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: 4Quasi-Supervised Strategies for Compound-Protein Interaction Prediction(John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.Article Citation - WoS: 16Citation - Scopus: 16Learning Control of Robot Manipulators in Task Space(John Wiley and Sons Inc., 2018) Doğan, Kadriye Merve; Tatlıcıoğlu, Enver; Zergeroğlu, Erkan; Çetin, KamilTwo important properties of industrial tasks performed by robot manipulators, namely, periodicity (i.e., repetitive nature) of the task and the need for the task to be performed by the end-effector, motivated this work. Not being able to utilize the robot manipulator dynamics due to uncertainties complicated the control design. In a seemingly novel departure from the existing works in the literature, the tracking problem is formulated in the task space and the control input torque is aimed to decrease the task space tracking error directly without making use of inverse kinematics at the position level. A repetitive learning controller is designed which “learns” the overall uncertainties in the robot manipulator dynamics. The stability of the closed-loop system and asymptotic end-effector tracking of a periodic desired trajectory are guaranteed via Lyapunov based analysis methods. Experiments performed on an in-house developed robot manipulator are presented to illustrate the performance and viability of the proposed controller.Conference Object Citation - Scopus: 12Incremental Itemset Mining Based on Matrix Apriori Algorithm(Springer Verlag, 2012) Oğuz, Damla; Ergenç, BelginDatabases are updated continuously with increments and re-running the frequent itemset mining algorithms with every update is inefficient. Studies addressing incremental update problem generally propose incremental itemset mining methods based on Apriori and FP-Growth algorithms. Besides inheriting the disadvantages of base algorithms, incremental itemset mining has challenges such as handling i) increments without re-running the algorithm, ii) support changes, iii) new items and iv) addition/deletions in increments. In this paper, we focus on the solution of incremental update problem by proposing the Incremental Matrix Apriori Algorithm. It scans only new transactions, allows the change of minimum support and handles new items in the increments. The base algorithm Matrix Apriori works without candidate generation, scans database only twice and brings additional advantages. Performance studies show that Incremental Matrix Apriori provides speed-up between 41% and 92% while increment size is varied between 5% and 100%.Article Citation - WoS: 9Citation - Scopus: 10Modelling Trip Distribution With Fuzzy and Genetic Fuzzy Systems(Taylor and Francis Ltd., 2013) Kompil, Mert; Çelik, Hüseyin MuratThis paper explores the potential capabilities of fuzzy and genetic fuzzy system approaches in urban trip distribution modelling with some new features. First, a simple fuzzy rule-based system (FRBS) and a novel genetic fuzzy rule-based system [GFRBS: a fuzzy system improved by a knowledge base learning process with genetic algorithms (GAs)] are designed to model intra-city passenger flows for Istanbul. Subsequently, their accuracy, applicability and generalizability characteristics are evaluated against the well-known gravity- and neural network (NN)-based trip distribution models. The overall results show that: traditional doubly constrained gravity models are still simple and efficient; NNs may not show expected performance when they are forced to satisfy trip constraints; simply-designed FRBSs, learning from observations and expertise, are both efficient and interpretable even if the data are large and noisy; and use of GAs in fuzzy rule-based learning considerably increases modelling performance, although it brings additional computation cost.Conference Object Citation - WoS: 1Citation - Scopus: 6Genetic Algorithm-Artificial Neural Network Model for the Prediction of Germanium Recovery From Zinc Plant Residues(Taylor and Francis Ltd., 2002) Akkurt, Sedat; Özdemir, Serhan; Tayfur, GökmenA multi-layer, feed-forward, back-propagation learning algorithm was used as an artificial neural network (ANN) tool to predict the extraction of germanium from zinc plant residues by sulphuric acid leaching. A genetic algorithm (GA) was used for the selection of training and testing data and a GA-ANN model of the germanium leaching system was created on the basis of the training data. Testing of the model yielded good error levels (r2 = 0.95). The model was employed to predict the response of the system to different values of the factors that affect the recovery of germanium and the results facilitate selection of the experimental conditions in which the optimum recovery will be achieved.