Compositional Analysis of Homeostasis of Gene Networks by Clustering Algorithms
Compositional Analysis of Homeostasis of Gene Networks by Clustering Algorithms
复制标题
DOI：
10.1007/978-3-319-94806-5_11
复制
发表时间：
2017-02
期刊：
影响因子：
--
通讯作者：
S. Ito;K. Osari;Shigeki Hagihara;N. Yonezaki
中科院分区：
文献类型：
--
作者：
S. Ito;K. Osari;Shigeki Hagihara;N. Yonezaki
在这项工作中，我们提出了一种成分方法来定性地分析基因网络的动态平衡。分析基因网络的动态平衡的问题在网络规格的大小中是完全的。由于问题的高度复杂性，只成功地分析了由几个基因组成的小网络。由于基因网络的动态平衡分析是基于线性时态逻辑公式的可实现性检验技术，因此我们可以应用一种组合算法来减轻可实现性问题的计算难度。为此，我们开发了一种聚类算法，以将网络规范划分为合适的大小，以利用组合算法。我们报告了用我们提出的方法对几个基因网络进行动态平衡分析的实验结果。我们的实验显示了相当大的改进，特别是在分析较大的网络时。
In this work we present a compositional approach to qualitatively analyse homeostasis of gene networks. The problem of analysing homeostasis of gene networks is 2EXPTIME-complete in the sizes of the network specifications. Due to this high complexity of the problem, only small networks consisting of a few genes were successfully analysed. Since the analysis of homeostasis of gene networks is based on the technique ofrealisabilitychecking of Linear Temporal Logic formulae, we can apply a compositional algorithm devised to mitigate the computational difficulty in realisability problems. For this, we develop a clustering algorithm to divide network specifications in suitable sizes to utilise the compositional algorithm. We report the experimental results of analyses of homeostasis of several gene networks with our proposed method. Our experiments show a fair improvement especially in the analyses of larger networks.