Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Book Part Citation - Scopus: 3ROSE: A Novel Approach for Protein Secondary Structure Prediction(Springer Science and Business Media Deutschland GmbH, 2021) Görmez, Yasin; Aydin, ZaferThree-dimensional structure of protein gives important information about protein’s function. Since it is time-consuming and costly to find the structure of protein by experimental methods, estimation of three-dimensional structures of proteins through computational methods has been an efficient alternative. One of the most important steps for the 3-D protein structure prediction is protein secondary structure prediction. Proteins which contain different number and sequences of amino acids may have similar structures. Thus, extracting appropriate input features has crucial importance for secondary structure prediction. In this study, a novel model, ROSE, is proposed for secondary structure prediction that obtains probability distributions as a feature vector by using two position specific scoring matrices obtained by PSIBLAST and HHblits. ROSE is a two-stage hybrid classifier that uses a one-dimensional bi-directional recurrent neural network at the first stage and a support vector machine at the second stage. It is also combined with DSPRED method, which employs dynamic Bayesian networks and a support vector machine. ROSE obtained comparable results to DSPRED in cross-validation experiments performed on a difficult benchmark and can be used as an alternative to protein secondary structure prediction. © 2021 Elsevier B.V., All rights reserved.Article Citation - WoS: 20Citation - Scopus: 19A Novel Integration of Mcdm Methods and Bayesian Networks: The Case of Incomplete Expert Knowledge(Springer, 2022-10-10) Kaya, Rukiye; Salhi, Said; Spiegler, VirginiaIn this study, we propose an effective integration of multi criteria decision making methods and Bayesian networks (BN) that incorporates expert knowledge. The novelty of this approach is that it provides decision support in case the experts have partial knowledge. We use decision-making trial and evaluation laboratory (DEMATEL) to elicit the causal graph of the BN based on the causal knowledge of the experts. BN provides the evaluation of alternatives based on the decision criteria which make up the initial decision matrix of the technique for order of preference by similarity to the ideal solution (TOPSIS). We then parameterize BN using Ranked Nodes which allows the experts to submit their knowledge with linguistic expressions. We propose the analytical hierarchy process to determine the weights of the decision criteria and TOPSIS to rank the alternatives. A supplier selection case study is conducted to illustrate the effectiveness of the proposed approach. Two evaluation measures, namely, the number of mismatches and the distance due to the mismatch are developed to assess the performance of the proposed approach. A scenario analysis with 5% to 20% of missing values with an increment of 5% is conducted to demonstrate that our approach remains robust as the level of missing values increases.