Publication detail

Syntax-Guided Optimal Synthesis for Chemical Reaction Networks

ČEŠKA, M. CARDELLI, L. FRANZLE, M. KWIATKOWSKA, M. LAURENTI, L. PAOLETTI, N. WHITBY, M.

Original Title

Syntax-Guided Optimal Synthesis for Chemical Reaction Networks

Type

conference paper

Language

English

Original Abstract

We study the problem of optimal syntax-guided synthesis of stochastic Chemical Reaction Networks (CRNs) that plays a fundamental role in design automation of molecular devices and in the construction of predictive biochemical models. We propose a sketching language for CRNs that concisely captures syntactic constraints on the network topology and allows its under-specification. Given a sketch, a correctness specification, and a cost function defined over the CRN syntax, our goal is to find a CRN that simultaneously meets the constraints, satisfies the specification and minimizes the cost function. To ensure computational feasibility of the synthesis process, we employ the Linear Noise Approximation allowing us to encode the synthesis problem as a satisfiability modulo theories problem over a set of parametric Ordinary Differential Equations (ODEs). We design and implement a novel algorithm for the optimal synthesis of CRNs that employs almost complete refutation procedure for SMT over reals and ODEs, and exploits a meta-sketching abstraction controlling the search strategy.  Through relevant case studies we demonstrate that our approach significantly improves the capability of existing methods for synthesis of biochemical systems and paves the way towards their automated and provably-correct design.

Keywords

chemical reaction network design automation optimal synthesis Linear Noise Approximation SMT solvers temporal logic  

Authors

ČEŠKA, M.; CARDELLI, L.; FRANZLE, M.; KWIATKOWSKA, M.; LAURENTI, L.; PAOLETTI, N.; WHITBY, M.

Released

2. 5. 2017

Publisher

Springer Verlag

Location

Heidelberg

ISBN

978-3-319-63390-9

Book

Proceedings of the 29th International Conference on Computer Aided Verification

Edition

Lecture Notes in Computer Science

Pages from

375

Pages to

395

Pages count

20

BibTex

@inproceedings{BUT146260,
  author="Milan {Češka} and Luca {Cardelli} and Martin {Franzle} and Marta {Kwiatkowska} and Luca {Laurenti} and Nicola {Paoletti} and Max {Whitby}",
  title="Syntax-Guided Optimal Synthesis for Chemical Reaction Networks",
  booktitle="Proceedings of the 29th International Conference on Computer Aided Verification",
  year="2017",
  series="Lecture Notes in Computer Science",
  volume="10427",
  pages="375--395",
  publisher="Springer Verlag",
  address="Heidelberg",
  doi="10.1007/978-3-319-63390-9\{_}20",
  isbn="978-3-319-63390-9"
}