Search results for: martingale difference sequence
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1686

Search results for: martingale difference sequence

1656 A Green Design for Assembly Model for Integrated Design Evaluation and Assembly and Disassembly Sequence Planning

Authors: Yuan-Jye Tseng, Fang-Yu Yu, Feng-Yi Huang

Abstract:

A green design for assembly model is presented to integrate design evaluation and assembly and disassembly sequence planning by evaluating the three activities in one integrated model. For an assembled product, an assembly sequence planning model is required for assembling the product at the start of the product life cycle. A disassembly sequence planning model is needed for disassembling the product at the end. In a green product life cycle, it is important to plan how a product can be disassembled, reused, or recycled, before the product is actually assembled and produced. Given a product requirement, there may be several design alternative cases to design the same product. In the different design cases, the assembly and disassembly sequences for producing the product can be different. In this research, a new model is presented to concurrently evaluate the design and plan the assembly and disassembly sequences. First, the components are represented by using graph based models. Next, a particle swarm optimization (PSO) method with a new encoding scheme is developed. In the new PSO encoding scheme, a particle is represented by a position matrix defining an assembly sequence and a disassembly sequence. The assembly and disassembly sequences can be simultaneously planned with an objective of minimizing the total of assembly costs and disassembly costs. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly and disassembly sequence planning problem. An example product is implemented and illustrated in this paper.

Keywords: green design, assembly and disassembly sequence planning, green design for assembly, particle swarm optimization.

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1655 A PN Sequence Generator based on Residue Arithmetic for Multi-User DS-CDMA Applications

Authors: Chithra R, Pallab Maji, Sarat Kumar Patra, Girija Sankar Rath

Abstract:

The successful use of CDMA technology is based on the construction of large families of encoding sequences with good correlation properties. This paper discusses PN sequence generation based on Residue Arithmetic with an effort to improve the performance of existing interference-limited CDMA technology for mobile cellular systems. All spreading codes with residual number system proposed earlier did not consider external interferences, multipath propagation, Doppler effect etc. In literature the use of residual arithmetic in DS-CDMA was restricted to encoding of already spread sequence; where spreading of sequence is done by some existing techniques. The novelty of this paper is the use of residual number system in generation of the PN sequences which is used to spread the message signal. The significance of cross-correlation factor in alleviating multi-access interference is also discussed. The RNS based PN sequence has superior performance than most of the existing codes that are widely used in DS-CDMA applications. Simulation results suggest that the performance of the proposed system is superior to many existing systems.

Keywords: Direct-Sequence Code Division Multiple Access (DSCDMA), Multiple-Access Interference (MAI), PN Sequence, Residue Number System (RNS).

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1654 Enhanced Imperialist Competitive Algorithm for the Cell Formation Problem Using Sequence Data

Authors: S. H. Borghei, E. Teymourian, M. Mobin, G. M. Komaki, S. Sheikh

Abstract:

Imperialist Competitive Algorithm (ICA) is a recent meta-heuristic method that is inspired by the social evolutions for solving NP-Hard problems. The ICA is a population-based algorithm which has achieved a great performance in comparison to other metaheuristics. This study is about developing enhanced ICA approach to solve the Cell Formation Problem (CFP) using sequence data. In addition to the conventional ICA, an enhanced version of ICA, namely EICA, applies local search techniques to add more intensification aptitude and embed the features of exploration and intensification more successfully. Suitable performance measures are used to compare the proposed algorithms with some other powerful solution approaches in the literature. In the same way, for checking the proficiency of algorithms, forty test problems are presented. Five benchmark problems have sequence data, and other ones are based on 0-1 matrices modified to sequence based problems. Computational results elucidate the efficiency of the EICA in solving CFP problems.

Keywords: Cell formation problem, Group technology, Imperialist competitive algorithm, Sequence data.

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1653 Application and Limitation of Parallel Modelingin Multidimensional Sequential Pattern

Authors: Mahdi Esmaeili, Mansour Tarafdar

Abstract:

The goal of data mining algorithms is to discover useful information embedded in large databases. One of the most important data mining problems is discovery of frequently occurring patterns in sequential data. In a multidimensional sequence each event depends on more than one dimension. The search space is quite large and the serial algorithms are not scalable for very large datasets. To address this, it is necessary to study scalable parallel implementations of sequence mining algorithms. In this paper, we present a model for multidimensional sequence and describe a parallel algorithm based on data parallelism. Simulation experiments show good load balancing and scalable and acceptable speedup over different processors and problem sizes and demonstrate that our approach can works efficiently in a real parallel computing environment.

Keywords: Sequential Patterns, Data Mining, ParallelAlgorithm, Multidimensional Sequence Data

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1652 Computational Analysis of the MembraneTargeting Domains of Plant-specific PRAF Proteins

Authors: Ewa Wywial, Shaneen M. Singh

Abstract:

The PRAF family of proteins is a plant specific family of proteins with distinct domain architecture and various unique sequence/structure traits. We have carried out an extensive search of the Arabidopsis genome using an automated pipeline and manual methods to verify previously known and identify unknown instances of PRAF proteins, characterize their sequence and build 3D structures of their individual domains. Integrating the sequence, structure and whatever little known experimental details for each of these proteins and their domains, we present a comprehensive characterization of the different domains in these proteins and their variant properties.

Keywords: PRAF proteins, homology modeling, Arabidopsisthaliana

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1651 Direct Sequence Spread Spectrum Technique with Residue Number System

Authors: M. I. Youssef, A. E. Emam, M. Abd Elghany

Abstract:

In this paper, a residue number arithmetic is used in direct sequence spread spectrum system, this system is evaluated and the bit error probability of this system is compared to that of non residue number system. The effect of channel bandwidth, PN sequences, multipath effect and modulation scheme are studied. A Matlab program is developed to measure the signal-to-noise ratio (SNR), and the bit error probability for the various schemes.

Keywords: Spread Spectrum, Direct sequence, Bit errorprobability and Residue number system.

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1650 Identification of Disease Causing DNA Motifs in Human DNA Using Clustering Approach

Authors: G. Tamilpavai, C. Vishnuppriya

Abstract:

Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: Bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM.

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1649 Optimization of Flexible Job Shop Scheduling Problem with Sequence Dependent Setup Times Using Genetic Algorithm Approach

Authors: Sanjay Kumar Parjapati, Ajai Jain

Abstract:

This paper presents optimization of makespan for ‘n’ jobs and ‘m’ machines flexible job shop scheduling problem with sequence dependent setup time using genetic algorithm (GA) approach. A restart scheme has also been applied to prevent the premature convergence. Two case studies are taken into consideration. Results are obtained by considering crossover probability (pc = 0.85) and mutation probability (pm = 0.15). Five simulation runs for each case study are taken and minimum value among them is taken as optimal makespan. Results indicate that optimal makespan can be achieved with more than one sequence of jobs in a production order.

Keywords: Flexible Job Shop, Genetic Algorithm, Makespan, Sequence Dependent Setup Times.

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1648 Dynamic Models versus Frailty Models for Recurrent Event Data

Authors: Entisar A. Elgmati

Abstract:

Recurrent event data is a special type of multivariate survival data. Dynamic and frailty models are one of the approaches that dealt with this kind of data. A comparison between these two models is studied using the empirical standard deviation of the standardized martingale residual processes as a way of assessing the fit of the two models based on the Aalen additive regression model. Here we found both approaches took heterogeneity into account and produce residual standard deviations close to each other both in the simulation study and in the real data set.

Keywords: Dynamic, frailty, misspecification, recurrent events.

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1647 Influence of Stacking Sequence and Temperature on Buckling Resistance of GFRP Infill Panel

Authors: Viriyavudh Sim, SeungHyun Kim, JungKyu Choi, WooYoung Jung

Abstract:

Glass Fiber Reinforced Polymer (GFRP) is a major evolution for energy dissipation when used as infill material for seismic retrofitting of steel frame, a basic PMC infill wall system consists of two GFRP laminates surrounding an infill of foam core. This paper presents numerical analysis in terms of buckling resistance of GFRP sandwich infill panels system under the influence of environment temperature and stacking sequence of laminate skin. Mode of failure under in-plane compression is studied by means of numerical analysis with ABAQUS platform. Parameters considered in this study are contact length between infill and frame, laminate stacking sequence of GFRP skin and variation of mechanical properties due to increment of temperature. The analysis is done with four cases of simple stacking sequence over a range of temperature. The result showed that both the effect of temperature and stacking sequence alter the performance of entire panel system. The rises of temperature resulted in the decrements of the panel’s strength. This is due to the polymeric nature of this material. Additionally, the contact length also displays the effect on the performance of infill panel. Furthermore, the laminate stiffness can be modified by orientation of laminate, which can increase the infill panel strength. Hence, optimal performance of the entire panel system can be obtained by comparing different cases of stacking sequence.

Keywords: Buckling resistance, GFRP infill panel, stacking sequence, temperature dependent.

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1646 Linking Business Process Models and System Models Based on Business Process Modelling

Authors: Faisal A. Aburub

Abstract:

Organizations today need to invest in software in order to run their businesses, and to the organizations’ objectives, the software should be in line with the business process. This research presents an approach for linking process models and system models. Particularly, the new approach aims to synthesize sequence diagram based on role activity diagram (RAD) model. The approach includes four steps namely: Create business process model using RAD, identify computerized activities, identify entities in sequence diagram and identify messages in sequence diagram. The new approach has been validated using the process of student registration in University of Petra as a case study. Further research is required to validate the new approach using different domains.

Keywords: Business process modelling, system models, role activity diagrams, sequence diagrams.

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1645 Fast Dummy Sequence Insertion Method for PAPR Reduction in WiMAX Systems

Authors: Peerapong Uthansakul, Sakkarin Chaokuntod, Monthippa Uthansakul

Abstract:

In literatures, many researches proposed various methods to reduce PAPR (Peak to Average Power Ratio). Among those, DSI (Dummy Sequence Insertion) is one of the most attractive methods for WiMAX systems because it does not require side information transmitted along with user data. However, the conventional DSI methods find dummy sequence by performing an iterative procedure until achieving PAPR under a desired threshold. This causes a significant delay on finding dummy sequence and also effects to the overall performances in WiMAX systems. In this paper, the new method based on DSI is proposed by finding dummy sequence without the need of iterative procedure. The fast DSI method can reduce PAPR without either delays or required side information. The simulation results confirm that the proposed method is able to carry out PAPR performances as similar to the other methods without any delays. In addition, the simulations of WiMAX system with adaptive modulations are also investigated to realize the use of proposed methods on various fading schemes. The results suggest the WiMAX designers to modify a new Signal to Noise Ratio (SNR) criteria for adaptation.

Keywords: WiMAX, OFDM, PAPR, Dummy SequenceInsertion method.

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1644 Optimization of Energy Consumption in Sequential Distillation Column

Authors: M.E. Masoumi, S. Kadkhodaie

Abstract:

Distillation column is one of the most common operations in process industries and is while the most expensive unit of the amount of energy consumption. Many ideas have been presented in the related literature for optimizing energy consumption in distillation columns. This paper studies the different heat integration methods in a distillation column which separate Benzene, Toluene, Xylene, and C9+. Three schemes of heat integration including, indirect sequence (IQ), indirect sequence with forward energy integration (IQF), and indirect sequence with backward energy integration (IQB) has been studied in this paper. Using shortcut method these heat integration schemes were simulated with Aspen HYSYS software and compared with each other with regarding economic considerations. The result shows that the energy consumption has been reduced 33% in IQF and 28% in IQB in comparison with IQ scheme. Also the economic result shows that the total annual cost has been reduced 12% in IQF and 8% in IQB regarding with IQ scheme. Therefore, the IQF scheme is most economic than IQB and IQ scheme.

Keywords: Optimization, Distillation Column Sequence, Energy Savings

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1643 Influence of the Line Parameters in Transmission Line Fault Location

Authors: Marian Dragomir, Alin Dragomir

Abstract:

In the paper, two fault location algorithms are presented for transmission lines which use the line parameters to estimate the distance to the fault. The first algorithm uses only the measurements from one end of the line and the positive and zero sequence parameters of the line, while the second one uses the measurements from both ends of the line and only the positive sequence parameters of the line. The algorithms were tested using a transmission grid transposed in MATLAB. In a first stage it was established a fault location base line, where the algorithms mentioned above estimate the fault locations using the exact line parameters. After that, the positive and zero sequence resistance and reactance of the line were calculated again for different ground resistivity values and then the fault locations were estimated again in order to compare the results with the base line results. The results show that the algorithm which uses the zero sequence impedance of the line is the most sensitive to the line parameters modifications. The other algorithm is less sensitive to the line parameters modification.

Keywords: Estimation algorithms, fault location, line parameters, simulation tool.

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1642 Sub-Impact Phenomenon of Elasto-Plastic Free-Free Beam during a Strike

Authors: H. Rong, X. C. Yin, J. Yang, Y. N. Shen

Abstract:

Based on Rayleigh beam theory, the sub-impacts of a free-free beam struck horizontally by a round-nosed rigid mass is simulated by the finite difference method and the impact-separation conditions. In order to obtain the sub-impact force, a uniaxial compression elastic-plastic contact model is employed to analyze the local deformation field on contact zone. It is found that the horizontal impact is a complicated process including the elastic plastic sub-impacts in sequence. There are two sub-zones of sub-impact. In addition, it found that the elastic energy of the free-free beam is more suitable for the Poisson collision hypothesis to explain compression and recovery processes.

Keywords: beam, sub-impact, elastic-plastic deformation, finite difference method.

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1641 Codes beyond Bits and Bytes: A Blueprint for Artificial Life

Authors: Rishabh Garg, Anuja Vyas, Aamna Khan, Muhammad Azwan Tariq

Abstract:

The present study focuses on integrating Machine Learning and Genomics, hereafter termed ‘GenoLearning’, to develop Artificial Life (AL). This is achieved by leveraging gene editing to imbue genes with sequences capable of performing desired functions. To accomplish this, a specialized sub-network of Siamese Neural Network (SNN), named Transformer Architecture specialized in Sequence Analysis of Genes (TASAG), compares two sequences: the desired and target sequences. Differences between these sequences are analyzed, and necessary edits are made on-screen to incorporate the desired sequence into the target sequence. The edited sequence can then be synthesized chemically using a Computerized DNA Synthesizer (CDS). The CDS fabricates DNA strands according to the sequence displayed on a computer screen, aided by microprocessors. These synthesized DNA strands can be inserted into an ovum to initiate further development, eventually leading to the creation of an Embot, and ultimately, an H-Bot. While this study aims to explore the potential benefits of Artificial Intelligence (AI) technology, it also acknowledges and addresses the ethical considerations associated with its implementation.

Keywords: Machine Learning, Genomics, Genetronics, DNA, Transformer, Siamese Neural Network, Gene Editing, Artificial Life, H-Bot, Zoobot.

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1640 Analysis of Sequence Moves in Successful Chess Openings Using Data Mining with Association Rules

Authors: R.M.Rani

Abstract:

Chess is one of the indoor games, which improves the level of human confidence, concentration, planning skills and knowledge. The main objective of this paper is to help the chess players to improve their chess openings using data mining techniques. Budding Chess Players usually do practices by analyzing various existing openings. When they analyze and correlate thousands of openings it becomes tedious and complex for them. The work done in this paper is to analyze the best lines of Blackmar- Diemer Gambit(BDG) which opens with White D4... using data mining analysis. It is carried out on the collection of winning games by applying association rules. The first step of this analysis is assigning variables to each different sequence moves. In the second step, the sequence association rules were generated to calculate support and confidence factor which help us to find the best subsequence chess moves that may lead to winning position.

Keywords: Blackmar-Diemer Gambit(BDG), Confidence, sequence Association Rules, Support.

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1639 A Study of Environmental Test Sequences for Electrical Units

Authors: Jung Ho Yang, Yong Soo Kim

Abstract:

Electrical units are operated by electrical and electronic components. An environmental test sequence is useful for testing electrical units to reduce reliability issues. This study introduces test sequence guidelines based on relevant principles and considerations for electronic testing according to International Standard IEC-60068-1 and the United States Military Standard MIL-STD-810G. Test sequences were then proposed based on the descriptions for each test. Finally, General Motors (GM) specification GMW3172 was interpreted and compared to IEC-60068-1 and MIL-STD-810G.

Keywords: Reliability, Environmental test sequence, Electrical units, IEC 60068-1, MIL-STD-810G.

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1638 Radio Frequency Identification Encryption via Modified Two Dimensional Logistic Map

Authors: Hongmin Deng, Qionghua Wang

Abstract:

A modified two dimensional (2D) logistic map based on cross feedback control is proposed. This 2D map exhibits more random chaotic dynamical properties than the classic one dimensional (1D) logistic map in the statistical characteristics analysis. So it is utilized as the pseudo-random (PN) sequence generator, where the obtained real-valued PN sequence is quantized at first, then applied to radio frequency identification (RFID) communication system in this paper. This system is experimentally validated on a cortex-M0 development board, which shows the effectiveness in key generation, the size of key space and security. At last, further cryptanalysis is studied through the test suite in the National Institute of Standards and Technology (NIST).

Keywords: Chaos encryption, logistic map, pseudo-random sequence, RFID.

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1637 Molecular Dynamics and Circular Dichroism Studies on Aurein 1.2 and Retro Analog

Authors: Safyeh Soufian, Hoosein Naderi-Manesh, Abdoali Alizadeh, Mohammad Nabi Sarbolouki

Abstract:

Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.

Keywords: Antimicrobial peptides, retro, molecular dynamic, circular dichroism.

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1636 Detecting Remote Protein Evolutionary Relationships via String Scoring Method

Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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1635 On λ− Summable of Orlicz Space of Gai Sequences of Fuzzy Numbers

Authors: N.Subramanian, S.Krishnamoorthy, S. Balasubramanian

Abstract:

In this paper the concept of strongly (λM)p - Ces'aro summability of a sequence of fuzzy numbers and strongly λM- statistically convergent sequences of fuzzy numbers is introduced.

Keywords: Fuzzy numbers, statistical convergence, Orlicz space, gai sequence.

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1634 End-to-End Spanish-English Sequence Learning Translation Model

Authors: Vidhu Mitha Goutham, Ruma Mukherjee

Abstract:

The low availability of well-trained, unlimited, dynamic-access models for specific languages makes it hard for corporate users to adopt quick translation techniques and incorporate them into product solutions. As translation tasks increasingly require a dynamic sequence learning curve; stable, cost-free opensource models are scarce. We survey and compare current translation techniques and propose a modified sequence to sequence model repurposed with attention techniques. Sequence learning using an encoder-decoder model is now paving the path for higher precision levels in translation. Using a Convolutional Neural Network (CNN) encoder and a Recurrent Neural Network (RNN) decoder background, we use Fairseq tools to produce an end-to-end bilingually trained Spanish-English machine translation model including source language detection. We acquire competitive results using a duo-lingo-corpus trained model to provide for prospective, ready-made plug-in use for compound sentences and document translations. Our model serves a decent system for large, organizational data translation needs. While acknowledging its shortcomings and future scope, it also identifies itself as a well-optimized deep neural network model and solution.

Keywords: Attention, encoder-decoder, Fairseq, Seq2Seq, Spanish, translation.

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1633 An Integrated Design Evaluation and Assembly Sequence Planning Model using a Particle Swarm Optimization Approach

Authors: Feng-Yi Huang, Yuan-Jye Tseng

Abstract:

In the traditional concept of product life cycle management, the activities of design, manufacturing, and assembly are performed in a sequential way. The drawback is that the considerations in design may contradict the considerations in manufacturing and assembly. The different designs of components can lead to different assembly sequences. Therefore, in some cases, a good design may result in a high cost in the downstream assembly activities. In this research, an integrated design evaluation and assembly sequence planning model is presented. Given a product requirement, there may be several design alternative cases to design the components for the same product. If a different design case is selected, the assembly sequence for constructing the product can be different. In this paper, first, the designed components are represented by using graph based models. The graph based models are transformed to assembly precedence constraints and assembly costs. A particle swarm optimization (PSO) approach is presented by encoding a particle using a position matrix defined by the design cases and the assembly sequences. The PSO algorithm simultaneously performs design evaluation and assembly sequence planning with an objective of minimizing the total assembly costs. As a result, the design cases and the assembly sequences can both be optimized. The main contribution lies in the new concept of integrated design evaluation and assembly sequence planning model and the new PSO solution method. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly planning problem. In this paper, an example product is tested and illustrated.

Keywords: assembly sequence planning, design evaluation, design for assembly, particle swarm optimization

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1632 Multiple Sequence Alignment Using Three- Dimensional Fragments

Authors: Layal Al Ait, Eduardo Corel, Kifah Tout, Burkhard Morgenstern

Abstract:

Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of using three-dimensional fragments – i.e. local threeway alignments -- in the alignment process instead of twodimensional ones. These three-dimensional fragments are gap-free alignments constituting of equal-length segments belonging to three distinct sequences. RESULTS: The obtained results showed good improvments over the performance of DIALIGN.

Keywords: DIALIGN, Multiple sequence alignment, Threedimensional fragments.

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1631 A System to Integrate and Manipulate Protein Database Using BioPerl and XML

Authors: Zurinahni Zainol, Rosalina Abdul Salam, Rosni Abdullah, Nur'Aini, Wahidah Husain

Abstract:

The size, complexity and number of databases used for protein information have caused bioinformatics to lag behind in adapting to the need to handle this distributed information. Integrating all the information from different databases into one database is a challenging problem. Our main research is to develop a tool which can be used to access and manipulate protein information from difference databases. In our approach, we have integrated difference databases such as Swiss-prot, PDB, Interpro, and EMBL and transformed these databases in flat file format into relational form using XML and Bioperl. As a result, we showed this tool can search different sizes of protein information stored in relational database and the result can be retrieved faster compared to flat file database. A web based user interface is provided to allow user to access or search for protein information in the local database.

Keywords: Protein sequence database, relational database, integrated database.

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1630 Comparison of Phylogenetic Trees of Multiple Protein Sequence Alignment Methods

Authors: Khaddouja Boujenfa, Nadia Essoussi, Mohamed Limam

Abstract:

Multiple sequence alignment is a fundamental part in many bioinformatics applications such as phylogenetic analysis. Many alignment methods have been proposed. Each method gives a different result for the same data set, and consequently generates a different phylogenetic tree. Hence, the chosen alignment method affects the resulting tree. However in the literature, there is no evaluation of multiple alignment methods based on the comparison of their phylogenetic trees. This work evaluates the following eight aligners: ClustalX, T-Coffee, SAGA, MUSCLE, MAFFT, DIALIGN, ProbCons and Align-m, based on their phylogenetic trees (test trees) produced on a given data set. The Neighbor-Joining method is used to estimate trees. Three criteria, namely, the dNNI, the dRF and the Id_Tree are established to test the ability of different alignment methods to produce closer test tree compared to the reference one (true tree). Results show that the method which produces the most accurate alignment gives the nearest test tree to the reference tree. MUSCLE outperforms all aligners with respect to the three criteria and for all datasets, performing particularly better when sequence identities are within 10-20%. It is followed by T-Coffee at lower sequence identity (<10%), Align-m at 20-30% identity, and ClustalX and ProbCons at 30-50% identity. Also, it is noticed that when sequence identities are higher (>30%), trees scores of all methods become similar.

Keywords: Multiple alignment methods, phylogenetic trees, Neighbor-Joining method, Robinson-Foulds distance.

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1629 Performance Analysis of a Free-Space Optical Code Division Multiple Access through Atmospheric Turbulence Channel

Authors: Tanveer Ahmed Bhuiyan, Samiul Hayder Choudhury, Asif Al - Rasheed, S.P. Majumder

Abstract:

In this paper, the effect of atmospheric turbulence on bit error probability in free-space optical CDMA scheme with Sequence Inverse Keyed (SIK) optical correlator receiver is analyzed. Here Intensity Modulation scheme is considered for transmission. The turbulence induced fading is described by the newly introduced gamma-gamma pdf[1] as a tractable mathematical model for atmospheric turbulence. Results are evaluated with Gold and Kasami code & it is shown that Gold sequence can be used for more efficient transmission than Kasami sequence in an atmospheric turbulence channel.

Keywords: CDMA, gamma-gamma pdf, atmospheric turbulence, Kasami, Gold, SIK, BER, Power Penalty, FSO.

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1628 Preserved Relative Differences between Regions of Different Thermal Scans

Authors: Tahir Majeed, Michael Handschuh, René Meier

Abstract:

Rheumatoid Arthritis patients have swelling and pain in joints of the hand. The regions where the patient feels pain also show increased body temperature. Thermal cameras can be used to detect the rise in temperature of the affected regions. To monitor the progression of Rheumatoid Arthritis, patients must visit the clinic regularly for scanning and examination. After scanning and evaluation, the dosage of the medicine is regulated accordingly. To monitor the disease progression over time, the correlation of the images between different visits must be established. It has been observed that the thermal measurements do not remain the same over time, even within a single scanning, when low-cost thermal cameras are used. In some situations, temperatures can vary as much as 2◦C within the same scanning sequence. In this paper, it has been shown that although the absolute temperature varies over time, the relative difference between different regions remains similar. Results have been computed over four scanning sequences and are presented.

Keywords: Relative thermal difference, rheumatoid arthritis, thermal imaging, thermal sensors.

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1627 FSM-based Recognition of Dynamic Hand Gestures via Gesture Summarization Using Key Video Object Planes

Authors: M. K. Bhuyan

Abstract:

The use of human hand as a natural interface for humancomputer interaction (HCI) serves as the motivation for research in hand gesture recognition. Vision-based hand gesture recognition involves visual analysis of hand shape, position and/or movement. In this paper, we use the concept of object-based video abstraction for segmenting the frames into video object planes (VOPs), as used in MPEG-4, with each VOP corresponding to one semantically meaningful hand position. Next, the key VOPs are selected on the basis of the amount of change in hand shape – for a given key frame in the sequence the next key frame is the one in which the hand changes its shape significantly. Thus, an entire video clip is transformed into a small number of representative frames that are sufficient to represent a gesture sequence. Subsequently, we model a particular gesture as a sequence of key frames each bearing information about its duration. These constitute a finite state machine. For recognition, the states of the incoming gesture sequence are matched with the states of all different FSMs contained in the database of gesture vocabulary. The core idea of our proposed representation is that redundant frames of the gesture video sequence bear only the temporal information of a gesture and hence discarded for computational efficiency. Experimental results obtained demonstrate the effectiveness of our proposed scheme for key frame extraction, subsequent gesture summarization and finally gesture recognition.

Keywords: Hand gesture, MPEG-4, Hausdorff distance, finite state machine.

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