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Meeting Report: BioSharing at ISMB 2010

Standards in genomic sciences 2010年第3期3卷 254-8页

作者： Dawn Field Susanna Sansone Edward F Delong Peter Sterk Iddo Friedberg Pascale Gaudet Susanna Lewis Renzo Kottmann Lynette Hirschman George Garrity Guy Cochrane John Wooley Folker Meyer Sarah Hunter Owen White Brian Bramlett Susan Gregurick Hilmar Lapp Sandra Orchard Philippe Rocca-Serra Alan Ruttenberg Nigam Shah Chris Taylor Anne Thessen Centre for Ecology & Hydrology Wallingford UK Oxford e-Research Centre University of Oxford Oxford UK Department of Biological Engineering Massachusetts Institue of Technology Cambridge USA Department of Microbiology Miami University Oxford USA Department of Computer Science and Software Engineering Miami University Oxford USA Swiss Institute of Bioinformatics Geneva 4 Switzerland Lawrence Berkeley National Laboratory Berkeley USA Microbial Genomics Group Max Planck Institute for Marine Microbiology & Jacobs University Bremen Bremen Germany Information Technology Center The MITRE Corporation Bedford USA Department of Microbiology and Molecular Genetics Michigan State University East Lansing USA European Molecular Biology Laboratory (EMBL) Outstation European Bioinformatics Institute (EBI) Cambridge UK University of California San Diego La Jolla USA Argonne National Laboratory Argonne USA Institute for Genome Sciences University of Maryland School of Medicine Baltimore USA Lux Bio Group Portland USA Biological Systems Science Division Department of Energy Washington DC USA National Evolutionary Synthesis Center (NESCent) Durham USA Science Commons c/o Massachusetts Institute of Technology Computer Science and Artificial Intelligence Laboratory Cambridge USA Stanford Center for Biomedical Informatics Research Stanford USA Marine Biological Laboratory USA

This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part of its M3 & BioSharing special interest group (SIG) workshop. The BioSharing event included invited talks from a range of community leaders and a panel discussion at the end of the day. The panel session led to the formal agreement among community leaders to join together to promote cross-community knowledge exchange and collaborations. A key focus of the newly formed Biosharing community will be linking up resources to promote real-world data sharing (virtuous cycle of data) and supporting compliance with data policies through the creation of a one-stop-portal of information. Further information about the newly established BioSharing effort can be found at http://***.

关键词： Community Leader Funding Agency Special Interest Group Panel Discussion Standardization Effort

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Particle filtering of point processes observation with application on the modeling of visual cortex neural spiking activity

Particle filtering of point processes observation with appli...

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International IEEE/EMBS Conference on Neural engineering, CNE

作者： Yousef Salimpour Hamid Soltanian-Zadeh Computational Neuroscience in School of Cognitive Sciences Institute of Studies in Fundamental Sciences Tehran Iran Department of Radiology Henry Ford Health System Detroit MI USA Control and Intelligent Processing Center of Excellence(CIPCE) Department of Electrical and Computer Engineering University of Tehran Tehran Iran

Recording of neural response to specific stimulus in a repeated trial is very common in neuroscience protocol. The perstimulus time histogram (PSTH) is a standard tool for analysis of neural response. However it could not capture the non-deterministic properties of the neuron especially in higher level cortical area such as inferior temporal cortex. The stochastic state point process filter theory is used for the estimation of the conditional intensity of the point process observation as a time varying firing rate and the particle filter is used to numerically estimate this density in time. The particle filters were applied to the results of the point process observation for compensating the Gaussian assumption. The results of applying point process modeling on a real data from inferior temporal cortex of macaque monkey indicates that, based on the assessment of goodness-of-fit, the neural spiking activity and biophysical property of neuron could be captured more accurately in compare to conventional methods.

关键词： Filtering Brain modeling Neurons Stochastic processes State estimation Particle filters Histograms Mathematical model Neural engineering Neuroscience

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Designing a home security system using sensor data fusion with dst and dsmt methods

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International Journal of engineering, Transactions A: Basics 2009年第1期22卷 13-20页

作者： Khalkhali, A. Moussavi Moshiri, B. Momeni, H.R. Telecommunication Infrastructure Company of Iran Ministry of Information and Communication Technology P.O. Box 14115-143 Tehran Iran Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran P.O. Box 14395-515 Tehran Iran Department of Electrical Engineering Tarbiat Modarres University P.O. Box 14115-143 Tehran Iran

Today due to the importance and necessity of implementing security systems in homes and other buildings, systems with higher certainty, lower cost and with sensor fusion methods are more attractive, as an applicable and high performance methods for the researchers. In this paper, the application of Dempster-Shafer evidential theory and also the newer, more general one Dezert-Smarandache theory for implementing as a home security system and also using sensor data fusion have been considered. The benefits of multisensor fusion with direct connection to the control unit, in comparison with the traditional single sensor systems, have been shown.

关键词： Sensor data fusion

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Feature shape and elevation based road classification and extraction on high spatial resolution remote sensing imageries

Feature shape and elevation based road classification and ex...

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International Conference on Geoinformatics

作者： Tao Tang Xiao Wang Joaquin Carbonara Zhixin Shi Department of Geography and Planning State University of New York University at Buffalo Buffalo NY USA Department of Mathematics State University of New York University at Buffalo Buffalo NY USA Center of Excellence of Document Analysis and Recognition (CEDAR) Department of Computer Science and Engineering State University of New York University at Buffalo USA

ISBN: (纸本)9781424445622

Classification and extraction of geospatial features from high spatial resolution imageries approved is one of the most significant steps for spatial database acquisition and updating in GIS. This research is to explore the methodologies of recognizing shape and elevation characteristics of spatial features on the remote sensed images. We focus on the road network classification and extraction among various features on the ground because it carries unique characteristic of elongation. We combined both a pattern recognition model of connected component labeling (CCL) in two dimensional image processing, and a three dimensional DEM elevation filtering model to extract the road and street features from high resolution imageries. Samples of digital aerial photographs in Erie County, New York were used to test the methodology. The results indicated that the correctness of road extraction in rural areas can reach 69.1%; that of completeness is 74.9%; and the overall quality is 73.1%. By contrast, the correctness in urban high-rise region is only 39.5%; that of completeness is 42.8%; and the overall quality is 32.8%.

关键词： Shape Roads Spatial resolution Remote sensing Feature extraction Image databases Spatial databases Geographic Information Systems Character recognition Image recognition

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HPMR: Prefetching and pre-shuffling in shared MapReduce computation environment

HPMR: Prefetching and pre-shuffling in shared MapReduce comp...

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IEEE International Conference on Cluster Computing

作者： Sangwon Seo Ingook Jang Kyungchang Woo Inkyo Kim Jin-Soo Kim Seungryoul Maeng Computer Science Department Korea Advanced Institute of Science and Technology South Korea Search Engineering Yahoo Inc. Seoul South Korea Advanced Software Center Samsung Advanced Institute of Technology South Korea School of Information and Comm. Sungkyunkwan University South Korea

MapReduce is a programming model that supports distributed and parallel processing for large-scale data-intensive applications such as machine learning, data mining, and scientific simulation. Hadoop is an open-source implementation of the MapReduce programming model. Hadoop is used by many companies including Yahoo!, Amazon, and Facebook to perform various data mining on large-scale data sets such as user search logs and visit logs. In these cases, it is very common to share the same computing resources by multiple users due to practical considerations about cost, system utilization, and manageability. However, Hadoop assumes that all cluster nodes are dedicated to a single user, failing to guarantee high performance in the shared MapReduce computation environment. In this paper, we propose two optimization schemes, prefetching and pre-shuffling, which improve the overall performance under the shared environment while retaining compatibility with the native Hadoop. The proposed schemes are implemented in the native Hadoop-0.18.3 as a plug-in component called HPMR (high performance MapReduce engine). Our evaluation on the Yahoo!Grid platform with three different workloads and seven types of test sets from Yahoo! shows that HPMR reduces the execution time by up to 73%.

关键词： Prefetching Large-scale systems Data mining Parallel programming Parallel processing Machine learning Computational modeling Open source software Facebook Costs

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Model based method for determining the minimum embedding dimension from solar activity chaotic time series

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International Journal of engineering, Transactions A: Basics 2008年第1期21卷 31-44页

作者： Mirmomeni, M. Lucas, C. Center of Excellence of Control and Intelligent Processing Department of Electrical and Computer Engineering University Tehran Iran

Predicting future behavior of chaotic time series system is a challenging area in the literature of nonlinear systems. The prediction's accuracy of chaotic time series is extremely dependent on the model and the learning algorithm. On the other hand the cyclic solar activity as one of the natural chaotic systems has significant effects on earth, climate, satellites and space missions. Several methods have been introduced for prediction of solar activity indices especially the sunspot number, which is a common measure of solar activity. In this paper, the problem of embedding dimension estimation for solar activity chaotic time series based on polynomial models is considered. The optimality of embedding dimension has an important role in computational efforts, Lyapunov exponents' analysis and efficiency of prediction. The method of this paper is based on the fact that the reconstructed dynamics of an attractor should be a smooth map, i.e. with no self intersection in the reconstructed attractor. To check this property, a local general polynomial autoregressive model is fitted to the given data and a canonical state space realization is considered. Then, the normalized one-step forward prediction error for different orders and various degrees of nonlinearity in polynomials is evaluated. Besides the estimation of the embedding dimension, a predictive model is obtained which can be used for prediction and estimation of the Lyapunov exponents. This algorithm is applied to indicate the minimum embedding dimension of sunspot numbers (SSN), Disturbance Storm Time or Dst. and Proton Flux indices are some of the most important among solar activity indices and results depict the power of the proposed method in embedding dimension estimation.

关键词： Polynomials

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Important scene analysis model using result importance and situation importance

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International Journal of Wireless and Mobile Computing 2009年第4期3卷 225-235页

作者： Hashimoto, Takako Katooka, Takashi Iizawa, Atsushi Kitagawa, Hiroyuki Software RandD Group RICOH Company Ltd. Bukyo-ku Tokyo 112-0002 Japan Department of Computer Science Graduate School of Systems and Information Engineering University of Tsukuba Tsukuba Ibaraki 305-8573 Japan Chiba University of Commerce Japan Network Solution and Services Center Global Marketing Group RICOH Company Ltd. Japan Ricoh IT Solutions Co. Ltd. Japan

Functional improvements to mobile terminals have made possible the spread of multimedia information delivery services. Especially for sports, a service that extracts important scenes and reports them to users has become popular. We take the approach that situational changes in a game's progress can be presented as state transitions, and devise an important scene analysis model based on Result Importance (RI), which represents each situation's actual importance, and Situation Importance (SI), which shows the degree of a chance at the situation. With our model, significant scenes are extracted dynamically. Experimental results indicate that the proposed method is very promising. Copyright © 2009 Inderscience Enterprises Ltd.

关键词： Multimedia systems

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Introduction of nano-seconds pulsed discharge plasma and its applications

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IEEJ Transactions on Fundamentals and Materials 2009年第1期129卷 7-14页

作者： Namihira, Takao Wang, Douyan Matsumoto, Takao Okada, Sho Akiyama, Hidenori Bioelectrics Research Center Kumamoto University 2-39-1 Kurokami Kumamoto 860-8555 Japan Priority Organization for Innovation and Excellence Kumamoto University 2-39-1 Kurokami Kumamoto 860-8555 Japan Department of Computer Science and Electrical Engineering Kumamoto University 2-39-1 Kurokami Kumamoto 860-8555 Japan Graduate School of Science and Technology Kumamoto University 2-39-1 Kurokami Kumamoto 860-8555 Japan

During the decades, the developments of high power semiconductor switch, magnetic core and etc have allowed us to manufacture the pulsed power source having higher energy transfer efficiency. As the results, the pulsed discharge has been recognized as one of the promised non-thermal plasma to practical use. In this paper, a generation process, electron energy, impedance and a temperature of the pulsed discharge plasma would be explained. In addition, a nano-seconds pulsed discharge plasma would be introduced as the non-thermal plasma processing giving us the highest energy efficiency and be demonstrated it. © 2009 The Institute of Electrical Engineers of Japan.

关键词： Electric discharges

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Modelling time dependent swelling potential of mudrock using laboratory tests and artificial neural network

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Transactions of the Institutions of Mining and Metallurgy, Section A: Mining Technology 2008年第1期117卷 32-41页

作者： Doostmohammadi, R. Moosavi, M. Araabi, B.N. Mining Engineering Department Zanjan University 5 km Tabriz road Zanjan Iran School of Mining Engineering University of Tehran Iran Control and Intelligent Processing Center of Excellence School of Electrical and Computer Engineering University of Tehran Iran

The focus of this research work is modelling time dependent swelling strain and pressure simultaneously in weak rock. Various swelling potential under different boundary conditions is considered. Free and semiconfined swelling strain and swelling pressure under oedometric condition are the most proposed tests for determination of the swelling potential of weak rock. In this paper, a modified swelling strain and pressure test is introduced using springs to provide deformable axial stiffness. The swelling strain and pressure of mudrock are modelled by artificial neural network for various swellable clay, carbonate, initial water content and different boundary stiffness, by using a combination of the proposed modified test along with the existing tests. This method correlates the results of laboratory tests with an acceptable accuracy. The proper operation of the developed model for predicting the time dependent swelling strain and pressure of mudrock under deformable and rigid axial boundaries is confirmed. © 2008 Institute of Materials, Minerals and Mining.

关键词： Neural networks

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Automatic verification of temporal properties of Air Traffic Management procedures using hybrid systems 7

Automatic verification of temporal properties of Air Traffic...

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7th EUROCONTROL Innovative Research Workshop and Exhibition: Disseminating ATM Innovative Research

作者： Di Benedetto, M.D. D'Innocenzo, A. Petriccone, A. Department of Electrical Engineering and Computer Science Center of Excellence DEWS University of L'Aquila Italy

In an Air Traffic Management context possible catastrophic events can take place because of error propagation in a multi-agent procedure [1]. In this paper we provide a mathematical framework based on hybrid systems theory for formal modeling of air traffic management applications. This framework can be used to model the dynamics of complex multi-agent systems in normal operative conditions, as well as in abnormal scenarios. The hybrid system framework allows description and detection of these errors and their effects on the evolution of procedures, as well as automatic verification of important properties such as safety and liveness. The ASEPIn Trail Procedure will be analyzed to illustrate the proposed methodology. We will describe the use of UPPAAL, a tool that can be used to model ASEP-ITP and to verify automatically the properties of interest including safety.

关键词： Hybrid systems

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