Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article Comparative Assessment of Smooth and Non-Smooth Optimization Solvers in HANSO Software(Balikesir University, 2021-10-27) Tor, Ali HakanThe aim of this study is to compare the performance of smooth and nonsmooth mization) software. The smooth optimization solver is the implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) method and the nonsmooth optimization solver is the Hybrid Algorithm for Nonsmooth Optimization. More precisely, the nonsmooth optimization algorithm is the combination of the BFGS and the Gradient Sampling Algorithm (GSA). We use well-known collection of academic test problems for nonsmooth optimization containing both convex and nonconvex problems. The motivation for this research is the importance of the comparative assessment of smooth optimization methods for solving nonsmooth optimization problems. This assessment will demonstrate how successful is the BFGS method for solving nonsmooth optimization problems in comparison with the nonsmooth optimization solver from HANSO. Performance profiles using the number iterations, the number of function evaluations and the number of subgradient evaluations are used to compare solvers.Article Citation - WoS: 3Citation - Scopus: 3MicroRNA Prediction Based on 3D Graphical Representation of RNA Secondary Structures(Tubitak Scientific & Technological Research Council Turkey, 2019-08-05) Sacar Demirci, Muserref Duygu; Demirci, Müşerref Duygu SaçarMicroRNAs (miRNAs) are posttranscriptional regulators of gene expression. While a miRNA can target hundreds of messenger RNA (mRNAs), an mRNA can be targeted by different miRNAs, not to mention that a single miRNA might have various binding sites in an mRNA sequence. Therefore, it is quite involved to investigate miRNAs experimentally. Thus, machine learning (ML) is frequently used to overcome such challenges. The key parts of a ML analysis largely depend on the quality of input data and the capacity of the features describing the data. Previously, more than 1000 features were suggested for miRNAs. Here, it is shown that using 36 features representing the RNA secondary structure and its dynamic 3D graphical representation provides up to 98% accuracy values. In this study, a new approach for ML-based miRNA prediction is proposed. Thousands of models are generated through classification of known human miRNAs and pseudohairpins with 3 classifiers: decision tree, naive Bayes, and random forest. Although the method is based on human data, the best model was able to correctly assign 96% of nonhuman hairpins from MirGeneDB, suggesting that this approach might be useful for the analysis of miRNAs from other species.Article Comparative Assessment of Smooth and Non-Smooth Optimization Solvers in Hanso Software(Ramazan Yaman, 2021-10-27) Tor, Ali HakanThe aim of this study is to compare the performance of smooth and nonsmooth mization) software. The smooth optimization solver is the implementation of the Broyden-Fletcher-Goldfarb-Shanno (BFGS) method and the nonsmooth optimization solver is the Hybrid Algorithm for Nonsmooth Optimization. More precisely, the nonsmooth optimization algorithm is the combination of the BFGS and the Gradient Sampling Algorithm (GSA). We use well-known collection of academic test problems for nonsmooth optimization containing both convex and nonconvex problems. The motivation for this research is the importance of the comparative assessment of smooth optimization methods for solving nonsmooth optimization problems. This assessment will demonstrate how successful is the BFGS method for solving nonsmooth optimization problems in comparison with the nonsmooth optimization solver from HANSO. Performance profiles using the number iterations, the number of function evaluations and the number of subgradient evaluations are used to compare solvers.