Stochastic mechanistic epidemiological models largely contribute to better understand pathogen emergence and spread, and assess control strategies at various scales (from within-host to transnational scale). However, developing realistic models which involve multi-disciplinary knowledge integration faces three major challenges in predictive epidemiology: lack of readability once translated into simulation code, low reproducibility and reusability, and long development time compared to outbreak time scale. We introduce here EMULSION, an artificial intelligence-based software intended to address those issues and 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 metapopulation). 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. EMULSION provides a command-line tool for checking models, producing model diagrams, running simulations, and plotting outputs. Written in Python 3, EMULSION runs on Linux, MacOS, and Windows. It is released under Apache-2.0 license. A comprehensive documentation with installation instructions, a tutorial and many examples are available from: https://sourcesup.renater.fr/www/emulsion-public.

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In order to recommend better control measures in public or animal health, epidemiologists incorporate ever-finer details in their models, from individual diversity to public policies, which often involve several observation scales. Due to the variety of modelling paradigms, it becomes more and more difficult to compare hypotheses and outcomes, all the more that the increased complexity of simulation programs is not yet counterbalanced by design principles nor by software engineering methods. We propose in this paper to use the multi-level agent-based paradigm to integrate existing methods within a common interface, provide a separation between concerns and reduce the part of code devoted to model designers. We illustrate our approach with an application to the Q fever disease in cattle.

The development of computational sciences has fostered major advances in life sciences, but also led to reproducibility and reliability issues, which become a crucial stake when simulations are aimed at assessing control measures, as in epidemiology. A broad use of software development methods is a useful remediation to reduce those problems, but preventive approaches, targeting not only implementation but also model design, are essential to sustainable enhancements. Among them, AI techniques, based on the separation between declarative and procedural concerns, and on knowledge engineering, offer promising solutions. Especially, multilevel multi-agent systems, deeply rooted in that culture, provide a generic way to integrate several epidemiological modeling paradigms within a homogeneous interface. We explain in this paper how this approach is used for building more generic, reliable and sustainable simulations, illustrated by real-case applications in cattle epidemiology.