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Ryan J Murphy

Publications and source records attributed to Ryan J Murphy.

3 recordsLinked to original sources

Adaptive therapy under parametric, structural, and measurement uncertainty

Adaptive therapy has emerged as a promising treatment strategy that exploits within-tumour competition to delay disease progression. Implementation, however, typically relies on indirect measurements of tumour burden and must account for potentially substantial patient heterogeneity. In this work, we capture patient-to-patient variability, parameter uncertainty, and imperfect biomarker measurements with a mathematical and statistical model that we calibrate to clinical prostate cancer data using a Bayesian inference framework. We use the resulting virtual cohort to demonstrate that, within the simple but now well-established Lotka-Volterra-based model, adaptive therapy robustly improves time-to-progression for the subset of patients that are predicted to eventually progress by the model. To account for other risk factors associated with larger tumour volumes, we introduce a new metric based on the risk of metastasis that demonstrates how adaptive therapy may be disadvantageous when sustained tumour burden is also considered. Given the ubiquity of uncertainty in oncology, we then describe several future modelling directions that also capture uncertainty in the temporal evolution of the underlying tumour or biomarker dynamics. Finally, we demonstrate how model misspecification and non-identifiability can lead to unreliable predictions, especially if uncertainty is inadequately captured.

q-bio.TO

A cautionary tale of model misspecification and identifiability

Mathematical models are routinely applied to interpret biological data, with common goals that include both prediction and parameter estimation. A challenge in mathematical biology, in particular, is that models are often complex and non-identifiable, while data are limited. Rectifying identifiability through simplification can seemingly yield more precise parameter estimates, albeit, as we explore in this perspective, at the potentially catastrophic cost of introducing model misspecification and poor accuracy. We demonstrate how uncertainty in model structure can be propagated through to uncertainty in parameter estimates using a semi-parametric Gaussian process approach that delineates parameters of interest from uncertainty in model terms. Specifically, we study generalised logistic growth with an unknown crowding function, and a spatially resolved process described by a partial differential equation with a time-dependent diffusivity parameter. Allowing for structural model uncertainty yields more robust and accurate parameter estimates, and a better quantification of remaining uncertainty. We conclude our perspective by discussing the connections between identifiability and model misspecification, and alternative approaches to dealing with model misspecification in mathematical biology.

stat.ME

Travelling waves in a free boundary mechanobiological model of an epithelial tissue

We consider a free boundary model of epithelial cell migration with logistic growth and nonlinear diffusion induced by mechanical interactions. Using numerical simulations, phase plane and perturbation analysis, we find and analyse travelling wave solutions with negative, zero, and positive wavespeeds. Unlike classical travelling wave solutions of reaction-diffusion equations, the travelling wave solutions that we explore have a well-defined front and are not associated with a heteroclinic orbit in the phase plane. We find leading order expressions for both the wavespeed and the density at the free boundary. Interestingly, whether the travelling wave solution invades or retreats depends only on whether the carrying capacity density corresponds to cells being in compression or extension.

nlin.PS