Egac

Abstract

Discovering relations between chemical reaction networks (CRNs) is a relevant problem in computational systems biology for model reduction, to explain if a given system can be seen as an abstraction of another one; and for model comparison, useful to establish an evolutionary path from simpler networks to more complex ones. This is also related to foundational issues in computer science regarding program equivalence, in light of the established interpretation of a CRN as a kernel programming language for concurrency. Criteria for deciding if two CRNs can be formally related have been recently developed, but these require that a candidate mapping be provided. Automatically finding candidate mappings is very hard in general since the search space essentially consists of all possible partitions of a set. In this paper we tackle this problem by developing a genetic algorithm for a class of CRNs called influence networks, which can be used to model a variety of biological systems including cell-cycle switches and gene networks. An extensive numerical evaluation shows that our approach can successfully establish relations between influence networks from the literature which cannot be found by exact algorithms due to their large computational requirements.

Language-based Abstractions for Dynamical Systems

“…Our own line of research [21,56,18,20,65,19,17,38] consists of a computer-science perspective to the abstraction problem, borrowing ideas from the concurrency theory community. We recast the ODE reduction problem to that of finding an appropriate equivalence relation over ODE variables, akin to classical models of computation based on labelled transition systems.…”

“…This paper briefly reviews our framework for ODE reduction. A more detailed tutorial-like presentation unifying the two approaches can be found in [65], while [18,56] address the more general problem of computing all differential equivalences of a model.…”