Rule-based epidemic models

Using graph rewriting to operationalize medical knowledge for the revision of concurrently applied clinical practice guidelines

Clinical practice guidelines (CPGs) are patient management tools that synthesize medical knowledge into an actionable format. CPGs are disease specific with limited applicability to the management of complex patients suffering from multimorbidity. For the management of these patients, CPGs need to be augmented with secondary medical knowledge coming from a variety of knowledge repositories. The operationalization of this knowledge is key to increasing CPGs' uptake in clinical practice. In this work, we propose an approach to operationalizing secondary medical knowledge inspired by graph rewriting. We assume that the CPGs can be represented as task network models, and provide an approach for representing and applying codified medical knowledge to a specific patient encounter. We formally define revisions that model and mitigate adverse interactions between CPGs and we use a vocabulary of terms to instantiate these revisions. We demonstrate the application of our approach using synthetic and clinical examples. We conclude by identifying areas for future work with the vision of developing a theory of mitigation that will facilitate the development of comprehensive decision support for the management of multimorbid patients.

Compositional modelling of immune response and virus transmission dynamics

Transmission models for infectious diseases are typically formulated in terms of dynamics between individuals or groups with processes such as disease progression or recovery for each individual captured phenomenologically, without reference to underlying biological processes. Furthermore, the construction of these models is often monolithic: they do not allow one to readily modify the processes involved or include the new ones, or to combine models at different scales. We show how to construct a simple model of immune response to a respiratory virus and a model of transmission using an easily modifiable set of rules allowing further refining and merging the two models together. The immune response model reproduces the expected response curve of PCR testing for COVID-19 and implies a long-tailed distribution of infectiousness reflective of individual heterogeneity. This immune response model, when combined with a transmission model, reproduces the previously reported shift in the population distribution of viral loads along an epidemic trajectory. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Transmission dynamics of SARS-CoV-2 in a strictly-Orthodox Jewish community in the UK

Some social settings such as households and workplaces, have been identified as high risk for SARS-CoV-2 transmission. Identifying and quantifying the importance of these settings is critical for designing interventions. A tightly-knit religious community in the UK experienced a very large COVID-19 epidemic in 2020, reaching 64.3% seroprevalence within 10 months, and we surveyed this community both for serological status and individual-level attendance at particular settings. Using these data, and a network model of people and places represented as a stochastic graph rewriting system, we estimated the relative contribution of transmission in households, schools and religious institutions to the epidemic, and the relative risk of infection in each of these settings. All congregate settings were important for transmission, with some such as primary schools and places of worship having a higher share of transmission than others. We found that the model needed a higher general-community transmission rate for women (3.3-fold), and lower susceptibility to infection in children to recreate the observed serological data. The precise share of transmission in each place was related to assumptions about the internal structure of those places. Identification of key settings of transmission can allow public health interventions to be targeted at these locations.

Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility

During the COVID-19 pandemic, mathematical modeling of disease transmission has become a cornerstone of key state decisions. To advance the state-of-the-art host viral modeling to handle future pandemics, many scientists working on related issues assembled to discuss the topics. These discussions exposed the reproducibility crisis that leads to inability to reuse and integrate models. This document summarizes these discussions, presents difficulties, and mentions existing efforts towards future solutions that will allow future model utility and integration. We argue that without addressing these challenges, scientists will have diminished ability to build, disseminate, and implement high-impact multi-scale modeling that is needed to understand the health crises we face.