EMULSION: transparent and flexible multiscale stochastic models in epidemiology
Stochastic mechanistic models are essential to predictive epidemiology, to better explore biological assumptions and anticipate effects of control measures on pathogen spread. Their development is usually long and iterative, involving multi-disciplinary knowledge integration. However, knowledge often becomes lost in model code, hindering late changes in assumptions and often making models appearing as black boxes to end-users. We introduce here EMULSION, an artificial intelligence-based software intended to help modellers focus on model design rather than programming. EMULSION defines a domain-specific language to make all components of an epidemiological model (structure, processes, parameters...) explicit as a structured text file. This file is readable by scientists from other fields (epidemiologists, biologists, economists), who can contribute to validate or revise assumptions at any stage of model development. It is then automatically processed by EMULSION generic simulation engine, preventing any discrepancy between model description and implementation. The modelling language and simulation architecture both rely on the combination of advanced artificial intelligence methods (knowledge representation and multi-level agent-based simulation), allowing several modelling paradigms (from compartment- to individual-based models) at several scales (up to metapopulations). The flexibility of EMULSION and its capability to support iterative modelling are illustrated here through examples of progressive complexity, including late revisions of core model assumptions. EMULSION is also currently used to model the spread of several diseases in real pathosystems (zoonoses such as Q fever or the vector-borne Rift Valley fever; or bovine respiratory diseases, with a focus on detection and treatment protocols). EMULSION provides a command-line tool for checking models, producing model diagrams, running simulations, and plotting outputs. Implemented in Python 3, EMULSION runs on Linux, MacOS, and soon Windows. It is released under Apache-2.0 license. A comprehensive documentation with installation instructions, tutorial and examples is available from: https://sourcesup.renater.fr/emulsion-public.