Analyzing Pathways Using SAT-Based Approaches

机译：使用基于SAT的方法分析路径

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A network of reactions is a commonly used paradigm for representing knowledge about a biological process. How does one understand such generic networks and answer queries using them? In this paper, we present a novel approach based on translation of generic reaction networks to Boolean weighted MaxSAT. The Boolean weighted MaxSAT instance is generated by encoding the equilibrium configurations of a reaction network by weighted boolean clauses. The important feature of this translation is that it uses reactions, rather than the species, as the boolean variables. Existing weighted MaxSAT solvers are used to solve the generated instances and find equilibrium configurations. This method of analyzing reaction networks is generic, flexible and scales to large models of reaction networks. We present a few case studies to validate our claims.

机译：反应网络是表示生物过程知识的常用范例。如何理解此类通用网络并使用它们回答查询？在本文中，我们提出了一种基于通用反应网络到布尔加权MaxSAT转换的新颖方法。布尔加权MaxSAT实例是通过使用加权布尔子句对反应网络的平衡配置进行编码而生成的。这种翻译的重要特征是它使用反应而不是种类作为布尔变量。现有的加权MaxSAT求解器用于求解生成的实例并找到平衡配置。这种分析反应网络的方法是通用的，灵活的，并且可以扩展到反应网络的大型模型。我们提供一些案例研究来验证我们的主张。

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来源
《International Conference on Algebraic Biology(AB 2007); 20070702-04; Castle of Hagenberg(AT)》|2007年|P.155-169|共15页
会议地点 Castle of Hagenberg(AT)
作者
Ashish Tiwari; Carolyn Talcott; Merrill Knapp; Patrick Lincoln; Keith Laderoute;
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作者单位

SRI International, Menlo Park, CA 94025;

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原文格式 PDF
正文语种 eng
中图分类代数、数论、组合理论;生物工程学（生物技术）;
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机译：使用基于SAT的方法分析途径

Analyzing Pathways Using SAT-Based Approaches

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