| 训练隐马尔可夫模型的BW-GA方法 |
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| 引用本文： | 文凤春,金人超,肖枝洪. 训练隐马尔可夫模型的BW-GA方法[J]. 计算机工程与应用, 2010, 46(17): 236-238. DOI: 10.3778/j.issn.1002-8331.2010.17.067 |
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| 作者姓名： | 文凤春 金人超 肖枝洪 |
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| 作者单位： | 1.华中农业大学 理学院，武汉 430073 2.华中科技大学 计算机科学与技术学院，武汉 430074 |
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| 基金项目： | 华中农业大学学科研究交叉基金 |
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| 摘 要： | Baum-Welch算法是训练HMMs的传统方法，该方法虽然收敛速度快，但容易陷入局部最优，影响了序列比对的质量。针对该算法存在的问题，结合生物遗传与进化的规律，设计了一种将传统方法与遗传算法相结合训练HMMs的BW-GA方法。根据序列比对的需要和HMMs的结构，定义了3种遗传操作和编码方式。用19条原核5sRNA序列对模型进行了训练，用BW-GA训练模型产生序列的对数似然概率比单独用传统方法训练的要高，产生序列比对的质量较好。
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| 关 键 词： | 多序列比对 隐马尔可夫模型 遗传算法 对数似然概率 |
| 收稿时间： | 2008-12-01 |
| 修稿时间： | 2009-2-10 |
New HMMs training method based on BW-GA |
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| WEN Feng-chun,JIN Ren-chao,XIAO Zhi-hong. New HMMs training method based on BW-GA[J]. Computer Engineering and Applications, 2010, 46(17): 236-238. DOI: 10.3778/j.issn.1002-8331.2010.17.067 |
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| Authors: | WEN Feng-chun JIN Ren-chao XIAO Zhi-hong |
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| Affiliation: | 1.Department of Science，Huazhong Agricultural University，Wuhan 430073，China 2.School of Computer Science and Technology，Huazhong University of Science and Technology，Wuhan 430074，China |
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| Abstract: | Traditional method for training HMMs is Baum-Welch algorithm which is noted for the rapid convergence.However,this method can only lead to local optimization and effects quantity of sequence alignment.In response to these problems for training HMMs using Baum-Welch algorithm and integration of laws in biological genetics and evolution,a new HMMs training method based on BW-GA that combines traditional method and genetic algorithm is proposed.According to the need of genetic alignment and structure of HMMs,three genetic operations and coding methods are designed.HMMs is trained with 19 nuclear 5sRNA sequences by applying BW-GA,which makes the sequences generated have a higher log-likelihood of probability than just applying traditional methods,and a better multi-sequence alignment is generated. |
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| Keywords: | multi-sequence alignment hidden markov models genetic algorithm log likelihood probability |
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