Accelerating Computation of DCM for ERP in MATLAB by External Function Calls to the GPU

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Title:	Accelerating Computation of DCM for ERP in MATLAB by External Function Calls to the GPU
Authors:	王尉任;Wang, Wei-Jen;Hsieh, I-Fan;Chen, Chun-Chuan
Contributors:	資訊電機學院資訊工程學系
Keywords:	Algorithms;Biology;Biomedical engineering;Combinatorial analysis;Complexity;Computer Graphics;Computer programming;Computer Science;Computer Simulation;Computing time;Constraint modelling;Electroencephalography;Event-related potentials;Evoked Potentials;Experimental data;Graphics processing units;Hardware;Hypotheses;Iterative methods;Matlab;Medicine;Memory;Models, Statistical;Neural networks;Optimization;Parallel processing;Performance enhancement;Registration;Software;Synthetic data;Therapeutic applications
Date:	2013-06-26
Issue Date:	2026-04-23 13:12:33 (UTC+8)
Publisher:	Public Library of Science;United States: Public Library of Science
Abstract:	摘要： This study aims to improve the performance of Dynamic Causal Modelling for Event Related Potentials (DCM for ERP) in MATLAB by using external function calls to a graphics processing unit (GPU). DCM for ERP is an advanced method for studying neuronal effective connectivity. DCM utilizes an iterative procedure, the expectation maximization (EM) algorithm, to find the optimal parameters given a set of observations and the underlying probability model. As the EM algorithm is computationally demanding and the analysis faces possible combinatorial explosion of models to be tested, we propose a parallel computing scheme using the GPU to achieve a fast estimation of DCM for ERP. The computation of DCM for ERP is dynamically partitioned and distributed to threads for parallel processing, according to the DCM model complexity and the hardware constraints. The performance efficiency of this hardware-dependent thread arrangement strategy was evaluated using the synthetic data. The experimental data were used to validate the accuracy of the proposed computing scheme and quantify the time saving in practice. The simulation results show that the proposed scheme can accelerate the computation by a factor of 155 for the parallel part. For experimental data, the speedup factor is about 7 per model on average, depending on the model complexity and the data. This GPU-based implementation of DCM for ERP gives qualitatively the same results as the original MATLAB implementation does at the group level analysis. In conclusion, we believe that the proposed GPU-based implementation is very useful for users as a fast screen tool to select the most likely model and may provide implementation guidance for possible future clinical applications such as online diagnosis. 其他題名： PLoS One 出版者： United States: Public Library of Science 出版日期： 2013-06-26 出處： PloS one, 2013-06, Vol.8 (6), p.e66599 資源來源： DOAJ Directory of Open Access Journals (WRLC) 版權： COPYRIGHT 2013 Public Library of Science 版權： 2013 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 版權： 2013 Wang et al 2013 Wang et al 識別號： ISSN: 1932-6203 識別號： EISSN: 1932-6203 識別號： DOI: 10.1371/journal.pone.0066599 識別號： PMID: 23840507
Appears in Collections:	[Department of Computer Science and information Engineering] journal & Dissertation

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