Syntax-Guided Optimal Synthesis for Chemical Reaction Networks

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216305%3A26230%2F17%3APU127274" target="_blank" >RIV/00216305:26230/17:PU127274 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1007/978-3-319-63390-9_20" target="_blank" >http://dx.doi.org/10.1007/978-3-319-63390-9_20</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/978-3-319-63390-9_20" target="_blank" >10.1007/978-3-319-63390-9_20</a>

Result language

angličtina

Original language name

Syntax-Guided Optimal Synthesis for Chemical Reaction Networks

Original language description

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.

Czech name

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Czech description

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Type

D - Article in proceedings

CEP classification

—

OECD FORD branch

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project

<a href="/en/project/GA16-17538S" target="_blank" >GA16-17538S: Relaxed equivalence checking for approximate computing</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Article name in the collection

Proceedings of the 29th International Conference on Computer Aided Verification

ISBN

978-3-319-63390-9

ISSN

—

e-ISSN

—

Number of pages

20

Pages from-to

375-395

Publisher name

Springer Verlag

Place of publication

Heidelberg

Event location

Heidelberg

Event date

May 2, 2017

Type of event by nationality

WRD - Celosvětová akce

UT code for WoS article

000431900900020