAs) are single-stranded, small, noncoding RNAs of about 22 nucleotides in length, which control gene expression at the posttranscriptional level through translational inhibition, degradation, adenylation, or destabilization of their target mRNAs. Although hundreds of miRNAs have been identified in various species, many more may still remain unknown. Therefore, discovery of new miRNA genes is an important step for understanding miRNA-mediated posttranscriptional regulation mechanisms. It seems that biological approaches to identify miRNA genes might be limited in their ability to detect rare miRNAs and are further limited to the tissues examined and the developmental stage of the organism under examination. These limitations have led to the development of sophisticated computational approaches attempting to identify possible miRNAs in silico. In this chapter, we discuss computational problems in miRNA prediction studies and review some of the many machine learning methods that have been tried to address the issues. © Springer Science+Business Media New York 2014.Conference Object Citation - Scopus: 1A Novel Feature To Predict Buggy Changes in a Software System(Springer, 2022) Yılmaz, Rahime; Nalçakan, Yağız; Haktanır, ElifResearchers have successfully implemented machine learning classifiers to predict bugs in a change file for years. Change classification focuses on determining if a new software change is clean or buggy. In the literature, several bug prediction methods at change level have been proposed to improve software reliability. This paper proposes a model for classification-based bug prediction model. Four supervised machine learning classifiers (Support Vector Machine, Decision Tree, Random Forrest, and Naive Bayes) are applied to predict the bugs in software changes, and performance of these four classifiers are characterized. We considered a public dataset and downloaded the corresponding source code and its metrics. Thereafter, we produced new software metrics by analyzing source code at class level and unified these metrics with the existing set. We obtained new dataset to apply machine learning algorithms and compared the bug prediction accuracy of the newly defined metrics. Results showed that our merged dataset is practical for bug prediction based experiments. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.Book Part Citation - WoS: 299Citation - Scopus: 406Introduction To Machine Learning(Humana Press, 2014) Baştanlar, Yalın; Özuysal, MustafaThe machine learning field, which can be briefly defined as enabling computers make successful predictions using past experiences, has exhibited an impressive development recently with the help of the rapid increase in the storage capacity and processing power of computers. Together with many other disciplines, machine learning methods have been widely employed in bioinformatics. The difficulties and cost of biological analyses have led to the development of sophisticated machine learning approaches for this application area. In this chapter, we first review the fundamental concepts of machine learning such as feature assessment, unsupervised versus supervised learning and types of classification. Then, we point out the main issues of designing machine learning experiments and their performance evaluation. Finally, we introduce some supervised learning methods.Article Citation - WoS: 30Machine Learning Methods for Microrna Gene Prediction(Humana Press, 2014) Saçar, Müşerref Duygu; Allmer, JensMicroRNAs (miRNAs) are single-stranded, small, noncoding RNAs of about 22 nucleotides in length, which control gene expression at the posttranscriptional level through translational inhibition, degradation, adenylation, or destabilization of their target mRNAs. Although hundreds of miRNAs have been identified in various species, many more may still remain unknown. Therefore, discovery of new miRNA genes is an important step for understanding miRNA-mediated posttranscriptional regulation mechanisms. It seems that biological approaches to identify miRNA genes might be limited in their ability to detect rare miRNAs and are further limited to the tissues examined and the developmental stage of the organism under examination. These limitations have led to the development of sophisticated computational approaches attempting to identify possible miRNAs in silico. In this chapter, we discuss computational problems in miRNA prediction studies and review some of the many machine learning methods that have been tried to address the issues.