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Investigating Memory optimization of Hash-index for Next Generation Sequencing on Multi-core Architecture

Investigating Memory Optimization of Hash-index for Next Gen...

26th IEEE international Parallel and Distributed Processing Symposium (IPDPS) / workshop on High Performance Data Intensive Computing

作者： Wang, Wendi Tang, Wen Li, Linchuan Tan, Guangming Zhang, Peiheng Sun, Ninghui Chinese Acad Sci Inst Comp Technol High Performance Comp Res Ctr Beijing 100864 Peoples R China

ISBN: (纸本)9780769546766

Next Generation Sequencing (NGS) is gaining interests due to the increased requirements and the decreased sequencing cost. The important and prerequisite step of most NGS applications is the mapping of short sequences, called reads, to the template reference sequences. Both the explosion of NGS data with over billions of reads generated each day and the data-intensive computations pose great challenges to the capability of existing computing systems. In this paper, we take a hash-index based algorithm (PerM) as an example to investigate the optimization approaches for accelerating NGS reads mapping on multi-core architectures. First, we propose a new parallel algorithm that reorders bucket access in hash index among multiple threads so that data locality in shared cache is improved. Second, in order to reduce the number of empty hash bucket, we propose a serialized hash index compression algorithm, which coincides with the sequential access nature of our new parallel algorithm. With reduced hash index size, it also becomes possible for us to use longer hash keys, which alleviates the hash conflicts and improves the query performance. Our experiment on an 8-socket 8-cores Intel Xeon X7550 SMP with 128 GB memory shows that the new parallel algorithm reduces LLC miss ratio to be 8% similar to 15% of the original algorithm and the overall performance is improved by 4 similar to 11 times (6 times avg.).

关键词： hashing Parallel algorithms core construction next generation sequencing locality data reading buckets

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Evaluating SPARQL Subqueries over P2P Overlay Networks

Evaluating SPARQL Subqueries over P2P Overlay Networks

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international workshop on Database and Expert Systems applications

作者： Liaquat Ali Georg Lausan University of Freiburg Germany Albert-Ludwigs-Universitat Freiburg Freiburg im Breisgau Baden-WÃ¼rttemberg DE

The introduction of subqueries is one of the most interesting features included in the latest SPARQL 1.1 specification. Existing distributed RDF storage and querying systems have not studied the evaluation of this newly included query feature. The evaluation of subqueries in distributed environment may be very inefficient and expensive in terms of query response time and bandwidth usage, particularly for the correlated subqueries where the inner query block is evaluated once for each solution of the outer query. In this paper, we study the problem of evaluating SPARQL subqueries over RDF data stored in 3nuts p2p network. We study semi join based optimization technique, and transformation algorithms to transform correlated queries to equivalent uncorrelated ones, that would make the distributed evaluation of such queries more efficient.

关键词： Resource description framework Peer to peer computing Databases optimization Syntactics Transforms

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Optimal multilevel thresholding using the modified adaptive particle swarm optimization

International Journal of Digital Content Technology and its ...

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international Journal of Digital Content Technology and its applications 2012年第15期6卷 208-219页

作者： Liu, Yi Mu, Caihong Kou, Weidong School of Electronic Engineering Xidian University Xi'an China School of Telecommunications Engineering Xidian University Xi'an China IBM Beijing China

The conventional multilevel thresholding methods are computational expensive since they exhaustively search the optimal thresholds to optimize the objective functions. In this paper, the modified adaptive particle swarm optimization (MAPSO) algorithm is proposed to overcome this drawback. The dynamic population (DP) strategy of the proposed algorithm enables the population size variable with the evolutionary state at run time. With the help of DP strategy, the population size can increase when the swarm converges and decrease when the swarm disperses. The MAPSO algorithm is used to find the optimal thresholds by maximizing the Otsu's objective function. The performance of the proposed algorithm has been validated on eight standard test images. The experimental results of 50 independent runs illustrate the best solution quality and stability of the MAPSO when compared with three other PSO algorithms.

关键词： Image segmentation

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Multi-dimensional commodity covering for tariff selection in transportation

Multi-dimensional commodity covering for tariff selection in...

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12th workshop on Algorithmic Approaches for Transportation Modelling, optimization, and Systems, ATMOS 2012

作者： König, Felix G. Matuschke, Jannik Richter, Alexander TomTom International BV An den Treptowers 1 12435 Berlin Germany Technische Universität Berlin Institut für Mathematik Straße des 17. Juni 136 10623 Berlin Germany

ISBN: (纸本)9783939897453

In this paper, we study a multi-dimensional commodity covering problem, which we encountered as a subproblem in optimizing large scale transportation networks in logistics. The problem asks for a selection of containers for transporting a given set of commodities, each commodity having different extensions of properties such as weight or volume. Each container can be selected multiple times and is specified by a fixed charge and capacities in the relevant properties. The task is to find a cost minimal collection of containers and a feasible assignment of the demand to all selected containers. From theoretical point of view, by exploring similarities to the well known SETCOVER problem, we derive NP-hardness and see that the non-approximability result known for set cover also carries over to our problem. For practical applications we need very fast heuristics to be integrated into a meta-heuristic framework that-depending on the context-either provide feasible near optimal solutions or only estimate the cost value of an optimal solution. We develop and analyze a flexible family of greedy algorithms that meet these challenges. In order to find best-performing configurations for different requirements of the meta-heuristic framework, we provide an extensive computational study on random and real world instance sets obtained from our project partner 4 flow AG. We outline a trade-off between running times and solution quality and conclude that the proposed methods achieve the accuracy and efficiency necessary for serving as a key ingredient in more complex meta-heuristics enabling the optimization of large-scale networks. © Felix G. König, Jannik Matuschke, and Alexander Richter.

关键词： Containers

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Optimal Energy Consumption and Throughput for Workflow applications on Distributed Architectures

Optimal Energy Consumption and Throughput for Workflow Appli...

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IEEE international workshop on Enabling Technologies: Infrastructure for Collaborative Enterprises (WET ICE)

作者： Abdallah Ben Othman Jean-Marc Nicod Laurent Philippe Veronika Rehn-Sonigo FEMTO-ST Institute CNRS / UFC / ENSMM UTBM Besancon France

In this paper we study both the throughput and the energy optimization problem for a distributed system subject to failures that executes a workflow at different speed levels. The application is modeled as a directed acyclic graph composed of typed tasks linked by dependency constraints. A continuous flow, or a great number of application instances has to be processed optimizing the collaborative system performance which implies to increase the throughput - the number of application instances processed by time unit - or to decrease the period - the time needed to output one instance of the system. The system is designed as a collaborative platform of distributed machines. Each machine collaborates with others by performing all the instances of at least one task of the DAG. The problem we tackle is to optimize the configuration of the platform. In this article we propose two polynomial algorithms that optimize the two objectives of period (i.e., throughput) and energy minimization and we prove that the proposed algorithms give optimal results. Our optimization approach is hierarchic in the sens that we either minimize the energy consumption for an optimal period or minimize the period for the optimal energy consumption.

关键词： Energy consumption Acceleration Throughput optimization Complexity theory Computational modeling Polynomials

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Advances in modeling and optimization techniques for microwave design

Advances in modeling and optimization techniques for microwa...

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IEEE MTT-S international Microwave workshop Series (IMWS)

作者： Qijun Zhang Carleton University Canada Tianjin University China

Summary form only given. Modeling and optimization of microwave and high-frequency/high-speed microelectronic devices and systems are important for achieving next generation information technology and communication systems. Increasing circuit size and design complexity, coupled with stringent design specifications and shorter design cycles, demand tools that are faster, more accurate and automated than possible today. Electromagnetic (EM)/physics-based design accuracies will be needed not only at the component level, but also at the circuit and system levels. Models with EM/physics-oriented accuracy but without the computational expense of direct EM/physics simulations are necessary. Recent applications of neural networks and space mapping for microwave design lead to new modeling and Computer-aided Design (CAD) with potential advantages in both speed and accuracy. applications are being made in modeling and design of microstrip and CPW circuits, multilayer interconnects, embedded passives, printed antennas, LTCC circuits, semiconductor devices, measurement standards, filters, amplifiers, mixers and so on. New CAD methods for optimization, statistical design, global modeling, and computational electromagnetics exploiting computational intelligence concepts are being developed. Advanced microwave CAD methodologies such as knowledge-aided design, knowledge-based neural networks, and space mapping are being developed. This leads to new opportunities combining equivalent circuit/empirical models, EM/physics simulation, behavioral modeling, neural network and space mapping optimization algorithms for fast and accurate design of high-frequency components and systems. This presentation provides an overview of the state of the art in these emerging directions. The presentations highlight implementable methodologies for automated modeling and design of RF/microwave components, circuits and systems. The presentation covers fundamental concepts and methodologies, industrial ap

关键词： Integrated circuit modeling Solid modeling Computational modeling Microwave filters Microwave amplifiers Microwave circuits Microwave communication

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Correlation-aware packet scheduling for multi-camera streaming

Correlation-aware packet scheduling for multi-camera streami...

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Packet Video

作者： Laura Toni Thomas Maugey Pascal Frossard University of California San Diego USA LTS4 Ecole Polytechnique Fédérale de Lausanne Switzerland

In multi-view applications, multiple cameras acquire the same scene from different perspectives, which results in correlated video streams. It becomes important to exploit this correlation at the acquisition side (i.e., in the source coding) or at the receiver side (i.e., during error-concealment). In this work, we propose a correlation-aware scheduling algorithm for multi-camera sets, in which information from all views need to be sent over a bottleneck channel to clients that decode the 3D scene captured by the cameras. Based on a novel rate-distortion model, that takes into account the correlation between sources, we propose a solution that minimizes the distortion in the scene reconstruction and adapts to temporal variations in the scene content. Simulation results show the gain of the scheduling algorithm when the correlation model is known in the optimization, compared to scheduling policies with no information about the correlation or with a priori camera selection algorithms.

关键词： Cameras Correlation PSNR Image reconstruction optimization Scheduling algorithms Scheduling

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Multi-classifier System Configuration Using Genetic algorithms

Multi-classifier System Configuration Using Genetic Algorith...

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international workshop on Frontiers in Handwriting Recognition

作者： D. Impedovo G. Pirlo D. Barbuzzi Dipartimento di Informatica Università degli Studi di Bari Bari Italy

Classifier combination is a powerful paradigm to deal with difficult pattern classification problems. As matter of this fact, multi-classifier systems have been widely adopted in many applications for which very high classification performance is necessary. Notwithstanding, multi-classifier system design is still an open problem. In fact, complexity of multi-classifiers systems make the theoretical evaluation of system performance very difficult and, consequently, also the design of a multi-classifier system. This paper presents a new approach for the design of a multi-classifier system. In particular, the problem of feature selection for a multi-classifier system is addressed and a genetic algorithm is proposed for automatic selecting the optimal set of features for each individual classifier of the multi-classifier system. The experimental results, carried out in the field of handwritten digit recognition, demonstrate the effectiveness of the proposed approach.

关键词： Genetic algorithms optimization Sociology Statistics Handwriting recognition Classification algorithms Machine learning

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Multiplex models for the optimum design of electrical machines

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international JOURNAL OF APPLIED ELECTROMAGNETICS AND MECHANICS 2011年第2-3期37卷 81-91页

作者： Brochet, Pascal Univ Lille Nord France Lille France

One promising way to address the problem of the synthesis of the design of electrical machines is to set it up as an optimization problem in order to benefit from the most effective optimization algorithms to solve it. Some consequences are here derived from this statement concerning the modeling of electrical machines, the formalization of the optimization problem and the required algorithms to solve it. They come from different experiments on the design of electrical machine, each one involving a particular methodology, and already reported. This way, a unified approach of multiplex model is proposed. Coupled with adapted multiobjective optimization algorithms it provides a powerful and promising way of designing electrical machines.

关键词： Design optimization multilevel multiobjective multiphysics electrical machine

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Design and technology solutions for high-efficiency high-speed motors

Design and technology solutions for high-efficiency high-spe...

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international Conference on Electrical Machines, ICEM

作者： F. Luise A. Tessarolo S. Pieri P. Raffin M. Di Chiara F. Agnolet M. Scalabrin Motor Generator and Drives Research and Development Ansaldo Sistemi Industriali S.p.A. Monfalcone Italy Industrial Engineering and Information Technology Department University of Trieste Italy

Over the last few decades an increasing sensitivity has been spreading towards energy saving technologies. In particular, as far as electric drives are concerned, a strong demand for high efficiency motors has been raising in many industry sectors. This paper describes the development of an innovative high-efficiency solution for highspeed motors targeted for industrial turbomachinery applications in the 500-1000 kW power range at 10000-15000 rpm The technology presented features a slotless stator and a magnetically-levitated Halbach permanent-magnet rotor. A full-scale motor prototype is being manufactured for the assessment of the proposed technology. Design optimization techniques, based on genetic algorithms and multi-disciplinary analysis tools, have been employed in the prototype design stage to maximize motor efficiency and performance figures. A multilevel cascaded-cell converter with optimized voltage output is under parallel development for motor supply. Prototype full-power and full-speed qualification tests are planned to take place within the current year to demonstrate the effectiveness of the design and technology presented in this paper.

关键词： Rotors Permanent magnet motors Prototypes Magnetic levitation optimization Stator windings

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