Inference of gene regulatory networks using s-system and differential evolution
Inference of gene regulatory networks using s-system and differential evolution
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DOI：
10.1145/1068009.1068079
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发表时间：
2005-06
期刊：
影响因子：
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通讯作者：
N. Noman;H. Iba
中科院分区：
文献类型：
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作者：
N. Noman;H. Iba
在这项工作中，我们提出了一种改进的进化方法来推断基因表达的时间序列数据的遗传网络的S-系统模型。我们采用差分进化（DE）来优化网络参数，以捕获基因表达数据中的动态。在一个初步的调查，我们确定适合DE的多模态和强非线性问题，如基因网络估计。提出了一种扩展的适应度函数，用于获得生物网络的稀疏结构。为了更准确地估计参数值，还建议了优化过程的增强。在遗传网络上使用不同数量的人工创建的时间序列数据进行实验，证明了所提出的方法的有效性。
In this work we present an improved evolutionary method for inferring S-system model of genetic networks from the time series data of gene expression. We employed Differential Evolution (DE) for optimizing the network parameters to capture the dynamics in gene expression data. In a preliminary investigation we ascertain the suitability of DE for a multimodal and strongly non-linear problem like gene network estimation. An extension of the fitness function for attaining the sparse structure of biological networks has been proposed. For estimating the parameter values more accurately an enhancement of the optimization procedure has been also suggested. The effectiveness of the proposed method was justified performing experiments on a genetic network using different numbers of artificially created time series data.