论文标题
参数布尔网络的平行一步控制
Parallel One-Step Control of Parametrised Boolean Networks
论文作者
论文摘要
布尔网络(BN)是一个简单的模型,用于研究生物系统的复杂动态行为。但是,可能很难收集足够的数据来精确地将生物系统的行为捕获到一组布尔功能中。可以使用参数化的布尔网络(PARBN)在某种程度上解决这些问题,因为它允许未指定的一些更新功能。在本文中,我们攻击具有异步语义的PARBN的控制问题。尽管在没有参数的情况下控制BNS有一项大量工作,但实际上尚未解决PARBNS控制问题。控制的目的是确保使用尽可能少的干预措施在给定状态下稳定系统。有很多方法可以控制BN动态。在这里,我们考虑了系统即时将系统扰动的一步方法。处理对PARBN的控制的天真方法是使用参数扫描,并使用已知的非批准BNS分别解决每个参数估值的控制问题。但是,随着PARBNS的参数空间在最坏情况下呈双重增长,这种方法效率很高。在本文中,我们为PARBNS的一步控制问题提出了一种新型的半符号算法,该算法建立在符号数据结构上,以避免扫描单个参数。我们评估了在实际生物学模型上的方法的性能。
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems. Nonetheless, it might be difficult to gather enough data to precisely capture the behavior of a biological system into a set of Boolean functions. These issues can be dealt with to some extent using parametrised Boolean networks (ParBNs), as it allows to leave some update functions unspecified. In this paper, we attack the control problem for ParBNs with asynchronous semantics. While there is an extensive work on controlling BNs without parameters, the problem of control for ParBNs has not been in fact addressed yet. The goal of control is to ensure the stabilisation of a system in a given state using as few interventions as possible. There are many ways to control BN dynamics. Here, we consider the one-step approach in which the system is instantaneously perturbed out of its actual state. A naive approach to handle control of ParBNs is using parameter scan and solve the control problem for each parameter valuation separately using known techniques for non-parametrised BNs. This approach is however highly inefficient as the parameter space of ParBNs grows doubly-exponentially in the worst case. In this paper, we propose a novel semi-symbolic algorithm for the one-step control problem of ParBNs, that builds on a symbolic data structures to avoid scanning individual parameters. We evaluate the performance of our approach on real biological models.