Modeling COVID-19 disease processes by remote elicitation of causal Bayesian networks from medical experts
Authors: Mascaro Steven , Wu Yue , Woodberry Owen , Nyberg Erik P. , Pearson Ross , Ramsay Jessica A. , Mace Ariel O. , Foley David A. , Snelling Thomas L. , Nicholson Ann E. ,   COVID BN Advisory Group, Semprini Alex , Martin Andrew , McLean-Tooke Andrew , Marais Ben , Tang Benjamin , McLeod Charlie , Blyth Christopher C. , Lemoh Chris , Waddington Claire , Nolan David , Raby Edward , Perez Gladymar , Marks Guy , Denholm Justin , Pilgram Lisa , Anstey Nicholas , Plebanski Magdalena , Boyd Mark , Borland Meredith L. , Maze Michael , John Mina , Middleton Paul , Craig Simon , Tong Steve Y.C. , Benson Susan , Richards Toby 
Published: March 2023

Abstract
Background
COVID-19 is a new multi-organ disease causing considerable worldwide morbidity and mortality. While many recognized pathophysiological mechanisms are involved, their exact causal relationships remain opaque. Better understanding is needed for predicting their progression, targeting therapeutic approaches, and improving patient outcomes. While many mathematical causal models describe COVID-19 epidemiology, none have described its pathophysiology.

Methods
In early 2020, we began developing such causal models. The SARS-CoV-2 virus’s rapid and extensive spread made this particularly difficult: no large patient datasets were publicly available; the medical literature was flooded with sometimes conflicting pre-review reports; and clinicians in many countries had little time for academic consultations. We used Bayesian network (BN) models, which provide powerful calculation tools and directed acyclic graphs (DAGs) as comprehensible causal maps. Hence, they can incorporate both expert opinion and numerical data, and produce explainable, updatable results. To obtain the DAGs, we used extensive expert elicitation (exploiting Australia’s exceptionally low COVID-19 burden) in structured online sessions. Groups of clinical and other specialists were enlisted to filter, interpret and discuss the literature and develop a current consensus. We encouraged inclusion of theoretically salient latent (unobservable) variables, likely mechanisms by extrapolation from other diseases, and documented supporting literature while noting controversies. Our method was iterative and incremental: systematically refining and validating the group output using one-on-one follow-up meetings with original and new experts. 35 experts contributed 126 hours face-to-face, and could review our products.

Results
We present two key models, for the initial infection of the respiratory tract and the possible progression to complications, as causal DAGs and BNs with corresponding verbal descriptions, dictionaries and sources. These are the first published causal models of COVID-19 pathophysiology.

Conclusions
Our method demonstrates an improved procedure for developing BNs via expert elicitation, which other teams can implement to model emergent complex phenomena. Our results have three anticipated applications: (i) freely disseminating updatable expert knowledge; (ii) guiding design and analysis of observational and clinical studies; (iii) developing and validating automated tools for causal reasoning and decision support. We are developing such tools for the initial diagnosis, resource management, and prognosis of COVID-19, parameterized using the ISARIC and LEOSS databases.