Reliable and efficient parameter estimation using approximate continuum limit descriptions of stochastic models

Abstract

Stochastic individual-based mathematical models are attractive for modelling biological phenomena because they naturally capture the stochasticity and variability that is often evident in biological data. Such models also allow us to track the motion of individuals within the population of interest. Unfortunately, capturing this microscopic detail means that simulation and parameter inference can become computationally expensive. One approach for overcoming this computational limitation is to coarse-grain the stochastic model to provide an approximate continuum model that can be solved using far less computational effort. However, coarse-grained continuum models can be biased or inaccurate, particularly for certain parameter regimes. In this work, we combine stochastic and continuum mathematical models in the context of lattice-based models of two-dimensional cell biology experiments by demonstrating how to simulate two commonly used experiments: cell proliferation assays and barrier assays. Our approach involves building a simple statistical model of the discrepancy between the expensive stochastic model and the associated computationally inexpensive coarse-grained continuum model. We form this statistical model based on a limited number of expensive stochastic model evaluations at design points sampled from a user-chosen distribution, corresponding to a computer experiment design problem. With straightforward design point selection schemes, we show that using the statistical model of the discrepancy in tandem with the computationally inexpensive continuum model allows us to carry out prediction and inference while correcting for biases and inaccuracies due to the continuum approximation. We demonstrate this approach by simulating a proliferation assay, where the continuum limit model is the well-known logistic ordinary differential equation, as well as a barrier assay where the continuum limit model is closely related to the well-known Fisher-KPP partial differential equation. We construct an approximate likelihood function for parameter inference, both with and without discrepancy correction terms. Using maximum likelihood estimation, we provide point estimates of the unknown parameters, and use the profile likelihood to characterise the uncertainty in these estimates and form approximate confidence intervals. For the range of inference problems considered, working with the continuum limit model alone leads to biased parameter estimation and confidence intervals with poor coverage. In contrast, incorporating correction terms arising from the statistical model of the model discrepancy allows us to recover the parameters accurately with minimal computational overhead. The main tradeoff is that the associated confidence intervals are typically broader, reflecting the additional uncertainty introduced by the approximation process. All algorithms required to replicate the results in this work are written in the open source Julia language and are available at GitHub.