Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions

TL;DR

This paper introduces a Bayesian framework with emulators for efficient global parameter searches in complex systems biology models, enabling uncertainty quantification and gene function evaluation.

Contribution

It presents a novel Bayesian emulation and history matching approach tailored for high-dimensional, complex biological models, improving parameter inference and uncertainty analysis.

Findings

Successfully applied to Arabidopsis root development models

Identified parameter sets consistent with observed data

Facilitated evaluation of gene functions in biological systems

Abstract

Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time relative to the needs of the analysis, and need to be compared to observed data. The correct analysis of such models usually requires a global parameter search, over a high dimensional parameter space, that incorporates and respects the most important sources of uncertainty. This can be an extremely difficult task, but it is essential for any meaningful inference or prediction to be made about any biological system. It hence represents a fundamental challenge for the whole of systems biology. Results: Bayesian statistical methodology for the uncertainty analysis of complex models is introduced, which is designed to address the high dimensional global parameter search problem. Bayesian emulators that mimic the systems biology model but which are extremely fast to evaluate are embedded within an iterative history match: an efficient method to search high dimensional spaces within a more formal statistical setting, while incorporating major sources of uncertainty. The approach is demonstrated via application to two models of hormonal crosstalk in Arabidopsis root development, which have 32 rate parameters, for which we identify the sets of rate parameter values that lead to acceptable matches to observed trend data. The biological consequences of the resulting comparison, including the evaluation of gene functions, are described.