Symbolic computation of differential equivalences

Journal article

Ordinary differential equations (ODEs) are widespread in many natural sciences including chemistry, ecology, and systems biology, and in disciplines such as control theory and electrical engineering. Building on the celebrated molecules-as-processes paradigm, they have become increasingly popular in computer science, with high-level languages and formal methods such as Petri nets, process algebra, and rule-based systems that are interpreted as ODEs.

We consider the problem of comparing and minimizing ODEs automatically. Influenced by traditional approaches in the theory of programming, we propose differential equivalence relations. We study them for a basic intermediate language, for which we have decidability results, that can be targeted by a class of high-level specifications. An ODE implicitly represents an uncountable state space, hence reasoning techniques cannot be borrowed from established domains such as probabilistic programs with finite-state Markov chain semantics. We provide novel symbolic procedures to check an equivalence and compute the largest one via partition refinement algorithms that use satisfiability modulo theories.

We illustrate the generality of our framework by showing that differential equivalences include (i) well-known notions for the minimization of continuous-time Markov chains (lumpability), (ii) bisimulations for chemical reaction networks recently proposed by Cardelli et al., and (iii) behavioral relations for process algebra with ODE semantics. Using ERODE, the tool that implements our techniques, we are able to detect equivalences in biochemical models from the literature that cannot be reduced using competing automatic techniques.

Authors: Cardelli, L; Tribastone, M; Tschaikowski, M; Vandin, A

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Elsevier
• Journal: Theoretical Computer Science
• Volume: 777
• Pages: 132-154
• Publication date: 2019-03-18
• Acceptance date: 2019-03-09
• DOI: 10.1016/j.tcs.2019.03.018
• ISSN: 0304-3975
• Language: English
• Keywords: quantitative equivalence relations; partition refinement; satisfiability modulo theory; ordinary differential equations