Inference and Uncertainty Quantification of Stochastic Gene Expression via Synthetic Models

Kaan Öcal, Michael U Gutmann, Guido Sanguinetti, Ramon Grima

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

Estimating uncertainty in model predictions is a central task in quantitative biology. Biological models at the single-cell level are intrinsically stochastic and nonlinear, creating formidable challenges for their statistical estimation which inevitably has to rely on approximations that trade accuracy for tractability. Despite intensive interest, a sweet spot in this trade off has not been found yet. We propose a flexible procedure for uncertainty quantification in a wide class of reaction networks describing stochastic gene expression including those with feedback. The method is based on creating a tractable coarse-graining of the model that is learned from simulations, a synthetic model, to approximate the likelihood function. We demonstrate that synthetic models can substantially outperform state-of-the-art approaches on a number of nontrivial systems and datasets, yielding an accurate and computationally viable solution to uncertainty quantification in stochastic models of gene expression.
Original languageEnglish
Article number20220153
Number of pages10
JournalJournal of the Royal Society. Interface
Volume19
Issue number192
DOIs
Publication statusPublished - 13 Jul 2022

Keywords / Materials (for Non-textual outputs)

  • Bayesian Inference
  • Uncertainty Quantification
  • Chemical Master Equation
  • Synthetic Likelihoods
  • Stochastic Modelling

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