Search results for: Clustering algorithm

Authors: Qing Lyu, Hang Zhu

Abstract:

Various flows in the network require to go through different types of middlebox. The improper placement of network middlebox and path assignment for flows could greatly increase the network latency and also decrease the performance of network. Minimizing the total end to end latency of all the ows requires to assign path for the incoming flows. In this paper, the flow path assignment problem in regard to the placement of various kinds of middlebox is studied. The flow path assignment problem is formulated to a linear programming problem, which is very time consuming. On the other hand, a naive greedy algorithm is studied. Which is very fast but causes much more latency than the linear programming algorithm. At last, the paper presents a heuristic algorithm named FPA, which takes bottleneck link information and estimated bandwidth occupancy into consideration, and achieves near optimal latency in much less time. Evaluation results validate the effectiveness of the proposed algorithm.

Keywords: Latency, Fast path assignment, Bottleneck link.

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Authors: A. A. Hossam-Eldin, E. N. Abdallah, M. S. El-Nozahy

Abstract:

The identification and elimination of bad measurements is one of the basic functions of a robust state estimator as bad data have the effect of corrupting the results of state estimation according to the popular weighted least squares method. However this is a difficult problem to handle especially when dealing with multiple errors from the interactive conforming type. In this paper, a self adaptive genetic based algorithm is proposed. The algorithm utilizes the results of the classical linearized normal residuals approach to tune the genetic operators thus instead of making a randomized search throughout the whole search space it is more likely to be a directed search thus the optimum solution is obtained at very early stages(maximum of 5 generations). The algorithm utilizes the accumulating databases of already computed cases to reduce the computational burden to minimum. Tests are conducted with reference to the standard IEEE test systems. Test results are very promising.

Keywords: Bad Data, Genetic Algorithms, Linearized Normal residuals, Observability, Power System State Estimation.

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Authors: Zong Chen

Abstract:

Motion estimation is a key problem in video processing and computer vision. Optical flow motion estimation can achieve high estimation accuracy when motion vector is small. Three-step search algorithm can handle large motion vector but not very accurate. A joint algorithm was proposed in this paper to achieve high estimation accuracy disregarding whether the motion vector is small or large, and keep the computation cost much lower than full search.

Keywords: Motion estimation, Block Matching, Optical flow, Three step search.

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Authors: J. Liu, Z. P. Yu, L. Xiong, Y. Feng, J. He

Abstract:

According to the independence, accuracy and controllability of the driving/braking torque of the distributed drive electric vehicle, a control strategy of differential drive assisted steering was designed. Firstly, the assisted curve under different speed and steering wheel torque was developed and the differential torques were distributed to the right and left front wheels. Then the steering return ability assisted control algorithm was designed. At last, the joint simulation was conducted by CarSim/Simulink. The result indicated: the differential drive assisted steering algorithm could provide enough steering drive-assisted under low speed and improve the steering portability. Along with the increase of the speed, the provided steering drive-assisted decreased. With the control algorithm, the steering stiffness of the steering system increased along with the increase of the speed, which ensures the driver’s road feeling. The control algorithm of differential drive assisted steering could avoid the understeer under low speed effectively.

Keywords: Differential assisted steering, control strategy, distributed drive electric vehicle.

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Authors: N. Arulanand, P. Dhara

Abstract:

Optimizing the parameters in the controller plays a vital role in the control theory and its applications. Optimizing the PID parameters is finding out the best value from the feasible solutions. Finding the optimal value is an optimization problem. Inverted Pendulum is a very good platform for control engineers to verify and apply different logics in the field of control theory. It is necessary to find an optimization technique for the controller to tune the values automatically in order to minimize the error within the given bounds. In this paper, the algorithmic concepts of Harmony search (HS) and Genetic Algorithm (GA) have been analyzed for the given range of values. The experimental results show that HS performs well than GA.

Keywords: Genetic Algorithm, Harmony Search Algorithm, Inverted Pendulum, PID Controller.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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Authors: Zohreh Sheikh Khozani, Wan Hanna Melini Wan Mohtar, Mojtaba Porhemmat

Abstract:

Prediction of wall shear stress in a rectangular channel, with non-homogeneous roughness distribution, was studied. Estimation of shear stress is an important subject in hydraulic engineering, since it affects the flow structure directly. In this study, the Genetic Algorithm Artificial (GAA) neural network is introduced as a hybrid methodology of the Artificial Neural Network (ANN) and modified Genetic Algorithm (GA) combination. This GAA method was employed to predict the wall shear stress. Various input combinations and transfer functions were considered to find the most appropriate GAA model. The results show that the proposed GAA method could predict the wall shear stress of open channels with high accuracy, by Root Mean Square Error (RMSE) of 0.064 in the test dataset. Thus, using GAA provides an accurate and practical simple-to-use equation.

Keywords: Artificial neural network, genetic algorithm, genetic programming, rectangular channel, shear stress.

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Authors: M.H. Ahmad Fadzil, Hurriyatul Fitriyah, Esa Prakasa, Hermawan Nugroho, S.H. Hussein, Azura Mohd. Affandi

Abstract:

Psoriasis is a chronic inflammatory skin condition which affects 2-3% of population around the world. Psoriasis Area and Severity Index (PASI) is a gold standard to assess psoriasis severity as well as the treatment efficacy. Although a gold standard, PASI is rarely used because it is tedious and complex. In practice, PASI score is determined subjectively by dermatologists, therefore inter and intra variations of assessment are possible to happen even among expert dermatologists. This research develops an algorithm to assess psoriasis lesion for PASI scoring objectively. Focus of this research is thickness assessment as one of PASI four parameters beside area, erythema and scaliness. Psoriasis lesion thickness is measured by averaging the total elevation from lesion base to lesion surface. Thickness values of 122 3D images taken from 39 patients are grouped into 4 PASI thickness score using K-means clustering. Validation on lesion base construction is performed using twelve body curvature models and show good result with coefficient of determinant (R2) is equal to 1.

Keywords: 3D digital imaging, base construction, PASI, psoriasis lesion thickness.

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Authors: J.R. Quevedo, E. Montañés, J. Ranilla, A. Bahamonde

Abstract:

The new framework the Higher Education is immersed in involves a complete change in the way lecturers must teach and students must learn. Whereas the lecturer was the main character in traditional education, the essential goal now is to increase the students' participation in the process. Thus, one of the main tasks of lecturers in this new context is to design activities of different nature in order to encourage such participation. Seminars are one of the activities included in this environment. They are active sessions that enable going in depth into specific topics as support of other activities. They are characterized by some features such as favoring interaction between students and lecturers or improving their communication skills. Hence, planning and organizing strategic seminars is indeed a great challenge for lecturers with the aim of acquiring knowledge and abilities. This paper proposes a method using Artificial Intelligence techniques to obtain student profiles from their marks and preferences. The goal of building such profiles is twofold. First, it facilitates the task of splitting the students into different groups, each group with similar preferences and learning difficulties. Second, it makes it easy to select adequate topics to be a candidate for the seminars. The results obtained can be either a guarantee of what the lecturers could observe during the development of the course or a clue to reconsider new methodological strategies in certain topics.

Keywords: artificial intelligence, clustering, organizingseminars, student profile

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Authors: Bogdan Walek, Cyril Klimes

Abstract:

This paper focuses on testing database of existing information system. At the beginning we describe the basic problems of implemented databases, such as data redundancy, poor design of database logical structure or inappropriate data types in columns of database tables. These problems are often the result of incorrect understanding of the primary requirements for a database of an information system. Then we propose an algorithm to compare the conceptual model created from vague requirements for a database with a conceptual model reconstructed from implemented database. An algorithm also suggests steps leading to optimization of implemented database. The proposed algorithm is verified by an implemented prototype. The paper also describes a fuzzy system which works with the vague requirements for a database of an information system, procedure for creating conceptual from vague requirements and an algorithm for reconstructing a conceptual model from implemented database.

Keywords: testing, database, relational database, information system, conceptual model, fuzzy, uncertain information, database testing, reconstruction, requirements, optimization

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Authors: Alawode Kehinde O., Jubril Abimbola M. Komolafe Olusola A.

Abstract:

This paper solves the environmental/ economic dispatch power system problem using the Non-dominated Sorting Genetic Algorithm-II (NSGA-II) and its hybrid with a Convergence Accelerator Operator (CAO), called the NSGA-II/CAO. These multiobjective evolutionary algorithms were applied to the standard IEEE 30-bus six-generator test system. Several optimization runs were carried out on different cases of problem complexity. Different quality measure which compare the performance of the two solution techniques were considered. The results demonstrated that the inclusion of the CAO in the original NSGA-II improves its convergence while preserving the diversity properties of the solution set.

Keywords: optimal power flow, multiobjective power dispatch, evolutionary algorithm

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Authors: Muhammad Haroon Siddiqui, Muhammad Rehan Khalid

Abstract:

This paper evaluates the performance of a novel algorithm for tracking of a mobile node, interms of execution time and root mean square error (RMSE). Particle Filter algorithm is used to track the mobile node, however a new technique in particle filter algorithm is also proposed to reduce the execution time. The stationary points were calculated through trilateration and finally by averaging the number of points collected for a specific time, whereas tracking is done through trilateration as well as particle filter algorithm. Wi-Fi signal is used to get initial guess of the position of mobile node in x-y coordinates system. Commercially available software “Wireless Mon" was used to read the WiFi signal strength from the WiFi card. Visual Cµ version 6 was used to interact with this software to read only the required data from the log-file generated by “Wireless Mon" software. Results are evaluated through mathematical modeling and MATLAB simulation.

Keywords: Particle Filter, Tracking, Wireless Local Area Network, WiFi, Trilateration

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

Abstract:

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: Maciej Norberciak

Abstract:

Timetabling problems are often hard and timeconsuming to solve. Most of the methods of solving them concern only one problem instance or class. This paper describes a universal method for solving large, highly constrained timetabling problems from different domains. The solution is based on evolutionary algorithm-s framework and operates on two levels – first-level evolutionary algorithm tries to find a solution basing on given set of operating parameters, second-level algorithm is used to establish those parameters. Tabu search is employed to speed up the solution finding process on first level. The method has been used to solve three different timetabling problems with promising results.

Keywords: Evolutionary algorithms, tabu search, timetabling.

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Authors: S. M. H. Karimian, F. S. Salehi, H. Alisadeghi

Abstract:

A two-dimensional moving mesh algorithm is developed to simulate the general motion of two rotating bodies with relative translational motion. The grid includes a background grid and two sets of grids around the moving bodies. With this grid arrangement rotational and translational motions of two bodies are handled separately, with no complications. Inter-grid boundaries are determined based on their distances from two bodies. In this method, the overset concept is applied to hybrid grid, and flow variables are interpolated using a simple stencil. To evaluate this moving mesh algorithm unsteady Euler flow is solved for different cases using dual-time method of Jameson. Numerical results show excellent agreement with experimental data and other numerical results. To demonstrate the capability of present algorithm for accurate solution of flow fields around moving bodies, some benchmark problems have been defined in this paper.

Keywords: Moving mesh, Overset grid, Unsteady Euler, Relative motion.

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Authors: Rajender Singh Chillar, Barjesh Kochar

Abstract:

All Text processing systems allow their users to search a pattern of string from a given text. String matching is fundamental to database and text processing applications. Every text editor must contain a mechanism to search the current document for arbitrary strings. Spelling checkers scan an input text for words in the dictionary and reject any strings that do not match. We store our information in data bases so that later on we can retrieve the same and this retrieval can be done by using various string matching algorithms. This paper is describing a new string matching algorithm for various applications. A new algorithm has been designed with the help of Rabin Karp Matcher, to improve string matching process.

Keywords: Algorithm, Complexity, Matching-patterns, Pattern, Rabin-Karp, String, text-processing.

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Authors: Hadjira Bentoumi, Pascal Gautron, Kadi Bouatouch

Abstract:

We present a method for fast volume rendering using graphics hardware (GPU). To our knowledge, it is the first implementation on the GPU. Based on the Shear-Warp algorithm, our GPU-based method provides real-time frame rates and outperforms the CPU-based implementation. When the number of slices is not sufficient, we add in-between slices computed by interpolation. This improves then the quality of the rendered images. We have also implemented the ray marching algorithm on the GPU. The results generated by the three algorithms (CPU-based and GPU-based Shear- Warp, GPU-based Ray Marching) for two test models has proved that the ray marching algorithm outperforms the shear-warp methods in terms of speed up and image quality.

Keywords: Volume rendering, graphics processors

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Authors: HangRok Lee, YongJe Choi, HoWon Kim

Abstract:

In recent years, it has been proposed security architecture for sensor network.[2][4]. One of these, TinySec by Chris Kalof, Naveen Sastry, David Wagner had proposed Link layer security architecture, considering some problems of sensor network. (i.e : energy, bandwidth, computation capability,etc). The TinySec employs CBC_mode of encryption and CBC-MAC for authentication based on SkipJack Block Cipher. Currently, This TinySec is incorporated in the TinyOS for sensor network security. This paper introduces TinyHash based on general hash algorithm. TinyHash is the module in order to replace parts of authentication and integrity in the TinySec. it implies that apply hash algorithm on TinySec architecture. For compatibility about TinySec, Components in TinyHash is constructed as similar structure of TinySec. And TinyHash implements the HMAC component for authentication and the Digest component for integrity of messages. Additionally, we define the some interfaces for service associated with hash algorithm.

Keywords: sensor network security, nesC, TinySec, TinyOS, Hash, HMAC, integrity

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Authors: Keunseok Cho, Sangbae Jeong, Hyungwook Chang, Minsoo Hahn

Abstract:

In this paper, a new encoding algorithm of spectral envelope based on NLMS in G.729.1 for VoIP is proposed. In the TDAC part of G.729.1, the spectral envelope and MDCT coefficients extracted in the weighted CELP coding error (lower-band) and the higher-band input signal are encoded. In order to reduce allocation bits for spectral envelope coding, a new quantization algorithm based on NLMS is proposed. Also, reduced bits are used to enhance sound quality. The performance of the proposed algorithm is evaluated by sound quality and bit reduction rates in clean and frame loss conditions.

Keywords: G.729.1, MDCT coefficient, NLMS, spectral envelope.

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Authors: Mubarak Saif Mohsen, Zurinahni Zainol, Rosalina Abdul Salam, Wahidah Husain

Abstract:

One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.

Keywords: Protein sequence algorithm, dynamic programming algorithm, multithread

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Authors: Daniela I. Borissova, Ivan C. Mustakerov

Abstract:

The paper addresses a problem of optimal staffing in open shop environment. The problem is to determine the optimal number of operators serving a given number of machines to fulfill the number of independent operations while minimizing staff idle. Using a Gantt chart presentation of the problem it is modeled as twodimensional cutting stock problem. A mixed-integer programming model is used to get minimal job processing time (makespan) for fixed number of machines' operators. An algorithm for optimal openshop staffing is developed based on iterative solving of the formulated optimization task. The execution of the developed algorithm provides optimal number of machines' operators in the sense of minimum staff idle and optimal makespan for that number of operators. The proposed algorithm is tested numerically for a real life staffing problem. The testing results show the practical applicability for similar open shop staffing problems.

Keywords: Integer programming, open shop problem, optimal staffing.

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Authors: Fayez M. Idris, Nehal I. AlZubaidi

Abstract:

Breast cancer detection techniques have been reported to aid radiologists in analyzing mammograms. We note that most techniques are performed on uncompressed digital mammograms. Mammogram images are huge in size necessitating the use of compression to reduce storage/transmission requirements. In this paper, we present an algorithm for the detection of microcalcifications in the JPEG2000 domain. The algorithm is based on the statistical properties of the wavelet transform that the JPEG2000 coder employs. Simulation results were carried out at different compression ratios. The sensitivity of this algorithm ranges from 92% with a false positive rate of 4.7 down to 66% with a false positive rate of 2.1 using lossless compression and lossy compression at a compression ratio of 100:1, respectively.

Keywords: Breast cancer, JPEG2000, mammography, microcalcifications.

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Authors: Songtao Chang, Yongji Wang, Lei Liu, Dangjun Zhao

Abstract:

Reentry trajectory optimization is a multi-constraints optimal control problem which is hard to solve. To tackle it, we proposed a new algorithm named CDEN(Constrained Differential Evolution Newton-Raphson Algorithm) based on Differential Evolution( DE) and Newton-Raphson.We transform the infinite dimensional optimal control problem to parameter optimization which is finite dimensional by discretize control parameter. In order to simplify the problem, we figure out the control parameter-s scope by process constraints. To handle constraints, we proposed a parameterless constraints handle process. Through comprehensive analyze the problem, we use a new algorithm integrated by DE and Newton-Raphson to solve it. It is validated by a reentry vehicle X-33, simulation results indicated that the algorithm is effective and robust.

Keywords: reentry vehicle, trajectory optimization, constraint optimal, differential evolution.

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Authors: P. Acharjee, S. K. Goswami

Abstract:

Particle Swarm Optimization (PSO) with elite PSO parameters has been developed for power flow analysis under practical constrained situations. Multiple solutions of the power flow problem are useful in voltage stability assessment of power system. A method of determination of multiple power flow solutions is presented using a hybrid of Particle Swarm Optimization (PSO) and local search technique. The unique and innovative learning factors of the PSO algorithm are formulated depending upon the node power mismatch values to be highly adaptive with the power flow problems. The local search is applied on the pbest solution obtained by the PSO algorithm in each iteration. The proposed algorithm performs reliably and provides multiple solutions when applied on standard and illconditioned systems. The test results show that the performances of the proposed algorithm under critical conditions are better than the conventional methods.

Keywords: critical conditions, ill-conditioned systems, localsearch technique, multiple power flow solutions, particle swarmoptimization.

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Authors: Maricar G. Misola, Bryan B. Navarro

Abstract:

Facility Layout Problem (FLP) is one of the essential problems of several types of manufacturing and service sector. It is an optimization problem on which the main objective is to obtain the efficient locations, arrangement and order of the facilities. In the literature, there are numerous facility layout problem research presented and have used meta-heuristic approaches to achieve optimal facility layout design. This paper presented genetic algorithm to solve facility layout problem; to minimize total cost function. The performance of the proposed approach was verified and compared using problems in the literature.

Keywords: Facility Layout Problem, Genetic Algorithm, Material Handling Cost, Meta-heuristic Approach.

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Authors: S. Khanpour, A. Movaghar

Abstract:

The one of best robust search technique on large scale search area is heuristic and meta heuristic approaches. Especially in issue that the exploitation of combinatorial status in the large scale search area prevents the solution of the problem via classical calculating methods, so such problems is NP-complete. in this research, the problem of winner determination in combinatorial auctions have been formulated and by assessing older heuristic functions, we solve the problem by using of genetic algorithm and would show that this new method would result in better performance in comparison to other heuristic function such as simulated annealing greedy approach.

Keywords: Bids, genetic algorithm, heuristic, metaheuristic, simulated annealing greedy.

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Authors: Deniz T. Sodiri, Venkat V S S Sastry

Abstract:

The paper presents an on-line recognition machine (RM) for continuous/isolated, dynamic and static gestures that arise in Flight Deck Officer (FDO) training. RM is based on generic pattern recognition framework. Gestures are represented as templates using summary statistics. The proposed recognition algorithm exploits temporal and spatial characteristics of gestures via dynamic programming and Markovian process. The algorithm predicts corresponding index of incremental input data in the templates in an on-line mode. Accumulated consistency in the sequence of prediction provides a similarity measurement (Score) between input data and the templates. The algorithm provides an intuitive mechanism for automatic detection of start/end frames of continuous gestures. In the present paper, we consider isolated gestures. The performance of RM is evaluated using four datasets - artificial (W TTest), hand motion (Yang) and FDO (tracker, vision-based ). RM achieves comparable results which are in agreement with other on-line and off-line algorithms such as hidden Markov model (HMM) and dynamic time warping (DTW). The proposed algorithm has the additional advantage of providing timely feedback for training purposes.

Keywords: On-line Recognition Algorithm, IsolatedDynamic/Static Gesture Recognition, On-line Markovian/DynamicProgramming, Training in Virtual Environments.

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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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Authors: K. Sivasubramanian, K. B. Jayanthi

Abstract:

Floorplanning plays a vital role in the physical design process of Very Large Scale Integrated (VLSI) chips. It is an essential design step to estimate the chip area prior to the optimized placement of digital blocks and their interconnections. Since VLSI floorplanning is an NP-hard problem, many optimization techniques were adopted in the literature. In this work, a music-inspired Harmony Search (HS) algorithm is used for the fixed die outline constrained floorplanning, with the aim of reducing the total chip area. HS draws inspiration from the musical improvisation process of searching for a perfect state of harmony. Initially, B*-tree is used to generate the primary floorplan for the given rectangular hard modules and then HS algorithm is applied to obtain an optimal solution for the efficient floorplan. The experimental results of the HS algorithm are obtained for the MCNC benchmark circuits.

Keywords: Floor planning, harmony search, non-slicing floorplan, very large scale integrated circuits.

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

Abstract:

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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