Interactions between Causal Structures in Graph Rewriting Systems

• Main Authors: Ioana Cristescu, Walter Fontana, Jean Krivine
• Format: Article
• Language: English
• Published: Open Publishing Association 2019-01-01
• Series: Electronic Proceedings in Theoretical Computer Science
• Online Access: http://arxiv.org/pdf/1901.00592v1

Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that explains how a system achieves a particular outcome given a set of rewrite rules. It is then useful to verify whether the mechanisms that emerge from a given model comply with empirical observations about their mutual interference. In this work, our objective is to determine whether a specific event in the mechanism for achieving X prevents or promotes the occurrence of a specific event in the mechanism for achieving Y. Such checks might also be used to hypothesize rules that would bring model mechanisms in compliance with observations. We define a rigorous framework for defining the concept of interference (positive or negative) between mechanisms induced by a system of graph-rewrite rules and for establishing whether an asserted influence can be realized given two mechanisms as an input.