Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware

机译：使用可重配置硬件加速Viterbi算法用于配置文件隐藏Markov模型

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Profile Hidden Markov Models (PHMMs) are used as a popular tool in bioinformatics for probabilistic sequence database searching. The search operation consists of computing the Viterbi score for each sequence in the database with respect to a given query PHMM. Because of the rapid growth of biological sequence databases, finding fast solutions is of highest importance to research in this area. Unfortunately, the required scan times of currently available sequential software implementations are very high. In this paper we show how reconfigurable hardware can be used as a computational platform to accelerate this application by two orders of magnitude.

机译：轮廓隐马尔可夫模型（PHMM）被用作生物信息学中用于概率序列数据库搜索的流行工具。搜索操作包括针对给定查询PHMM计算数据库中每个序列的维特比得分。由于生物序列数据库的快速增长，寻找快速解决方案对于这一领域的研究至关重要。不幸的是，当前可用的顺序软件实现所需的扫描时间非常长。在本文中，我们展示了如何将可重新配置的硬件用作计算平台，以将该应用程序加速两个数量级。

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来源
《International Conference on Computational Science(ICCS 2006) pt.1; 20060528-31; Reading(GB)》|2006年|P.522-529|共8页
会议地点 Reading(GB)
作者
Timothy F. Oliver; Bertil Schmidt; Yanto Jakop; Douglas L. Maskell;
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作者单位

School of Computer Engineering, Nanyang Technological University, Singapore 639798;

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原文格式 PDF
正文语种 eng
中图分类计算技术、计算机技术;
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专利

1. Reconfigurable Hardware Accelerator for Profile Hidden Markov Models [J] . Atef Ibrahim, Hamed Elsimary, Abdullah Aljumah, Arabian Journal for Science and Engineering. Section A, Sciences . 2016,第8期

机译：可重新配置的硬件加速器，隐藏马尔可夫模型
2. FPGA implementation of logarithmic versions of Baum-Welch and Viterbi algorithms for reduced precision hidden Markov models [J] . Pietras M., Klesk P. Bulletin of the Polish Academy of Sciences. Technical Sciences . 2017,第6期

机译：FPGA实现BAUM-WELCH和Viterbi算法的对数形式，降低精密隐马尔可夫模型
3. VITERBI ALGORITHMS FOR HIDDEN SEMI-MARKOV MODELS WITH APPLICATION TO DNA ANALYSIS [J] . Pertsinidou Christina-Elisavet, Limnios Nikolaos RAIRO Operation Research . 2015,第3期

机译：隐含半马尔可夫模型的维特比算法在DNA分析中的应用
4. Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware [C] . Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, International Conference on Computational Science pt.1 . 2006

机译：None
5. Multi-genome annotation of genome fragments using hidden Markov model profiles [D] . Menor, Mark. 2007

机译：使用隐藏的Markov模型图谱对基因组片段进行多基因组注释
6. Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training [O] . Tin Y Lam, Irmtraud M Meyer 2010

机译：使用随机期望最大化（EM）训练和Viterbi训练来训练隐马尔可夫模型参数的高效算法
7. Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware [O] . Timothy F. Oliver, Bertil Schmidt, Yanto Jakop, 2006

机译：使用可重构硬件加速概要文件隐藏马尔可夫模型的维特比算法

Accelerating the Viterbi Algorithm for Profile Hidden Markov Models Using Reconfigurable Hardware

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