Search results for: Protein sequence algorithm

Authors: G. Parmar, R. Prasad, S. Mukherjee

Abstract:

The authors present an algorithm for order reduction of linear dynamic systems using the combined advantages of stability equation method and the error minimization by Genetic algorithm. The denominator of the reduced order model is obtained by the stability equation method and the numerator terms of the lower order transfer function are determined by minimizing the integral square error between the transient responses of original and reduced order models using Genetic algorithm. The reduction procedure is simple and computer oriented. It is shown that the algorithm has several advantages, e.g. the reduced order models retain the steady-state value and stability of the original system. The proposed algorithm has also been extended for the order reduction of linear multivariable systems. Two numerical examples are solved to illustrate the superiority of the algorithm over some existing ones including one example of multivariable system.

Keywords: Genetic algorithm, Integral square error, Orderreduction, Stability equation method.

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Authors: V. K. Banga, Y. Singh, R. Kumar

Abstract:

In this paper, we have proposed a low cost optimized solution for the movement of a three-arm manipulator using Genetic Algorithm (GA) and Analytical Hierarchy Process (AHP). A scheme is given for optimizing the movement of robotic arm with the help of Genetic Algorithm so that the minimum energy consumption criteria can be achieved. As compared to Direct Kinematics, Inverse Kinematics evolved two solutions out of which the best-fit solution is selected with the help of Genetic Algorithm and is kept in search space for future use. The Inverse Kinematics, Fitness Value evaluation and Binary Encoding like tasks are simulated and tested. Although, three factors viz. Movement, Friction and Least Settling Time (or Min. Vibration) are used for finding the Fitness Function / Fitness Values, however some more factors can also be considered.

Keywords: Inverse Kinematics, Genetic Algorithm (GA), Analytical Hierarchy Process (AHP), Fitness Value, Fitness Function.

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Authors: Diogen Babuc

Abstract:

The question that is a motivation of writing is how many devote themselves to discovering something in the world of science where much is discerned and revealed, but at the same time, much is unknown. The insightful elements of this algorithm are the ciphering and deciphering algorithms of Playfair, Caesar, and Vigen`ere. Only a few of their main properties are taken and modified, with the aim of forming a specific functionality of the algorithm called Latin Djokovic. Specifically, a string is entered as input data. A key k is given, with a random value between the values a and b = a+3. The obtained value is stored in a variable with the aim of being constant during the run of the algorithm. In correlation to the given key, the string is divided into several groups of substrings, and each substring has a length of k characters. The next step involves encoding each substring from the list of existing substrings. Encoding is performed using the basis of Caesar algorithm, i.e. shifting with k characters. However, that k is incremented by 1 when moving to the next substring in that list. When the value of k becomes greater than b + 1, it will return to its initial value. The algorithm is executed, following the same procedure, until the last substring in the list is traversed. Using this polyalphabetic method, ciphering and deciphering of strings are achieved. The algorithm also works for a 100-character string. The x character is not used when the number of characters in a substring is incompatible with the expected length. The algorithm is simple to implement, but it is questionable if it works better than the other methods, from the point of view of execution time and storage space.

Keywords: Ciphering and deciphering, Authentic Algorithm, Polyalphabetic Cipher, Random Key, methods comparison.

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Authors: Sayani Sil, Sukanta Das

Abstract:

This paper reports a distributed mutual exclusion algorithm for mobile Ad-hoc networks. The network is clustered hierarchically. The proposed algorithm considers the clustered network as a logical tree and develops a token passing scheme to get the mutual exclusion. The performance analysis and simulation results show that its message requirement is optimal, and thus the algorithm is energy efficient.

Keywords: Critical section, Distributed mutual exclusion, MobileAd-hoc network, Token-based algorithms.

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Authors: Basit Shahzad, Muhammad Tanvir Afzal

Abstract:

Many algorithms are available for sorting the unordered elements. Most important of them are Bubble sort, Heap sort, Insertion sort and Shell sort. These algorithms have their own pros and cons. Shell Sort which is an enhanced version of insertion sort, reduces the number of swaps of the elements being sorted to minimize the complexity and time as compared to insertion sort. Shell sort improves the efficiency of insertion sort by quickly shifting values to their destination. Average sort time is O(n1.25), while worst-case time is O(n1.5). It performs certain iterations. In each iteration it swaps some elements of the array in such a way that in last iteration when the value of h is one, the number of swaps will be reduced. Donald L. Shell invented a formula to calculate the value of ?h?. this work focuses to identify some improvement in the conventional Shell sort algorithm. ''Enhanced Shell Sort algorithm'' is an improvement in the algorithm to calculate the value of 'h'. It has been observed that by applying this algorithm, number of swaps can be reduced up to 60 percent as compared to the existing algorithm. In some other cases this enhancement was found faster than the existing algorithms available.

Keywords: Algorithm, Computation, Shell, Sorting.

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Authors: Alexey V. Klyuev, Valery P. Samarin, Viktor F. Klyuev, Andrey V. Klyuev

Abstract:

A power measurement algorithm of the input mix components of the noise signal and pulse interference is considered. The algorithm efficiency analysis has been carried out for different interference-to-signal ratio. Algorithm performance features have been explored by numerical experiment results.

Keywords: Noise signal, pulse interference, signal power, spectrum width, detection.

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Authors: Doaa Hegazy, Joachim Denzler

Abstract:

SoftBoost is a recently presented boosting algorithm, which trades off the size of achieved classification margin and generalization performance. This paper presents a performance evaluation of SoftBoost algorithm on the generic object recognition problem. An appearance-based generic object recognition model is used. The evaluation experiments are performed using a difficult object recognition benchmark. An assessment with respect to different degrees of label noise as well as a comparison to the well known AdaBoost algorithm is performed. The obtained results reveal that SoftBoost is encouraged to be used in cases when the training data is known to have a high degree of noise. Otherwise, using Adaboost can achieve better performance.

Keywords: SoftBoost algorithm, AdaBoost algorithm, Generic object recognition.

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Authors: Wan-Ting Lin, Chuen-Horng Lin, Tsung-Ho Wu, Yung-Kuan Chan

Abstract:

This study aims to segment objects using the K-means algorithm for texture features. Firstly, the algorithm transforms color images into gray images. This paper describes a novel technique for the extraction of texture features in an image. Then, in a group of similar features, objects and backgrounds are differentiated by using the K-means algorithm. Finally, this paper proposes a new object segmentation algorithm using the morphological technique. The experiments described include the segmentation of single and multiple objects featured in this paper. The region of an object can be accurately segmented out. The results can help to perform image retrieval and analyze features of an object, as are shown in this paper.

Keywords: k-mean, multiple objects, segmentation, texturefeatures.

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Authors: Tom Snir, Eitan Rubin

Abstract:

Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: Gökhan Silahtaroğlu

Abstract:

Decision tree algorithms have very important place at classification model of data mining. In literature, algorithms use entropy concept or gini index to form the tree. The shape of the classes and their closeness to each other some of the factors that affect the performance of the algorithm. In this paper we introduce a new decision tree algorithm which employs data (attribute) folding method and variation of the class variables over the branches to be created. A comparative performance analysis has been held between the proposed algorithm and C4.5.

Keywords: Classification, decision tree, split, pruning, entropy, gini.

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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: Sumitra Nuanmeesri, Kanate Ploydanai

Abstract:

Many companies have excel, it is economy and well perform to use in material requirement planning (MRP) on excel. For several products, it, however, is complex problem to link the relationship between the tables of products because the relationship depends on bill of material (BOM). This paper presents algorithm to create MRP on excel, and links relationship between tables. The study reveals MRP that is created by the algorithm which is easier and faster than MRP that created by human. By this technique, MRP on excel might be good ways to improve a productivity of companies.

Keywords: Material requirement planning, Algorithm, Spreadsheet.

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Authors: B. Coşgun, Ö. Öztürk

Abstract:

Canola is a specific edible type of rapeseed, developed in the 1970s, which contains about 40 percent oil. This research was carried out to determine the yield and some quality characteristics of some winter canola cultivars during the 2010-2011 vegetation period in Central Anatolia of Turkey. In this research; Oase, Dante, Californium, Excalibur, Elvis, ES Hydromel, Licord, Orkan, Vectra, Nelson, Champlain and NK Petrol winter canola varieties were used as material. The field experiment was set up in a “Randomized Complete Block Design” with three replications on 21 September 2010. In this research; seed yield, oil content, protein content, oil yield and protein yield were examined. As a result of this research; seed yield, oil content, oil yield and protein yield (except protein content) were significant differences between the cultivars. The highest seed yield (6348 kg ha-1) was obtained from the NK Petrol, while the lowest seed yield (3949 kg ha-1) was determined from the Champlain cultivar was obtained. The highest oil content (46.73%) was observed from Oase and the lowest value was obtained from Vectra (41.87%) cultivar. The highest oil yield (2950 kg ha-1) was determined from NK Petrol while the least value (1681 kg ha-1) was determined from Champlain cultivar. The highest protein yield (1539.3 kg ha-1) was obtained from NK Petrol and the lowest protein yield (976.5 kg ha-1) was obtained from Champlain cultivar. The main purpose of the cultivation of oil crops, to increase the yield of oil per unit area. According the result of this research, NK Petrol cultivar which ranks first with regard to both seed yield and oil yield between cultivars as the most suitable winter canola cultivar of local conditions.

Keywords: Cultivar, Oil yield, Rapeseed, Seed Yield.

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Authors: Young-Seok Choi

Abstract:

This paper proposes a complementary combination scheme of affine projection algorithm (APA) filters with different order of input regressors. A convex combination provides an interesting way to keep the advantage of APA having different order of input regressors. Consequently, a novel APA which has the rapid convergence and the reduced steady-state error is derived. Experimental results show the good properties of the proposed algorithm.

Keywords: Adaptive filter, affine projection algorithm, convex combination, input order.

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Authors: Alaa E. Abdallah, M. Bsoul, Emad E. Abdallah, Ahmad Al-Khasawneh, Muath Alzghool

Abstract:

Due to the limited lifetime of the nodes in ad hoc and sensor networks, energy efficiency needs to be an important design consideration in any routing algorithm. It is known that by employing a virtual backbone in a wireless network, the efficiency of any routing scheme for the network can be improved. One common design for routing protocols in mobile ad hoc networks is to use positioning information; we use the node-s geometric locations to introduce an algorithm that can construct the virtual backbone structure locally in 3D environment. The algorithm construction has a constant time.

Keywords: Virtual backbone, dominating set, UDG.

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Authors: Nidal F. Shilbayeh, Belal AbuHaija, Zainab N. Al-Qudsy

Abstract:

In this paper, we propose a new robust and secure system that is based on the combination between two different transforms Discrete wavelet Transform (DWT) and Contourlet Transform (CT). The combined transforms will compensate the drawback of using each transform separately. The proposed algorithm has been designed, implemented and tested successfully. The experimental results showed that selecting the best sub-band for embedding from both transforms will improve the imperceptibility and robustness of the new combined algorithm. The evaluated imperceptibility of the combined DWT-CT algorithm which gave a PSNR value 88.11 and the combination DWT-CT algorithm improves robustness since it produced better robust against Gaussian noise attack. In addition to that, the implemented system shored a successful extraction method to extract watermark efficiently.

Keywords: DWT, CT, Digital Image Watermarking, Copyright Protection.

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Authors: Shu-Xin Miao

Abstract:

In this note, we discuss the convergence behavior of a modified inexact Uzawa algorithm for solving generalized saddle point problems, which is an extension of the result obtained in a recent paper [Z.H. Cao, Fast Uzawa algorithm for generalized saddle point problems, Appl. Numer. Math., 46 (2003) 157-171].

Keywords: Saddle point problem, inexact Uzawa algorithm, convergence behavior.

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Authors: Jinghua Zhang, Charles B. Owen, Jinsheng Xu

Abstract:

A new hybrid coding method for compressing animated polygonal meshes is presented. This paper assumes the simplistic representation of the geometric data: a temporal sequence of polygonal meshes for each discrete frame of the animated sequence. The method utilizes a delta coding and an octree-based method. In this hybrid method, both the octree approach and the delta coding approach are applied to each single frame in the animation sequence in parallel. The approach that generates the smaller encoded file size is chosen to encode the current frame. Given the same quality requirement, the hybrid coding method can achieve much higher compression ratio than the octree-only method or the delta-only method. The hybrid approach can represent 3D animated sequences with higher compression factors while maintaining reasonable quality. It is easy to implement and have a low cost encoding process and a fast decoding process, which make it a better choice for real time application.

Keywords: animated polygonal meshes, compression, deltacoding, octree.

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Authors: Fawzi Irshaid, Fatiha Dilmi, Khaled Tarawneh, Raji Hadeth, Adnan Jaran, Ahad Al-Khatib

Abstract:

P16/INK4A is tumor suppressor protein that plays a critical role in cell cycle regulation. Loss of P16 protein expression has been implicated in pathogenesis of many cancers, including lymphoma. Therefore, we sought to investigate if loss of P16 protein expression is associated with lymphoma and/or any specific lymphoma subtypes (Hodgkin-s lymphoma (HL) and nonHodgkin-s lymphoma (NHL)). Fifty-five lymphoma cases consisted of 30 cases of HL and 25 cases of NHL, with an age range of 3 to 78 years, were examined for loss of P16 by immunohistochemical technique using a specific antibody reacting against P16. In total, P16 loss was seen in 33% of all lymphoma cases. P16 loss was identified in 47.7% of HL cases. In contrast, only 16% of NHL showed loss of P16. Loss of P16 was seen in 67% of HL patients with 50 years of age or older, whereas P16 loss was found in only 42% of HL patients with less than 50 years of age. P16 loss in HL is somewhat higher in male (55%) than in female (30%). In subtypes of HL, P16 loss was found exclusively in all cases of lymphocyte depletion, lymphocyte predominance and unclassified cases, whereas P16 loss was seen in 39% of mixed cellularity and 29% of nodular sclerosis cases. In low grade NHL patients, P16 loss was seen in approximately one-third of cases, whereas no or very rare of P16 loss was found in intermediate and high grade cases. P16 loss did not show any correlation with age or gender of NHL patients. In conclusion, the high rate of P16 loss seen in our study suggests that loss of P16 expression plays a critical role in the pathogenesis of lymphoma, particularly with HL.

Keywords: B-cells, immunostaining, P16 protein, Reed-Sternberg cells, tumors.

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Authors: Bhawna Tandon, Shiv Narayan, Jagdish Kumar

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This study proposes the transformation of nonlinear Magnetic Levitation System into linear one, via state and feedback transformations using explicit algorithm. This algorithm allows computing explicitly the linearizing state coordinates and feedback for any nonlinear control system, which is feedback linearizable, without solving the Partial Differential Equations. The algorithm is performed using a maximum of N-1 steps where N being the dimension of the system.

Keywords: Explicit Algorithm, Feedback Linearization, Nonlinear control, Magnetic Levitation System.

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Authors: Olufunke O. Ezekiel, Ogugua C. Aworh

Abstract:

Solid state fermentation of cassava peel with emphasis on protein enrichment using Trichoderma viride was evaluated. The effect of five variables: moisture content, pH, particle size (p), nitrogen source and incubation temperature; on the true protein and total sugars of cassava peel was investigated. The optimum fermentation period was established to be 8 days. Total sugars were 5-fold higher at pH 6 relative to pH 4 and 7-fold higher when cassava peels were fermented at 30oC relative to 25oC as well as using ammonium sulfate as the nitrogen source relative to urea or a combination of both. Total sugars ranged between 123.21mg/g at 50% initial moisture content to 374mg/g at 60% and from 190.59mg/g with particle size range of 2.00>p>1.41mm to 310.10mg/g with 4.00>p>3.35mm.True protein ranged from 229.70 mg/g at pH 4 to 284.05 mg/g at pH 6; from 200.87 mg/g with urea as nitrogen source and to 254.50mg/g with ammonium sulfate; from 213.82mg/g at 50% initial moisture content to 254.50mg/g at 60% moisture content, from 205.75mg/g in cassava peel with 5.6>p> 4.75mm to 268.30 in cassava peel with particle size 4.00>p>3.35mm, from 207.57mg/g at 25oC to 254.50mg/g at 30oC Cassava peel with particle size 4.00>p>3.35 mm and initial moisture content of 60% at pH 6.0, 30oC incubation temperature with ammonium sulfate (10g N / kg substrate) was most suitable for protein enrichment with Trichoderma viride. Crude protein increased from 4.21 % in unfermented cassava peel samples to 10.43 % in fermented samples.

Keywords: Cassava peel, Solid state fermentation, Trichoderma viride, Total sugars, True protein.

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Authors: Bainian Li, Kongsheng Zhang, Jian Xu

Abstract:

In this paper we study the fuzzy c-mean clustering algorithm combined with principal components method. Demonstratively analysis indicate that the new clustering method is well rather than some clustering algorithms. We also consider the validity of clustering method.

Keywords: FCM algorithm, Principal Components Analysis, Clustervalidity

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Authors: Doru Anastasiu Popescu, Dan Rădulescu

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In this paper, we determine the similarity of two HTML web applications. We are going to use a genetic algorithm in order to determine the most significant web pages of each application (we are not going to use every web page of a site). Using these significant web pages, we will find the similarity value between the two applications. The algorithm is going to be efficient because we are going to use a reduced number of web pages for comparisons but it will return an approximate value of the similarity. The binary trees are used to keep the tags from the significant pages. The algorithm was implemented in Java language.

Keywords: Tag, HTML, web page, genetic algorithm, similarity value, binary tree.

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Authors: Adnan Al-Smadi, Mahmoud Smadi

Abstract:

This paper presents an algorithm for reconstructing phase and magnitude responses of the impulse response when only the output data are available. The system is driven by a zero-mean independent identically distributed (i.i.d) non-Gaussian sequence that is not observed. The additive noise is assumed to be Gaussian. This is an important and essential problem in many practical applications of various science and engineering areas such as biomedical, seismic, and speech processing signals. The method is based on evaluating the bicepstrum of the third-order statistics of the observed output data. Simulations results are presented that demonstrate the performance of this method.

Keywords: Cepstrum, bicepstrum, third order statistics

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Authors: Tijani Delleji, Mourad Zribi, Ahmed Ben Hamida

Abstract:

This paper discusses EM algorithm and Bootstrap approach combination applied for the improvement of the satellite image fusion process. This novel satellite image fusion method based on estimation theory EM algorithm and reinforced by Bootstrap approach was successfully implemented and tested. The sensor images are firstly split by a Bayesian segmentation method to determine a joint region map for the fused image. Then, we use the EM algorithm in conjunction with the Bootstrap approach to develop the bootstrap EM fusion algorithm, hence producing the fused targeted image. We proposed in this research to estimate the statistical parameters from some iterative equations of the EM algorithm relying on a reference of representative Bootstrap samples of images. Sizes of those samples are determined from a new criterion called 'hybrid criterion'. Consequently, the obtained results of our work show that using the Bootstrap EM (BEM) in image fusion improve performances of estimated parameters which involve amelioration of the fused image quality; and reduce the computing time during the fusion process.

Keywords: Satellite image fusion, Bayesian segmentation, Bootstrap approach, EM algorithm.

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Authors: Sana Bouzaida, Anis Sakly, Faouzi M'Sahli

Abstract:

In this paper, a TSK-type Neuro-fuzzy Inference System that combines the features of fuzzy sets and neural networks has been applied for the identification of MIMO systems. The procedure of adapting parameters in TSK model employs a Shuffled Frog Leaping Algorithm (SFLA) which is inspired from the memetic evolution of a group of frogs when seeking for food. To demonstrate the accuracy and effectiveness of the proposed controller, two nonlinear systems have been considered as the MIMO plant, and results have been compared with other learning methods based on Particle Swarm Optimization algorithm (PSO) and Genetic Algorithm (GA).

Keywords: Identification, Shuffled frog Leaping Algorithm (SFLA), TSK-type neuro-fuzzy model.

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Authors: Shazia Javed, Noor Atinah Ahmad

Abstract:

In this paper an efficient incomplete factorization preconditioner is proposed for the Least Mean Squares (LMS) adaptive filter. The proposed preconditioner is approximated from a priori knowledge of the factors of input correlation matrix with an incomplete strategy, motivated by the sparsity patter of the upper triangular factor in the QRD-RLS algorithm. The convergence properties of IPLMS algorithm are comparable with those of transform domain LMS(TDLMS) algorithm. Simulation results show efficiency and robustness of the proposed algorithm with reduced computational complexity.

Keywords: Autocorrelation matrix, Cholesky's factor, eigenvalue spread, Markov input.

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Authors: Tomohiro Hachino, Kenji Shimoda, Hitoshi Takata

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This paper presents a method of model selection and identification of Hammerstein systems by hybridization of the genetic algorithm (GA) and particle swarm optimization (PSO). An unknown nonlinear static part to be estimated is approximately represented by an automatic choosing function (ACF) model. The weighting parameters of the ACF and the system parameters of the linear dynamic part are estimated by the linear least-squares method. On the other hand, the adjusting parameters of the ACF model structure are properly selected by the hybrid algorithm of the GA and PSO, where the Akaike information criterion is utilized as the evaluation value function. Simulation results are shown to demonstrate the effectiveness of the proposed hybrid algorithm.

Keywords: Hammerstein system, identification, automatic choosing function model, genetic algorithm, particle swarm optimization.

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Authors: S. K. Satpathy, S. Panda, K. K. Nagwanshi, S. K. Nayak, C. Ardil

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Removing noise from the any processed images is very important. Noise should be removed in such a way that important information of image should be preserved. A decisionbased nonlinear algorithm for elimination of band lines, drop lines, mark, band lost and impulses in images is presented in this paper. The algorithm performs two simultaneous operations, namely, detection of corrupted pixels and evaluation of new pixels for replacing the corrupted pixels. Removal of these artifacts is achieved without damaging edges and details. However, the restricted window size renders median operation less effective whenever noise is excessive in that case the proposed algorithm automatically switches to mean filtering. The performance of the algorithm is analyzed in terms of Mean Square Error [MSE], Peak-Signal-to-Noise Ratio [PSNR], Signal-to-Noise Ratio Improved [SNRI], Percentage Of Noise Attenuated [PONA], and Percentage Of Spoiled Pixels [POSP]. This is compared with standard algorithms already in use and improved performance of the proposed algorithm is presented. The advantage of the proposed algorithm is that a single algorithm can replace several independent algorithms which are required for removal of different artifacts.

Keywords: Filtering, Decision Based Algorithm, noise, imagerestoration.

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Authors: Manuel Ceballos, Juan Nunez, Angel F. Tenorio

Abstract:

The set of all abelian subalgebras is computationally obtained for any given finite-dimensional Lie algebra, starting from the nonzero brackets in its law. More concretely, an algorithm is described and implemented to compute a basis for each nontrivial abelian subalgebra with the help of the symbolic computation package MAPLE. Finally, it is also shown a brief computational study for this implementation, considering both the computing time and the used memory.

Keywords: Solvable Lie algebra, maximal abelian dimension, algorithm.

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