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Identifying, tabulating, and analyzing contacts between branched neuron morphologies

IBM JOURNAL OF RESEARCH AND DEVELOPMENT 2008年第1-2期52卷 43-55页

作者： Kozloski, J. Sfyrakis, K. Hill, S. Schuermann, F. Peck, C. Markram, H. IBM Corp Div Res Thomas J Watson Res Ctr Yorktown Hts NY 10598 USA Ecole Polytech Fed Lausanne Blue Brain Lab Brain Mind Inst Fac Sci Vie CH-1015 Lausanne Switzerland IBM Corp Div Res Thomas J Watson Res Ctr CH-1015 Lausanne Switzerland

Simulating neural tissue requires the construction of models of the anatomical structure and physiological function of neural microcircuitry. The Blue Brain Project is simulating the microcircuitry of a neocortical column with very high structural and physiological precision. This paper describes how we model anatomical structure by identifying, tabulating, and analyzing contacts between 104 neurons in a morphologically precise model of a column. A contact occurs when one element touches another, providing the opportunity for the subsequent creation of a simulated synapse. The architecture of our application divides the problem of detecting and analyzing contacts among thousands of processors on the IBM Blue Gene/L (TM) supercomputer. Data required for contact tabulation is encoded with geometrical data for contact detection and is exchanged among processors. Each processor selects a subset of neurons and then iteratively 1) divides the number of points that represents each neuron among column subvolumes, 2) detects contacts in a subvolume, 3) tabulates arbitrary categories of local contacts, 4) aggregates and analyzes global contacts, and 5) revises the contents of a column to achieve a statistical objective. Computing, analyzing, and optimizing local data in parallel across distributed global data objects involve problems common to other domains (such as three-dimensional image processing and registration). Thus, we discuss the generic nature of the application architecture.

关键词： NEURONS image processing IMAGING systems SIMULATION methods OPTICAL data processing COMPUTER graphics MOLECULAR biology MORPHOGENESIS

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Towards universal code generator generation

Towards universal code generator generation

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IPDPS 2008 - 22nd IEEE International parallel and distributed processing Symposium

作者： Richards, Timothy Walters ii, Edward K. Moss, J. Eliot B. Palmer, Trek Weems, Charles C. Department of Computer Science University of Massachusetts Amherst MA United States

ISBN: (纸本)9781424416943

One of the most difficult tasks a compiler writer faces is the construction of the code generator. The code generator is that part of the compiler that translates compiler intermediate representation (IR) into instructions for a target machine. Unfortunately, implementing a code generator "by hand" is a difficult, time consuming, and error prone task. The details of both the IR and target instruction set must be carefully considered in order to generate correct and efficient code. This, in turn, requires an expert in both the compiler internals as well as the target machine. Even an expert, however, can produce a code generator that is difficult to verify and debug. In this paper we present a universal approach for automating the construction of correct code generators. In particular, we show that both the compiler IR and target instruction set semantics can be described by a machine description language and leveraged by a heuristic search procedure to derive code generator patterns. We then utilize formal methods to determine if the IR and target sequence pairs that make up these patterns are semantically equivalent. ©2008 IEEE.

关键词： Formal methods

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Massively parallel electrical conductivity imaging of the subsurface: Applications to hydrocarbon exploration

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Journal of Physics: Conference Series 2009年第1期180卷

作者： Gregory A Newman Michael Commer Lawrence Berkeley National Laboratory MS-90-1116 Berkeley CA 94720 USA

Three-dimensional (3D) geophysical imaging is now receiving considerable attention for electrical conductivity mapping of potential offshore oil and gas reservoirs. The imaging technology employs controlled source electromagnetic (CSEM) and magnetotelluric (MT) fields and treats geological media exhibiting transverse anisotropy. Moreover when combined with established seismic methods, direct imaging of reservoir fluids is possible. Because of the size of the 3D conductivity imaging problem, strategies are required exploiting computational parallelism and optimal meshing. The algorithm thus developed has been shown to scale to tens of thousands of processors. In one imaging experiment, 32,768 tasks/processors on the IBM Watson Research Blue Gene/L supercomputer were successfully utilized. Over a 24 hour period we were able to image a large scale field data set that previously required over four months of processing time on distributed clusters based on Intel or AMD processors utilizing 1024 tasks on an InfiniBand fabric. Electrical conductivity imaging using massively parallel computational resources produces results that cannot be obtained otherwise and are consistent with timeframes required for practical exploration problems.

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GPU-accelerated KLT tracking with monte-carlo-based feature reselection

GPU-accelerated KLT tracking with monte-carlo-based feature ...

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Digital image Computing: Techniques and Applications, DICTA 2008

作者： Ohmer, Julius Fabian Redding, Nicholas J. DSTO Intelligence Surveillance Reconnaissance Division P.O. Box 1500 Edinburgh SA 5111 Australia

ISBN: (纸本)9780769534565

Many computer vision methods rely on frame reg- istration information obtained with algorithms such as the Kanade-Lucas-Tomasi (KLT) feature tracker, which is known for its excellent performance in that area. Various research groups proposed methods to ex- tend its performance, both in terms of execution time and stability. Recent research has shown that cur- rent graphics processing units (GPUs) have proven to be very eficient SIMD parallel processing architectures that can be used to speed up the execution time of the KLT algorithm by an order of a magnitude compared with an ordinary CPU implementation and thus mak- ing it suitable for real-time applications on commodity hardware. Previous publications demonstrated the use of the GPU for the tracking and image processing part of the KLT algorithm. One essential, but computation- ally demanding step of the KLT algorithm is the fea- ture selection step. It injects fresh feature points into the existing point set and thus enables the KLT to con- tinuously track points throughout an image sequence. Those sequences can contain rapid movements or they may be of low quality. In such situations, features di- minish rapidly and the step must be performed poten- tially for every frame. Thus, the performance of the otherwise eficient GPU implementation declines sub- stantially, as this step includes a sorting operation on the sparse feature map, which is diffcult to implement eficiently on the GPU. We use the KLT algorithm to calculate a stable frame registration with high accuracy using the feature point set. We found that maintain- ing a well distributed feature set through frequent in- jections of points is an essential requirement. In this paper we will demonstrate an alternative feature rese- lection method that can be eficiently implemented on the GPU. It is a Monte-Carlo-based approximation of the original method and leads to very good tracking re- sults with just a fraction of the computational cost. © 2008 IEEE.

关键词： Graphics processing unit

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Correction of the motion blur alteration in the human lymphocyte micro-nucleus image based on Wiener'S deconvolution

Correction of the motion blur alteration in the human lympho...

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16th IMEKO TC4 International Symposium on Exploring New Frontiers of Instrumentation and methods for Electrical and Electronic Measurements;13th International Workshop on ADC Modelling and Testing - IMEKO TC4 - TC21 Joint Session

作者： Grimaldi, Domenico Lamonaca, Francesco Macrí, Carmelo Dept. of Electronics Computer and System Sciences University of Calabria 87036 Rende - CS Italy

ISBN: (纸本)9788890314933

The image correction based on the Wiener's deconvolution is proposed by evaluating the Point-Spread Function (PSF) for motion blur alteration. This correction is experimented to reduce the number of rejected images by the pre-processing procedure pointed out to correct detection of the Micro Nucleuses into human lymphocyte images acquired from the image Flow Cytometer. The proposed correction operates in conjunction with (i) the spatial filters, pointed out to correct the bad exposure, the Gaussian out of focus and the Gaussian noise, and (ii) the Wiener's deconvolution with PSF particularized for Gaussian out of focus alteration with high intensity. The heavy computation burden of correction based on each one Wiener's deconvolution compared with that based on spatial filters suggests to use each one of the Wiener's deconvolution to process the rejected images from the spatial filters, only, and not all acquired images. According to this consideration and to speed up the complete pre-processing correction procedure, the implementation is based on the computing distributed service implemented by using the LabVIEW Shared Variables. The criteria to establish the number of PCs to be used is experimental evaluated.

关键词： Gaussian noise (electronic)

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SPADE - Scheduler for parallel and distributed Execution from mobile devices

SPADE - Scheduler for Parallel and Distributed Execution fro...

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6th International Workshop on Middleware for Pervasive and Ad-Hoc Computing, MPAC 2008 - Held at the ACM/IFIP/USENIX 9th International Middleware Conference, Middleware 2008

作者： Nuno Silva, João Veiga, Luís Ferreira, Paulo INESC-ID Technical University of Lisbon Portugal

ISBN: (纸本)9781605583648

Mobile computing devices, such as mobile phones or even ultra-mobile PC's, are becoming more and more powerful. Because of this fact, users are starting to use these devices to execute tasks that until a few years ago would only be executed on a desktop PC, e.g. picture manipulation, or text editing. Furthermore, these devices, are by now almost continuously connected, either by Wi-Fi or 3G UMTS links. Nevertheless power consumption is still a major factor on these mobile devices usage, restricting autonomy. While users should be able to employ mobile computing devices to perform these tasks with convenience, it would improve performance and reduce battery drain if the bulk processing of such tasks could be offloaded to remote hosts accessible by the same user. To accomplish this, we present SPADE, a middleware to deploy remote and parallel execution of some commodity applications to solve complex problems, from mobile devices, without any special programming effort, and by simply defining several data input sets. In SPADE, jobs are composed of simpler tasks that will be executed on remote computers. The user states what files should be processed by each task, what application will be launched and defines the application arguments. By using SPADE any user can, for instance, accelerate a batch image manipulation by using otherwise idle remote computers, while releasing the mobile device for other tasks. In order to make SPADE usable by a wide set of computer users we implemented two ideas: i) the execution code is a commodity piece of software already installed on the remote computers (e.g. image processing applications), and ii) the definition of the data sets to be remotely processed is done in a simple and intuitive way. The results are promising as the speedups accomplished are near optimal, while reducing power consumption, and SPADE allows the easy and efficient deployment of jobs on remote hosts. Copyright 2008 ACM.

关键词： Mobile devices

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Clusters versus FPGAs for Spectral Mixture Analysis-Based Lossy Hyperspectral Data Compression

Clusters versus FPGAs for Spectral Mixture Analysis-Based Lo...

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Conference on Satellite Data Compression, Communications and Archiving IV

作者： Plaza, Antonio J. Univ Extremadura Dept Technol Comp & Commun E-10071 Caceres Spain

ISBN: (纸本)9780819473042

The increasing number of airborne and satellite platforms that incorporate hyperspectral imaging spectrometers has soon created the need for efficient storage, transmission and data compression methodologies. In particular, hyperspectral data compression is expected to play a crucial role in many remote sensing applications. Many efforts have been devoted to designing and developing lossless and lossy algorithms for hyperspectral imagery. However, most available lossy compression approaches have largely overlooked the impact of mixed pixels and subpixel targets, which can be accurately modeled and uncovered by resorting to the wealth of spectral information provided by hyperspectral image data. In this paper, we develop a simple lossy compression technique which relies on the concept of spectral unmixing, one of the most popular approaches to deal with mixed pixels and subpixel targets in hyperspectral analysis. The proposed method uses a two-stage approach in which the purest spectral signatures (also called endmembers) are first extracted from the input data, and then used to express mixed pixels as linear combinations of endmembers. Analytical and experimental results are presented in the context of a real application, using hyperspectral data collected by NASA's Jet Propulsion Laboratory over the World Trade Center area in New York City, right after the terrorist attacks of September 11th. These data are used in this work to evaluate the impact of compression using different methods on spectral signature quality for accurate detection of hot spot fires. Two parallel implementations are developed for the proposed lossy compression algorithm: a multiprocessor implementation tested on Thunderhead, a massively parallel Beowulf cluster at NASA's Goddard Space Flight Center, and a hardware implementation developed on a Xilinx Virtex-ii FPGA device. Combined, these parts offer a thoughtful perspective on the potential and emerging challenges of incorporating parallel d

关键词： Hyperspectral imaging data compression parallel implementations clusters of computers field programmable gate arrays (FPGAs)

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A Transformation Framework for Communicating Multiprocessor-Tasks

A Transformation Framework for Communicating Multiprocessor-...

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16th Euromicro Conference on parallel, distributed and Network-Based processing (PDP 2008)

作者： Jorg Dummler Thomas Rauber Gudula Runger Chemnitz University of Technology Germany Angewandte Informatik II Bayreuth University Germany

parallel programming models based on a mixture of task and data parallelism have shown to be successful in addressing the increasing communication overhead of distributed memory platforms with a large number of processors. In these models, an application is decomposed into a set of parallel tasks that can run on an arbitrary number of processors. The communication between different tasks is allowed only at the start and the end of a task, thus limiting the possible communication patterns and the potential granularity of the tasks. In this paper, we consider an extended parallel programming model that additionally supports communication between running parallel tasks. We describe a specification language for applications in the new programming model and propose a transformation framework for a step-wise derivation of an executable message passing program from the specification language. The advantages of the approach are demonstrated for solution methods for ordinary differential equations.

关键词： Specification languages parallel programming Chemical technology Computer science parallel processing Message passing Processor scheduling Application software Differential equations Scalability

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Compact Ultrasound Scanner with Simultaneous parallel Channel Data Acquisition Capabilities

Compact Ultrasound Scanner with Simultaneous Parallel Channe...

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IEEE Ultrasonics Symposium

作者： Mo, L. DeBusschere, D. McLaughlin, G. Napolitano, D. Bai, W. Fowkes, K. Irish, A. Wang, X. Fowlkes, J. B. Carson, P. L. ZONARE Med Syst Inc Mountain View CA 94043 USA Univ Michigan Hlth Syst Ann Arbor MI 48109 USA

ISBN: (纸本)9781424424283

The research package for a commercially available compact ultrasound system has been significantly expanded with two major enhancements: 1) a command-and-control system from an external computer that provides support for adjustment of imaging parameter values and for acquisition of raw data for off-line processing;2) a single-zone research imaging mode that supports the receive data capture from 64 transducer channels simultaneously over multiple image frames. Two calibration studies using a 5-10 MHz linear array are presented. The first study involved pulse-echo imaging of line targets in a hypo-echoic phantom. Line spread functions of up to 4 cm depth are shown to be in good qualitative agreement with FIELD ii simulations. The second study pertained to photoacoustic imaging of a human hair fiber, using an effective 128-element receive aperture achieved by combining channel data acquired with the left and right 64-element apertures. A photoacoustic B-mode image was obtained by standard ultrasound beamforming and detection methods.

关键词： compact ultrasound channel data photoacoustic

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A neocortex model implementation on reconfigurable logic with streaming memory

A neocortex model implementation on reconfigurable logic wit...

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International Symposium on parallel and distributed processing (IPDPS)

作者： Christopher N. Vutsinas Tarek M. Taha Kenneth L. Rice Department of Electrical and Computer Engineering Clemson University Clemson SC USA

In this paper we study the acceleration of a new class of cognitive processing applications based on the structure of the neocortex. Our focus is on a model of the visual cortex used for image recognition developed by George and Hawkins. We propose techniques to accelerate the algorithm using reconfigurable logic, specifically a streaming memory architecture utilizing available off-chip memory. We discuss the design of a streaming memory access unit enabling a large number of processing elements to be placed on a single FPGA thus increasing throughput. We present an implementation of our approach on a Cray XD1 and discuss possible extension to further increase throughput. Our results indicate that using a two FPGA design with streaming memory gives a speedup of 71.9 times over a purely software implementation.

关键词： Reconfigurable logic Application software Brain modeling Field programmable gate arrays Concurrent computing Bayesian methods Computer architecture Acceleration image recognition Streaming media

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