Self-organizing map approaches for the haplotype assembly problem
文献类型：期刊论文
| 作者 | Wu, Ling-Yun1 ; Li, Zhenping2; Wang, Rui-Sheng3; Zhang, Xiang-Sun1; Chen, Luonan4
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| 刊名 | MATHEMATICS AND COMPUTERS IN SIMULATION
 |
| 出版日期 | 2009-06-01 |
| 卷号 | 79期号:10页码:3026-3037 |
| 关键词 | SNP Haplotype assembly Minimum error correction Self-organizing maps Neural network |
| ISSN号 | 0378-4754 |
| DOI | 10.1016/j.matcom.2009.01.021 |
| 英文摘要 | Haplotype assembly is to reconstruct a pair of haplotypes from SNP values observed in a set of individual DNA fragments. In this paper, we focus on studying minimum error correction (MEC) model for the haplotype assembly problem and explore self-organizing map (SOM) methods for this problem. Specifically, haplotype assembly by MEC is formulated into an integer linear programming model. Since the MEC problem is NP-hard and thus cannot be solved exactly within acceptable running time for large-scale instances, we investigate the ability of classical SOMs to solve the haplotype assembly problem with MEC model. Then, aiming to overcome the limits of classical SOW a novel SOM approach is proposed for the problem. Extensive computational experiments on both synthesized and real datasets show that the new SOM-based algorithm can efficiently reconstruct haplotype pairs in a very high accuracy under realistic parameter settings. Comparison with previous methods also confirms the superior performance of the new SOM approach. (C) 2009 IMACS. Published by Elsevier B.V. All rights reserved. |
| 资助项目 | Academic Human Resources Development in Institutions of Higher Learning ; National Natural Science Foundation of China[10631070] ; National Natural Science Foundation of China[60503004] ; National Natural Science Foundation of China[60873205] ; Foundation of Beijing Wuzi University ; Beijing Natural Science Foundation[1092011] ; JSPS-NSFC Scientific Cooperation Program[10711140116] |
| WOS研究方向 | Computer Science ; Mathematics |
| 语种 | 英语 |
| WOS记录号 | WOS:000267312200005 |
| 出版者 | ELSEVIER SCIENCE BV |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/7910]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Zhang, Xiang-Sun |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, Beijing 100080, Peoples R China 2.Beijing Wuzi Univ, Sch Informat, Beijing 101149, Peoples R China 3.Renmin Univ China, Dept Math, Beijing 100872, Peoples R China 4.Osaka Sangyo Univ, Dept Elect Engn & Elect, Osaka 5748530, Japan |
| 推荐引用方式 GB/T 7714 | Wu, Ling-Yun,Li, Zhenping,Wang, Rui-Sheng,et al. Self-organizing map approaches for the haplotype assembly problem[J]. MATHEMATICS AND COMPUTERS IN SIMULATION,2009,79(10):3026-3037. |
| APA | Wu, Ling-Yun,Li, Zhenping,Wang, Rui-Sheng,Zhang, Xiang-Sun,&Chen, Luonan.(2009).Self-organizing map approaches for the haplotype assembly problem.MATHEMATICS AND COMPUTERS IN SIMULATION,79(10),3026-3037. |
| MLA | Wu, Ling-Yun,et al."Self-organizing map approaches for the haplotype assembly problem".MATHEMATICS AND COMPUTERS IN SIMULATION 79.10(2009):3026-3037. |
入库方式： OAI收割
来源：数学与系统科学研究院
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