Rule-based epidemic models

This paper gives an introduction to rule-based modelling applied to topics in infectious diseases. Rule-based models generalise reaction-based models with reagents that have internal state and may be bound together to form complexes, as in chemistry. Rule-based modelling is directly transferable from molecular biology to epidemiology and allows us to express a broad class of models for processes of interest in epidemiology that would not otherwise be feasible in compartmental models. This includes dynamics commonly found in compartmental models such as the spread of a virus from an infectious to a susceptible population, and more complex dynamics outside the typical scope of such models such as social behaviours and decision-making, testing capacity constraints, and tracing of people exposed to a virus but not yet symptomatic. We propose that such dynamics are well-captured with rule-based models, and that doing so combines intuitiveness and transparency of representation with scalability and compositionality. We demonstrate this feasibility of our approach using a suite of seven models to describe a spread of infectious diseases under different scenarios: wearing masks, infection via fomites and prevention by hand-washing, the concept of vector-borne diseases, testing and contact tracing interventions, disease propagation within motif-structured populations with shared environments such as schools, and superspreading events. The machine-readable description of these models corresponds closely to the mathematical description and also functions as a human-readable format so that one knows readily "what is in the model".