论文标题

生物医学和神经科学的计算逻辑

Computational Logic for Biomedicine and Neurosciences

论文作者

de Maria, Elisabetta, Despeyroux, Joelle, Felty, Amy, Liò, Pietro, Olarte, Carlos, Bahrami, Abdorrahim

论文摘要

我们在这里提倡将计算逻辑用于系统生物学,作为一个\ emph {unified and Safe}框架,非常适合对生物系统的动态行为进行建模,表达其特性并验证这些属性。潜在的候选逻辑应具有传统的证明理论谱系(包括归纳或依次的微积分表现,享有切割和专注力),并应配备经过认证的证明工具。除了提供可靠的框架之外,这还允许我们生物系统的正确编码。对于系统生物学的百分比,尤其是生物医学,到目前为止,对于建模部分,三个候选逻辑:全部基于线性逻辑。所研究的特性及其证明是在非常表达的(非线性)电感逻辑中形式化的:电感构造的计算(CIC)。到目前为止,我们考虑过的示例相对简单。但是,所有这些都在COQ系统中带有正式的半自动证明,该证明实现了CIC。在神经科学中,我们直接使用CIC和COQ来对神经元和一些简单的神经元电路进行建模,并证明其某些动态特性。 %在生物医学中,多膜途径相互作用的研究以及临床和电子健康记录数据应有助于药物发现和疾病诊断。未来的工作包括使用更多的自动侵略。这应该使我们能够指定和研究更现实的例子,从长远来看,以提供疾病诊断和治疗预后的系统。

We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The potential candidate logics should have a traditional proof theoretic pedigree (including either induction, or a sequent calculus presentation enjoying cut-elimination and focusing), and should come with certified proof tools. Beyond providing a reliable framework, this allows the correct encodings of our biological systems. % For systems biology in general and biomedicine in particular, we have so far, for the modeling part, three candidate logics: all based on linear logic. The studied properties and their proofs are formalized in a very expressive (non linear) inductive logic: the Calculus of Inductive Constructions (CIC). The examples we have considered so far are relatively simple ones; however, all coming with formal semi-automatic proofs in the Coq system, which implements CIC. In neuroscience, we are directly using CIC and Coq, to model neurons and some simple neuronal circuits and prove some of their dynamic properties. % In biomedicine, the study of multi omic pathway interactions, together with clinical and electronic health record data should help in drug discovery and disease diagnosis. Future work includes using more automatic provers. This should enable us to specify and study more realistic examples, and in the long term to provide a system for disease diagnosis and therapy prognosis.

扫码加入交流群

加入微信交流群

微信交流群二维码

扫码加入学术交流群,获取更多资源