Browsing by Subject "Optimization techniques"

Now showing 1 - 5 of 5
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    Effects of additional independent noise in binary composite hypothesis-testing problems
    (IEEE, 2009-09) Bayram, Suat; Gezici, Sinan
    Performance of some suboptimal detectors can be improved by adding independent noise to their observations. In this paper, the effects of adding independent noise to observations of a detector are investigated for binary composite hypothesistesting problems in a generalized Neyman-Pearson framework. Sufficient conditions are derived to determine when performance of a detector can or cannot be improved via additional independent noise. Also, upper and lower limits are derived on the performance of a detector in the presence of additional noise, and statistical characterization of optimal additional noise is provided. In addition, two optimization techniques are proposed to calculate the optimal additional noise. Finally, simulation results are presented to investigate the theoretical results. © 2009 IEEE.
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    Examining the annealing schedules for RNA design algorithm
    (IEEE, 2016-07) Erhan, H. E.; Sav, Sinem; Kalashnikov, S.; Tsang, H. H.
    RNA structures are important for many biological processes in the cell. One important function of RNA are as catalytic elements. Ribozymes are RNA sequences that fold to form active structures that catalyze important chemical reactions. The folded structure for these RNA are very important; only specific conformations maintain these active structures, so it is very important for RNA to fold in a specific way. The RNA design problem describes the prediction of an RNA sequence that will fold into a given RNA structure. Solving this problem allows researchers to design RNA; they can decide on what folded secondary structure is required to accomplish a task, and the algorithm will give them a primary sequence to assemble. However, there are far too many possible primary sequence combinations to test sequentially to see if they would fold into the structure. Therefore we must employ heuristics algorithms to attempt to solve this problem. This paper introduces SIMARD, an evolutionary algorithm that uses an optimization technique called simulated annealing to solve the RNA design problem. We analyzes three different cooling schedules for the annealing process: 1) An adaptive cooling schedule, 2) a geometric cooling schedule, and 3) a geometric cooling schedule with warm up. Our results show that an adaptive annealing schedule may not be more effective at minimizing the Hamming distance between the target structure and our folded sequence's structure when compared with geometric schedules. The results also show that warming up in a geometric cooling schedule may be useful for optimizing SIMARD. © 2016 IEEE.
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    G-network modelling based abnormal pathway detection in gene regulatory networks
    (Springer, London, 2012) Kim H.; Atalay, Rengül; Gelenbe, E.
    Gene expression centered gene regulatory networks studies can provide insight into the dynamics of pathway activities that depend on changes in their environmental conditions. Thus we propose a new pathway analysis approach to detect differentially behaving pathways in abnormal conditions based on G-network theory. Using this approach gene regulatory network model parameters are estimated from normal and abnormal samples using optimization techniques with corresponding constraints. We show that in a "p53 network" application, the proposed method effectively detects anomalous activated/inactivated pathways related with MDM2, ATM/ATR and RB1 genes, which could not be observed from previous analyses of gene regulatory network normal and abnormal behaviour. © 2012 Springer-Verlag London Limited.
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    Low-order controller design for haptic systems under delayed feedback
    (2012) Liacu, B.; Koru, A. T.; Özbay, Hitay; Niculescu, S. -I.; Andriot, C.
    In this paper, we consider PD controller design for haptic systems under delayed feedback. More precisely, we present a complete stability analysis of a haptic system where local dynamics are described by some second-order mechanical dynamics. Next, using two optimization techniques (H ∞ and stability margin optimization) we propose an optimal choice for the controller gains. The derived results are tested on a three degree of freedom real-time experimental platform to illustrate the theoretical results. © 2012 IFAC.
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    Projections onto convex sets (POCS) based optimization by lifting
    (IEEE, 2013) Çetin, A. Enis; Bozkurt, Alican; Günay, Osman; Habiboglu, Yusuf Hakan; Köse, K.; Onaran, İbrahim; Tofighi, Mohammad; Sevimli, Rasim Akın
    A new optimization technique based on the projections onto convex space (POCS) framework for solving convex and some non-convex optimization problems are presented. The dimension of the minimization problem is lifted by one and sets corresponding to the cost function are defined. If the cost function is a convex function in RN the corresponding set which is the epigraph of the cost function is also a convex set in RN+1. The iterative optimization approach starts with an arbitrary initial estimate in R N+1 and an orthogonal projection is performed onto one of the sets in a sequential manner at each step of the optimization problem. The method provides globally optimal solutions in total-variation, filtered variation, l1, and entropic cost functions. It is also experimentally observed that cost functions based on lp; p < 1 may be handled by using the supporting hyperplane concept. The new POCS based method can be used in image deblurring, restoration and compressive sensing problems. © 2013 IEEE.