Efficient parametric inference for stochastic biological systems with measured variability

DOI10.1515/SAGMB-2013-0061zbMATH Open1296.92042arXiv1403.8057OpenAlexW2964335983WikidataQ51088040 ScholiaQ51088040MaRDI QIDQ461689FDOQ461689

Authors: Iain G. Johnston 

Publication date: 13 October 2014

Published in: Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Abstract: Stochastic systems in biology often exhibit substantial variability within and between cells. This variability, as well as having dramatic functional consequences, provides information about the underlying details of the system's behaviour. It is often desirable to infer properties of the parameters governing such systems given experimental observations of the mean and variance of observed quantities. In some circumstances, analytic forms for the likelihood of these observations allow very efficient inference: we present these forms and demonstrate their usage. When likelihood functions are unavailable or difficult to calculate, we show that an implementation of approximate Bayesian computation (ABC) is a powerful tool for parametric inference in these systems. However, the calculations required to apply ABC to these systems can also be computationally expensive, relying on repeated stochastic simulations. We propose an ABC approach that cheaply eliminates unimportant regions of parameter space, by addressing computationally simple mean behaviour before explicitly simulating the more computationally demanding variance behaviour. We show that this approach leads to a substantial increase in speed when applied to synthetic and experimental datasets.

Full work available at URL: https://arxiv.org/abs/1403.8057

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zbMATH Keywords

approximate Bayesian computationparametric inferencecellular noise

Mathematics Subject Classification ID

General biostatistics (92B15)

Cites Work

• Sequential Monte Carlo without likelihoods
• Approximate Bayesian computational methods
• Title not available (Why is that?)
• Stochastic modelling for systems biology.
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Cited In (7)

• Accounting for extrinsic variability in the estimation of stochastic rate constants
• Quantum parameter estimation via dispersive measurement in circuit QED
• Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models
• Slight parameter changes detection in biological models: a multiresolution approach
• Inferring stochastic rates from heterogeneous snapshots of particle positions
• Stochastic models for evolving cellular populations of mitochondria: disease, development, and ageing
• Parallelized Parameter Estimation of Biological Pathway Models

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