Analyzing Pathways Using SAT-Based Approaches
Analyzing Pathways Using SAT-Based Approaches
复制标题
使用基于 SAT 的方法分析路径
DOI：
10.1007/978-3-540-73433-8_12
复制
发表时间：
2007
影响因子：
3
通讯作者：
K. Laderoute
中科院分区：
文献类型：
--
作者：
A. Tiwari;C. Talcott;M. Knapp;P. Lincoln;K. Laderoute
反应网络是表示生物过程知识的常用范例。如何理解这种通用网络并使用它们回答查询？在本文中，我们提出了一种新的方法的基础上翻译的通用反应网络布尔加权MaxSAT。布尔加权MaxSAT实例通过对反应网络的平衡构型进行加权布尔子句编码而生成。这种转换的重要特征是它使用反应而不是物种作为布尔变量。现有的加权MaxSAT求解器用于解决生成的实例，并找到平衡配置。该方法具有通用性、灵活性和可扩展性，适用于大型反应网络模型。我们提出了一些案例研究来验证我们的主张。
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.