Search results for: Genetic Regulatory Networks (GRNs)

Authors: Hamid Barati, Ali Movaghar, Ali Barati, Arash Azizi Mazreah , Ehsan Shahsavari Gogheri, Faranak Mohsenzadeh

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The communication networks development and advancement during two last decades has been toward a single goal and that is gradual change from circuit-switched networks to packed switched ones. Today a lot of networks operates are trying to transform the public telephone networks to multipurpose packed switch. This new achievement is generally called "next generation networks". In fact, the next generation networks enable the operators to transfer every kind of services (sound, data and video) on a network. First, in this report the definition, characteristics and next generation networks services and then ad-hoc networks role in the next generation networks are studied.

Keywords: NGNs services, Ad-hoc Networks, NGN.

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Authors: S. M. Khalessizadeh, R. Zaefarian, S.H. Nasseri, E. Ardil

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Today, Genetic Algorithm has been used to solve wide range of optimization problems. Some researches conduct on applying Genetic Algorithm to text classification, summarization and information retrieval system in text mining process. This researches show a better performance due to the nature of Genetic Algorithm. In this paper a new algorithm for using Genetic Algorithm in concept weighting and topic identification, based on concept standard deviation will be explored.

Keywords: Genetic Algorithm, Text Mining, Term Weighting, Concept Extraction, Concept Distribution.

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Authors: S.Baskar, P.S.Ramkumar, R.Kesavan

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This paper presents a new heuristic algorithm useful for long-term planning of survivable WDM networks. A multi-period model is formulated that combines network topology design and capacity expansion. The ability to determine network expansion schedules of this type becomes increasingly important to the telecommunications industry and to its customers. The solution technique consists of a Genetic Algorithm that allows generating several network alternatives for each time period simultaneously and shortest-path techniques to deduce from these alternatives a least-cost network expansion plan over all time periods. The multi-period planning approach is illustrated on a realistic network example. Extensive simulations on a wide range of problem instances are carried out to assess the cost savings that can be expected by choosing a multi-period planning approach instead of an iterative network expansion design method.

Keywords: Wavelength Division Multiplexing, Genetic Algorithm, Network topology, Multi-period reliable network planning

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Authors: C. M. A. Robles G., R. A. Hernandez-Becerril

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We board the problem of creating a seismic alert system, based upon artificial neural networks, trained by using the well-known back-propagation and genetic algorithms, in order to emit the alarm for the population located into a specific city, about an eminent earthquake greater than 4.5 Richter degrees, and avoiding disasters and human loses. In lieu of using the propagation wave, we employed the magnitude of the earthquake, to establish a correlation between the recorded magnitudes from a controlled area and the city, where we want to emit the alarm. To measure the accuracy of the posed method, we use a database provided by CIRES, which contains the records of 2500 quakes incoming from the State of Guerrero and Mexico City. Particularly, we performed the proposed method to generate an issue warning in Mexico City, employing the magnitudes recorded in the State of Guerrero.

Keywords: Seismic Alert System, Artificial Neural Networks, Genetic Algorithms.

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Authors: P. Subbaraj, V. Rajasekaran

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This paper presents a new approach using Combined Artificial Neural Network (CANN) module for daily peak load forecasting. Five different computational techniques –Constrained method, Unconstrained method, Evolutionary Programming (EP), Particle Swarm Optimization (PSO), and Genetic Algorithm (GA) – have been used to identify the CANN module for peak load forecasting. In this paper, a set of neural networks has been trained with different architecture and training parameters. The networks are trained and tested for the actual load data of Chennai city (India). A set of better trained conventional ANNs are selected to develop a CANN module using different algorithms instead of using one best conventional ANN. Obtained results using CANN module confirm its validity.

Keywords: Combined ANN, Evolutionary Programming, Particle Swarm Optimization, Genetic Algorithm and Peak load forecasting.

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Authors: K. Vijayalakshmi, S. Radhakrishnan

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In this paper we have proposed a novel dynamic least cost multicast routing protocol using hybrid genetic algorithm for IP networks. Our protocol finds the multicast tree with minimum cost subject to delay, degree, and bandwidth constraints. The proposed protocol has the following features: i. Heuristic local search function has been devised and embedded with normal genetic operation to increase the speed and to get the optimized tree, ii. It is efficient to handle the dynamic situation arises due to either change in the multicast group membership or node / link failure, iii. Two different crossover and mutation probabilities have been used for maintaining the diversity of solution and quick convergence. The simulation results have shown that our proposed protocol generates dynamic multicast tree with lower cost. Results have also shown that the proposed algorithm has better convergence rate, better dynamic request success rate and less execution time than other existing algorithms. Effects of degree and delay constraints have also been analyzed for the multicast tree interns of search success rate.

Keywords: Dynamic Group membership change, Hybrid Genetic Algorithm, Link / node failure, QoS Parameters.

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Authors: Amod P. Vaze

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Genetic Algorithm has been used to solve wide range of optimization problems. Some researches conduct on applying Genetic Algorithm to analog circuit design automation. These researches show a better performance due to the nature of Genetic Algorithm. In this paper a modified Genetic Algorithm is applied for analog circuit design automation. The modifications are made to the topology of the circuit. These modifications will lead to a more computationally efficient algorithm.

Keywords: Genetic algorithm, analog circuits, design.

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Authors: Frank Emmert-Streib, Matthias Dehmer

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Inferring the network structure from time series data is a hard problem, especially if the time series is short and noisy. DNA microarray is a technology allowing to monitor the mRNA concentration of thousands of genes simultaneously that produces data of these characteristics. In this study we try to investigate the influence of the experimental design on the quality of the result. More precisely, we investigate the influence of two different types of random single gene perturbations on the inference of genetic networks from time series data. To obtain an objective quality measure for this influence we simulate gene expression values with a biologically plausible model of a known network structure. Within this framework we study the influence of single gene knock-outs in opposite to linearly controlled expression for single genes on the quality of the infered network structure.

Keywords: Dynamic Bayesian networks, microarray data, structure learning, Markov chain Monte Carlo.

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Authors: Sung Hoon Jung

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In this paper, we propose a selective mutation method for improving the performances of genetic algorithms. In selective mutation, individuals are first ranked and then additionally mutated one bit in a part of their strings which is selected corresponding to their ranks. This selective mutation helps genetic algorithms to fast approach the global optimum and to quickly escape local optima. This results in increasing the performances of genetic algorithms. We measured the effects of selective mutation with four function optimization problems. It was found from extensive experiments that the selective mutation can significantly enhance the performances of genetic algorithms.

Keywords: Genetic algorithm, selective mutation, function optimization

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Authors: Grigorios N. Beligiannis, Georgios A. Tsirogiannis, Panayotis E. Pintelas

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In this contribution, a way to enhance the performance of the classic Genetic Algorithm is proposed. The idea of restarting a Genetic Algorithm is applied in order to obtain better knowledge of the solution space of the problem. A new operator of 'insertion' is introduced so as to exploit (utilize) the information that has already been collected before the restarting procedure. Finally, numerical experiments comparing the performance of the classic Genetic Algorithm and the Genetic Algorithm with restartings, for some well known test functions, are given.

Keywords: Genetic Algorithms, Restartings, Search space exploration, Search space exploitation.

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Authors: Bashar Al-Shboul, Sung-Hyon Myaeng

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K-Means (KM) is considered one of the major algorithms widely used in clustering. However, it still has some problems, and one of them is in its initialization step where it is normally done randomly. Another problem for KM is that it converges to local minima. Genetic algorithms are one of the evolutionary algorithms inspired from nature and utilized in the field of clustering. In this paper, we propose two algorithms to solve the initialization problem, Genetic Algorithm Initializes KM (GAIK) and KM Initializes Genetic Algorithm (KIGA). To show the effectiveness and efficiency of our algorithms, a comparative study was done among GAIK, KIGA, Genetic-based Clustering Algorithm (GCA), and FCM [19].

Keywords: Clustering, Genetic Algorithms, K-means.

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Authors: C. Rajan, K. Geetha, C. Rasi Priya, R. Sasikala

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Nature is a great source of inspiration for solving complex problems in networks. It helps to find the optimal solution. Metaheuristic algorithm is one of the nature-inspired algorithm which helps in solving routing problem in networks. The dynamic features, changing of topology frequently and limited bandwidth make the routing, challenging in MANET. Implementation of appropriate routing algorithms leads to the efficient transmission of data in mobile ad hoc networks. The algorithms that are inspired by the principles of naturally-distributed/collective behavior of social colonies have shown excellence in dealing with complex optimization problems. Thus some of the bio-inspired metaheuristic algorithms help to increase the efficiency of routing in ad hoc networks. This survey work presents the overview of bio-inspired metaheuristic algorithms which support the efficiency of routing in mobile ad hoc networks.

Keywords: Ant colony optimization algorithm, Genetic algorithm, naturally inspired algorithms and particle swarm optimization algorithm.

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Authors: Yongzhong Wu, Ping Ji

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This paper proposes a genetic algorithm based on a new replacement strategy to solve the quadratic assignment problems, which are NP-hard. The new replacement strategy aims to improve the performance of the genetic algorithm through well balancing the convergence of the searching process and the diversity of the population. In order to test the performance of the algorithm, the instances in QAPLIB, a quadratic assignment problem library, are tried and the results are compared with those reported in the literature. The performance of the genetic algorithm is promising. The significance is that this genetic algorithm is generic. It does not rely on problem-specific genetic operators, and may be easily applied to various types of combinatorial problems.

Keywords: Quadratic assignment problem, Genetic algorithm, Replacement strategy, QAPLIB.

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Authors: H. Kazemi Karegar, S. Jalilzadeh, V. Nabaei, A. Shabani

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In this paper, the problem of finding the optimal topological configuration of a deregulated distribution network is considered. The new features of this paper are proposing a multiobjective function and its application on deregulated distribution networks for finding the optimal configuration. The multi-objective function will be defined for minimizing total Energy Supply Costs (ESC) and energy losses subject to load flow constraints. The optimal configuration will be obtained by using Binary Genetic Algorithm (BGA).The proposed method has been tested to analyze a sample and a practical distribution networks.

Keywords: Binary Genetic Algorithm, Deregulated Distribution Network, Minimizing Cost, Reconfiguration.

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Authors: H. Shayeghi, H. A. Shayanfar, G. Azimi

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Short-Term Load Forecasting (STLF) plays an important role for the economic and secure operation of power systems. In this paper, Continuous Genetic Algorithm (CGA) is employed to evolve the optimum large neural networks structure and connecting weights for one-day ahead electric load forecasting problem. This study describes the process of developing three layer feed-forward large neural networks for load forecasting and then presents a heuristic search algorithm for performing an important task of this process, i.e. optimal networks structure design. The proposed method is applied to STLF of the local utility. Data are clustered due to the differences in their characteristics. Special days are extracted from the normal training sets and handled separately. In this way, a solution is provided for all load types, including working days and weekends and special days. We find good performance for the large neural networks. The proposed methodology gives lower percent errors all the time. Thus, it can be applied to automatically design an optimal load forecaster based on historical data.

Keywords: Feed-forward Large Neural Network, Short-TermLoad Forecasting, Continuous Genetic Algorithm.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

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The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Gary Marlin Sandquist

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Currently, a large number of license activities (Early Site Permits, Combined Operating License, reactor certifications, etc.), are pending for review before the United States Nuclear Regulatory Commission (US NRC). Much of the senior staff at the NRC is now committed to these review and licensing actions. To address this additional workload, the NRC has recruited a large number of new Regulatory Staff for dealing with these and other regulatory actions such as the US Fleet of Research and Test Reactors (RTRs). These reactors pose unusual demands on Regulatory Staff since the US Fleet of RTRs, although few (32 Licensed RTRs as of 2010), they represent a broad range of reactor types, operations, and research and training aspects that nuclear reactor power plants (such as the 104 LWRs) do not pose. The NRC must inspect and regulate all these facilities. This paper addresses selected training topics and regulatory activities providedNRC Inspectors for RTRs.

Keywords: Regulations, Research and Test Reactors, Training, US NRC

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Authors: Panpan Xu, Shulin Sui, Zongjie Du

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Genetic algorithm is widely used in optimization problems for its excellent global search capabilities and highly parallel processing capabilities; but, it converges prematurely and has a poor local optimization capability in actual operation. Simulated annealing algorithm can avoid the search process falling into local optimum. A hybrid genetic algorithm based on simulated annealing is designed by combining the advantages of genetic algorithm and simulated annealing algorithm. The numerical experiment represents the hybrid genetic algorithm can be applied to solve the function optimization problems efficiently.

Keywords: Genetic algorithm, Simulated annealing, Hybrid genetic algorithm, Function optimization.

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Authors: Maria E. Manioudaki, Panayiota Poirazi

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Yeast cells live in a constantly changing environment that requires the continuous adaptation of their genomic program in order to sustain their homeostasis, survive and proliferate. Due to the advancement of high throughput technologies, there is currently a large amount of data such as gene expression, gene deletion and protein-protein interactions for S. Cerevisiae under various environmental conditions. Mining these datasets requires efficient computational methods capable of integrating different types of data, identifying inter-relations between different components and inferring functional groups or 'modules' that shape intracellular processes. This study uses computational methods to delineate some of the mechanisms used by yeast cells to respond to environmental changes. The GRAM algorithm is first used to integrate gene expression data and ChIP-chip data in order to find modules of coexpressed and co-regulated genes as well as the transcription factors (TFs) that regulate these modules. Since transcription factors are themselves transcriptionally regulated, a three-layer regulatory cascade consisting of the TF-regulators, the TFs and the regulated modules is subsequently considered. This three-layer cascade is then modeled quantitatively using artificial neural networks (ANNs) where the input layer corresponds to the expression of the up-stream transcription factors (TF-regulators) and the output layer corresponds to the expression of genes within each module. This work shows that (a) the expression of at least 33 genes over time and for different stress conditions is well predicted by the expression of the top layer transcription factors, including cases in which the effect of up-stream regulators is shifted in time and (b) identifies at least 6 novel regulatory interactions that were not previously associated with stress-induced changes in gene expression. These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully model biological pathways and capture quantitative dependencies between distant regulators and downstream genes.

Keywords: gene modules, artificial neural networks, yeast, stress

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Authors: M. Hadi Mashinchi, M. Reza Mashinchi, Siti Mariyam H. J. Shamsuddin

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In this paper a genetic algorithms approach for solving the linear and quadratic fuzzy equations Ãx̃=B̃ and Ãx̃² + B̃x̃=C̃ , where Ã, B̃, C̃ and x̃ are fuzzy numbers is proposed by genetic algorithms. Our genetic based method initially starts with a set of random fuzzy solutions. Then in each generation of genetic algorithms, the solution candidates converge more to better fuzzy solution x̃_b . In this proposed method the final reached x̃_b is not only restricted to fuzzy triangular and it can be fuzzy number.

Keywords: Fuzzy coefficient, fuzzy equation, genetic algorithms.

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

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Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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Authors: Razagh Hafezi, Ahmad Keshavarz, Vida Moshfegh

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This paper presents a novel algorithm of stereo correspondence with rank transform. In this algorithm we used the genetic algorithm to achieve the accurate disparity map. Genetic algorithms are efficient search methods based on principles of population genetic, i.e. mating, chromosome crossover, gene mutation, and natural selection. Finally morphology is employed to remove the errors and discontinuities.

Keywords: genetic algorithm, morphology, rank transform, stereo correspondence

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Authors: Mohammad Ali Tabarzad, Caro Lucas, Ali Hamzeh

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Adaptive Genetic Algorithms extend the Standard Gas to use dynamic procedures to apply evolutionary operators such as crossover, mutation and selection. In this paper, we try to propose a new adaptive genetic algorithm, which is based on the statistical information of the population as a guideline to tune its crossover, selection and mutation operators. This algorithms is called Statistical Genetic Algorithm and is compared with traditional GA in some benchmark problems.

Keywords: Genetic Algorithms, Statistical Information ofthe Population, PAUX, SSO.

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Authors: Konstantinos C. Giotopoulos, Christos E. Alexakos, Grigorios N. Beligiannis, Spiridon D.Likothanassis

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In this contribution an innovative platform is being presented that integrates intelligent agents and evolutionary computation techniques in legacy e-learning environments. It introduces the design and development of a scalable and interoperable integration platform supporting: I) various assessment agents for e-learning environments, II) a specific resource retrieval agent for the provision of additional information from Internet sources matching the needs and profile of the specific user and III) a genetic algorithm designed to extract efficient information (classifying rules) based on the students- answering input data. The agents are implemented in order to provide intelligent assessment services based on computational intelligence techniques such as Bayesian Networks and Genetic Algorithms. The proposed Genetic Algorithm (GA) is used in order to extract efficient information (classifying rules) based on the students- answering input data. The idea of using a GA in order to fulfil this difficult task came from the fact that GAs have been widely used in applications including classification of unknown data. The utilization of new and emerging technologies like web services allows integrating the provided services to any web based legacy e-learning environment.

Keywords: Bayesian Networks, Computational Intelligencetechniques, E-learning legacy systems, Service Oriented Integration, Intelligent Agents, Genetic Algorithms.

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Authors: J. Tospornsampan, I. Kita, M. Ishii, Y. Kitamura

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In this paper a combination approach of two heuristic-based algorithms: genetic algorithm and tabu search is proposed. It has been developed to obtain the least cost based on the split-pipe design of looped water distribution network. The proposed combination algorithm has been applied to solve the three well-known water distribution networks taken from the literature. The development of the combination of these two heuristic-based algorithms for optimization is aimed at enhancing their strengths and compensating their weaknesses. Tabu search is rather systematic and deterministic that uses adaptive memory in search process, while genetic algorithm is probabilistic and stochastic optimization technique in which the solution space is explored by generating candidate solutions. Split-pipe design may not be realistic in practice but in optimization purpose, optimal solutions are always achieved with split-pipe design. The solutions obtained in this study have proved that the least cost solutions obtained from the split-pipe design are always better than those obtained from the single pipe design. The results obtained from the combination approach show its ability and effectiveness to solve combinatorial optimization problems. The solutions obtained are very satisfactory and high quality in which the solutions of two networks are found to be the lowest-cost solutions yet presented in the literature. The concept of combination approach proposed in this study is expected to contribute some useful benefits in diverse problems.

Keywords: GAs, Heuristics, Looped network, Least-cost design, Pipe network, Optimization, TS

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Authors: Anwar Jarndal

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In this paper, a genetic-neural-network (GNN) based large-signal model for GaN HEMTs is presented along with its parameters extraction procedure. The model is easy to construct and implement in CAD software and requires only DC and S-parameter measurements. An improved decomposition technique is used to model self-heating effect. Two GNN models are constructed to simulate isothermal drain current and power dissipation, respectively. The two model are then composed to simulate the drain current. The modeling procedure was applied to a packaged GaN-on-Si HEMT and the developed model is validated by comparing its large-signal simulation with measured data. A very good agreement between the simulation and measurement is obtained.

Keywords: GaN HEMT, computer-aided design & modeling, neural networks, genetic optimization.

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Authors: Frank Emmert Streib, Matthias Dehmer, Gökhan H. Bakır, Max Mühlhauser

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In this paper we investigate the influence of external noise on the inference of network structures. The purpose of our simulations is to gain insights in the experimental design of microarray experiments to infer, e.g., transcription regulatory networks from microarray experiments. Here external noise means, that the dynamics of the system under investigation, e.g., temporal changes of mRNA concentration, is affected by measurement errors. Additionally to external noise another problem occurs in the context of microarray experiments. Practically, it is not possible to monitor the mRNA concentration over an arbitrary long time period as demanded by the statistical methods used to learn the underlying network structure. For this reason, we use only short time series to make our simulations more biologically plausible.

Keywords: Dynamic Bayesian networks, structure learning, gene networks, Markov chain Monte Carlo, microarray data.

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Authors: Jana Chvalkovska, Petr Jansky, Petr Teply

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The impact assessment in its various forms has recently become a very important part of policy-making and legislation in many different countries. Regulatory impact assessment (RIA) is yet another set of analytical methods deployed in the legislation of the European Union, of many developed countries as well as in many developing ones such as Mexico, Malaysia and Philippines. The aim of this paper is to provide a theoretical background for economic models in regulatory impact assessment and an overview of their application especially on the financial market in the Czech Republic. We found out an inadequate application of these models, what makes room for further research in this field.

Keywords: regulatory impact assessment, RIA, impact evaluation, building societies, Czech Republic

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Authors: A. R. Malekpour, A.R. Seifi

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This paper discusses a genetic algorithm (GA) based optimal load shedding that can apply for electrical distribution networks with and without dispersed generators (DG). Also, the proposed method has the ability for considering constant and variable capacity deficiency caused by unscheduled outages in the bulked generation and transmission system of bulked power supply. The genetic algorithm (GA) is employed to search for the optimal load shedding strategy in distribution networks considering DGs in two cases of constant and variable modelling of bulked power supply of distribution networks. Electrical power distribution systems have a radial network and unidirectional power flows. With the advent of dispersed generations, the electrical distribution system has a locally looped network and bidirectional power flows. Therefore, installed DG in the electrical distribution systems can cause operational problems and impact on existing operational schemes. Introduction of DGs in electrical distribution systems has introduced many new issues in operational and planning level. Load shedding as one of operational issue has no exempt. The objective is to minimize the sum of curtailed load and also system losses within the frame-work of system operational and security constraints. The proposed method is tested on a radial distribution system with 33 load points for more practical applications.

Keywords: DG, Load shedding, Optimization, Capacity Deficiency Modelling.

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Authors: M. A. Sharbafi, M. Shakiba Herfeh, Caro Lucas, A. Mohammadi Nejad

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Several researchers have proposed methods about combination of Genetic Algorithm (GA) and Fuzzy Logic (the use of GA to obtain fuzzy rules and application of fuzzy logic in optimization of GA). In this paper, we suggest a new method in which fuzzy decision making is used to improve the performance of genetic algorithm. In the suggested method, we determine the alleles that enhance the fitness of chromosomes and try to insert them to the next generation. In this algorithm we try to present an innovative vaccination in the process of reproduction in genetic algorithm, with considering the trade off between exploration and exploitation.

Keywords: Genetic Algorithm, Fuzzy Decision Making.

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