Model-Checking Signal Transduction Networks through Decreasing Reachability Sets
Model-Checking Signal Transduction Networks through Decreasing Reachability Sets
复制标题
通过减少可达性集对信号传导网络进行模型检查
DOI：
--
复制
发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Qinsi Wang
中科院分区：
文献类型：
--
作者：
Koen Claessen;J. Fisher;Samin S. Ishtiaq;Nir Piterman;Qinsi Wang
我们考虑定性网络的模型检查，这是生物学中信号转导网络建模的一种流行的形式。由于缺乏初始状态，定性网络的一个独特特征是“减少可达集”。简单地说，在i步之后未访问的状态将不会在每i步之后访问i步。我们使用这个特征来创建一个特定结构的定性网络的所有路径的紧凑表示。将这种紧凑的路径表示与LTL模型检查相结合，可以显著提高性能。特别是，对于最近的白血病模型，我们的方法比标准方法至少快5倍，在某些情况下快100倍。我们的方法增强了生物学家使用的迭代假设驱动的实验过程，使可执行的生物模型快速周转。
We consider model checking of Qualitative Networks, a popular formalism for modeling signal transduction networks in biology. One of the unique features of qualitative networks, due to them lacking initial states, is that of "reducing reachability sets". Simply put, a state that is not visited after i steps will not be visited after i′ steps for every i′>i. We use this feature to create a compact representation of all the paths of a qualitative network of a certain structure. Combining this compact path representation with LTL model checking leads to significant acceleration in performance. In particular, for a recent model of Leukemia, our approach works at least 5 times faster than the standard approach and up to 100 times faster in some cases. Our approach enhances the iterative hypothesis-driven experimentation process used by biologists, enabling fast turn-around of executable biological models.
影响因子：
1.1
作者：
Heath, John;Kwiatkowska, Marta;Tymchyshyn, Oksana
通讯作者：
Tymchyshyn, Oksana