Symbolic computation of differential equivalences

Luca Cardelli, Mirco Tribastone, Max Tschaikowski, Andrea Vandin

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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 highlevel 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 highlevel 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. With a prototype implementation we are able to detect equivalences in biochemical models from the literature that cannot be reduced using competing automatic techniques.

Original languageEnglish
JournalACM SIGPLAN Notices
Volume51
Issue number1
Pages (from-to)137-150
Number of pages14
ISSN1523-2867
DOIs
Publication statusPublished - 8 Apr 2016
Externally publishedYes

Keywords

  • Ordinary differential equations
  • Partition refinement
  • Quantitative equivalence relations
  • Satisfiability modulo theory

Cite this