Improved Approach for Haplotype Inference Based on Markov Chain

机译：基于马尔可夫链的单倍型推理的改进方法

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Variable-order Markov model (VMM) is an important statistical method for haplotype inference problem. It is well-suited for sparse marker maps and large-scale data. The existing algorithm, HaploRec, solves VMM by a greedy algorithm with pruning strategy. We present an improved Expectation-Maximization (EM) algorithm for VMM, which is based on dynamic programming (DP). The computational experimental results with simulated and real data show that the proposed algorithm can greatly improve the accuracy of VMM with an acceptable running time.The methods described in this paper are implemented in a software package, HMC, which is available from the internet.

机译：变阶马尔可夫模型（VMM）是单倍型推断问题的重要统计方法。它非常适合稀疏标记图和大规模数据。现有的算法HaploRec通过带有修剪策略的贪婪算法来求解VMM。我们为VMM提出了一种改进的期望最大化（EM）算法，该算法基于动态编程（DP）。模拟和真实数据的计算实验结果表明，所提出的算法可以在可接受的运行时间下极大地提高VMM的精度。本文描述的方法在HMC软件包中实现，可从Internet上获得。

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《Optimization and Systems Biology》|2008年|212-223|共12页
会议地点 Lijiang(CN);Lijiang(CN)
作者
DO Q.V.; rnMEBARKI A.; rnHECK J.V.; rnSAADA R.AMI;
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作者单位

Ling-Yun Wu@Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China--Ji-Hong Zhang@School of International Business, Beijing Foreign Studies University, Beijing 100089, China--Raymond Chan@Department of Mathematics, Chinese University of Hong Kong, Hong Kong--;

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正文语种 eng
中图分类生物工程学（生物技术）;
关键词
Haplotype Inference; SNP; Markov Chain; Dynamic Programming;

机译：单倍型推断； SNP；马尔可夫链；动态规划;

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1. Bounding inferences for large-scale continuous-time Markov chains: A new approach based on lumping and imprecise Markov chains [J] . Erreygers Alexander, De Bock Jasper 高分子論文集 . 2019,第Deca期

机译：大规模连续时间马尔可夫链的边界推论：一种基于集总和不精确马尔可夫链的新方法
2. Bayesian Inference with Markov Chain Monte Carlo-Based Numerical Approach for Input Model Updating [J] . Wu Lingzi, Ji Wenying, AbouRizk Simaan M. Journal of Computing in Civil Engineering . 2020,第1期

机译：基于马尔可夫链蒙特卡罗的贝叶斯推断数值模型更新
3. Haplotype inference based on Hidden Markov Models in the QTL-MAS 2010 multi-generational dataset [J] . Carl Nettelblad BMC proceedings. . 2011,第S3期

机译：QTL-MAS 2010多代数据集中基于隐马尔可夫模型的单倍型推断
4. Improved Approach for Haplotype Inference Based on Markov Chain [C] . Ling-Yun Wu, Ji-Hong Zhang, Raymond Chan International Symposium on Optimization and Systems Biology . 2008

机译：基于马尔可夫链的单倍型推理的改进方法
5. Haplotype inference using a hidden Markov model with efficient Markov chain sampling. [D] . Sun, Shuying. 2007

机译：使用具有有效马尔可夫链采样的隐藏马尔可夫模型的单倍型推断。
6. A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns [O] . Jihua Wu, Guo-Bo Chen, Degui Zhi, 2014

机译：使用确定的单倍型和单倍型模式对聚类基因的当前数据进行单倍型推断的隐马尔可夫模型
7. Improved Approach for Haplotype Inference Based on Markov Chain ∗ [O] . Ling-yun Wu, Ji-hong Zhang Raymond Chan 2008

机译：基于马尔可夫链*的单倍型推理的改进方法

Improved Approach for Haplotype Inference Based on Markov Chain

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