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bioRxiv · 10.1101/2023.09.03.555060

Leveraging artificial intelligence and software engineering methods in epidemiology for the co-creation of decision-support tools based on mechanistic models

Picault, S.·Niang, G.·Sicard, V.·Sorin-Dupont, B.·Assie, S.·Ezanno, P.
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Abstract

Epidemiological modelling is a key lever for infectious disease control and prevention on farms. It makes it possible to understand the spread of pathogens, but also to compare intervention scenarios even in counterfactual situations. However, the actual capability of decision makers to use mechanistic models to support timely interventions is limited. This study demonstrates how artificial intelligence (AI) techniques can make mechanistic epidemiological models more accessible to farmers and veterinarians, and how to transform such models into user-friendly decision-support tools (DST). By leveraging knowledge representation methods, such as the textual formalization of model components through a domain-specific language (DSL), the co-design of mechanistic models and decision-support tools becomes more efficient and collaborative. This facilitates the integration of explicit expert knowledge and practical insights into the modelling process. Furthermore, the utilization of AI and software engineering enables the automation of web application generation based on existing mechanistic models. This automation simplifies the development of DST, as tool designers can focus on identifying users needs and specifying expected features and meaningful presentations of outcomes, instead of wasting time in writing code to wrap models into web apps. To illustrate the practical application of this approach, we consider the example of Bovine Respiratory Disease (BRD), a tough challenge in fattening farms where young beef bulls often develop BRD shortly after being allocated into pens. BRD is a multi-factorial, multi-pathogen disease that is difficult to anticipate and control, often resulting in the massive use of antimicrobials to mitigate its impact on animal health, welfare, and economic losses. The decision-support tool developed from an existing mechanistic BRD model empowers users, including farmers and veterinarians, to customize scenarios based on their specific farm conditions. It enables them to anticipate the effects of various pathogens, compare the epidemiological and economic outcomes associated with different farming practices, and decide how to balance the reduction of disease impact and the reduction of antimicrobial usage (AMU). The generic method presented in this article illustrates the potential of artificial intelligence (AI) and software engineering methods to enhance the co-creation of decision-support tools based on mechanistic models in veterinary epidemiology. The corresponding pipeline is distributed as an open-source software. By leveraging these advancements, this research aims to bridge the gap between theoretical models and the practical usage of their outcomes on the field. HighlightsO_LIAI make mechanistic epidemiological models usable to support decisions on farms C_LIO_LITextual knowledge representation fosters co-design of mechanistic models and tools C_LIO_LIAI and software engineering automate web app generation to ease disease control C_LI

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Picault, S., Niang, G., Sicard, V., Sorin-Dupont, B., Assie, S., Ezanno, P.. 2023-09-04. Leveraging artificial intelligence and software engineering methods in epidemiology for the co-creation of decision-support tools based on mechanistic models. https://doi.org/10.1101/2023.09.03.555060

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