Efficient finite-difference method for computing sensitivities of biochemical reactions

Research output: Contribution to journalArticleScientificpeer-review

Researchers

Research units

  • University of Trento
  • University of Pisa

Abstract

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking stochastic noise into account. This paper proposes a new finite-difference method for efficiently computing sensitivities of biochemical reactions. We employ propensity bounds of reactions to couple the simulation of the nominal and perturbed processes. The exactness of the simulation is preserved by applying the rejection-based mechanism. For each simulation step, the nominal and perturbed processes under our coupling strategy are synchronized and often jump together, increasing their positive correlation and hence reducing the variance of the estimator. The distinctive feature of our approach in comparison with existing coupling approaches is that it only needs to maintain a single data structure storing propensity bounds of reactions during the simulation of the nominal and perturbed processes. Our approach allows to compute sensitivities of many reaction rates simultaneously. Moreover, the data structure does not require to be updated frequently, hence improving the computational cost. This feature is especially useful when applied to large reaction networks. We benchmark our method on biological reaction models to prove its applicability and efficiency.

Details

Original languageEnglish
Pages (from-to)1-20
JournalProceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences
Volume474
Issue number2218
Publication statusPublished - 1 Oct 2018
MoE publication typeA1 Journal article-refereed

    Research areas

  • Finite-difference sensitivity analysis, Rejection-based simulation, Stochastic simulation

ID: 30099127