Tag Archives: Epidemiology

Flu and Coronavirus Simulator – A geospatial agent-based simulator for analyzing COVID-19 spread and public health measures on local regions

By Imran Mahmood

A Summary of: Mahmood et al. (2020)

In this paper we reviewed the lessons learned during the development of the ‘Flu and Coronavirus Simulator’ (FACS) and compare our chosen Agent-based Simulation approach with the conventional disease modelling approaches.

FACS provides an open-ended platform for the specification and implementation of the primary components of Agent-Based Simulation (ABS): (i) Agents; (ii) Virtual environment and (iii) Rule-set using a systematic Simulation Development Approach. FACS inherits features of a comprehensive simulation framework from its ancestors: (i) FLEE (Groen & Arabnejad, 2015) and (ii) FabSim3 (Groen & Arabnejad 2014). Where, FLEE mainly specializes in ABS complex dynamics e.g., agent movements; FabSim3 provides the ability to simulate a large population of agents with microscopic details using remote supercomputers. The combination of this legacy code offers numerous benefits including high performance, high scalability, and greater re-usability through a model coupling. Hence it provides an open-ended API for modellers and programmers to use it for further scientific research and development. FACS generalizes the process of disease modelling and provides a template to model any infectious disease. Thus allowing: (i) non-programmers (e.g., epidemiologists and healthcare data scientists) to use the framework as a disease modelling suite; and (ii) providing an open-ended API for modellers and programmers to use it for further scientific research and development. FACS offers a built-in location graph construction tool that allows the import of large spatial data-sets (e.g., Open Street Map), automated parsing and pre-processing of the spatial data, and generating buildings of various types, thus allowing ease in the synthesis of the virtual environment for the region under consideration. FACS provides a realistic disease transmission algorithm with the ability to capture population interactions and demographic patterns e.g., age diversity, daily life activities, mobility patterns, exposure at the street-level or in public transportation, use, or no use of face mask, assumptions of exposure within closed quarters.

We believe our approach has proven to be quite productive in modelling complex systems like epidemic spread in large regions due to ever-changing model requirements, multi-resolution abstraction, non-linear system dynamics, rule-based heuristics, and above all large-scale computing requirements. During the development of this framework, we learned that the real-world abstraction changes more rapidly than in other circumstances. For instance, the concept of social distancing and lockdown scenarios have evolved significantly since early March. Therefore, rapid changes in the ABS model were necessary. Model building in these cases benefits more from using a bottom-up approach like ABS, as opposed to any centralized analytical solution.

References

Groen, D., & Arabnejad, H. (2014). Fabsim3. GitHub. https://github.com/djgroen/FabSim3

Groen, D., & Arabnejad, H. (2015). Flee. GitHub. https:// github.com/djgroen/flee

Mahmood, I.,  Arabnejad, H., Suleimenova, D., Sassoon, I.,  Marshan, A.,  Serrano-Rico, A.,  Louvieris, P., Anagnostou, A., Taylor, S.J.E., Bell, D. & Groen, D. (2020) FACS: a geospatial agent-based simulator for analysing COVID-19 spread and public health measures on local regions, Journal of Simulation, DOI: 10.1080/17477778.2020.1800422


Mahmood, I. (2020) Flu and Coronavirus Simulator - A geospatial agent-based simulator for analyzing COVID-19 spread and public health measures on local regions. Review of Artificial Societies and Social Simulation, 10th Sept 2020. https://rofasss.org/2020/09/10/facs/


 

Get out of your silos and work together!

By Peer-Olaf Siebers and Sudhir Venkatesan

(A contribution to the: JASSS-Covid19-Thread)

The JASSS position paper ‘Computational Models That Matter During a Global Pandemic Outbreak: A Call to Action’ (Squazzoni et al 2020) calls on the scientific community to improve the transparency, access, and rigour of their models. A topic that we think is equally important and should be part of this list is the quest to more “interdisciplinarity”; scientific communities to work together to tackle the difficult job of understanding the complex situation we are currently in and be able to give advice.

The modelling/simulation community in the UK (and more broadly) tend to work in silos. The two big communities that we have been exposed to are the epidemiological modelling community, and social simulation community. They do not usually collaborate with each other despite working on very similar problems and using similar methods (e.g. agent-based modelling). They publish in different journals, use different software, attend different conferences, and even sometimes use different terminology to refer to the same concepts.

The UK pandemic response strategy (Gov.UK 2020) is guided by advice from the Scientific Advisory Group for Emergencies (SAGE), which in turn has comprises three independent expert groups- SPI-M (epidemic modellers), SPI-B (experts in behaviour change from psychology, anthropology and history), and NERVTAG (clinicians, epidemiologists, virologists and other experts). Of these, modelling from member SPI-M institutions has played an important role in informing the UK government’s response to the ongoing pandemic (e.g. Ferguson et al 2020). Current members of the SPI-M belong to what could be considered the ‘epidemic modelling community’. Their models tend to be heavily data-dependent which is justifiable given that their most of their modelling focus on viral transmission parameters. However, this emphasis on empirical data can sometimes lead them to not model behaviour change or model it in a highly stylised fashion, although more examples of epidemic-behaviour models appear in recent epidemiological literature (e.g. Verelst et al 2016; Durham et al 2012; van Boven et al 2008; Venkatesan et al 2019). Yet, of the modelling work informing the current response to the ongoing pandemic, computational models of behaviour change are prominently missing. This, from what we have seen, is where the ‘social simulation’ community can really contribute their expertise and modelling methodologies in a very valuable way. A good resource for epidemiologists in finding out more about the wide spectrum of modelling ideas are the Social Simulation Conference Proceeding Programmes (e.g. SSC2019 2019). But unfortunately, the public health community, including policymakers, are either unaware of these modelling ideas or are unsure of how these are relevant to them.

As pointed out in a recent article, one important concern with how behaviour change has possibly been modelled in the SPI-M COVID-19 models is the assumption that changes in contact rates resulting from a lockdown in the UK and the USA will mimic those obtained from surveys performed in China, which unlikely to be valid given the large political and cultural differences between these societies (Adam 2020). For the immediate COVID-19 response models, perhaps requiring cross-disciplinary validation for all models that feed into policy may be a valuable step towards more credible models.

Effective collaboration between academic communities relies on there being a degree of familiarity, and trust, with each other’s work, and much of this will need to be built up during inter-pandemic periods (i.e. “peace time”). In the long term, publishing and presenting in each other’s journals and conferences (i.e. giving the opportunity for other academic communities to peer-review a piece of modelling work), could help foster a more collaborative environment, ensuring that we are in a much better to position to leverage all available expertise during a future emergency. We should aim to take the best across modelling communities and work together to come up with hybrid modelling solutions that provide insight by delivering statistics as well as narratives (Moss 2020). Working in silos is both unhelpful and inefficient.

References

Adam D (2020) Special report: The simulations driving the world’s response to COVID-19. How epidemiologists rushed to model the coronavirus pandemic. Nature – News Feature. https://www.nature.com/articles/d41586-020-01003-6 [last accessed 07/04/2020]

Durham DP, Casman EA (2012) Incorporating individual health-protective decisions into disease transmission models: A mathematical framework. Journal of The Royal Society Interface. 9(68), 562-570

Ferguson N, Laydon D, Nedjati Gilani G, Imai N, Ainslie K, Baguelin M, Bhatia S, Boonyasiri A, Cucunuba Perez Zu, Cuomo-Dannenburg G, Dighe A (2020) Report 9: Impact of non-pharmaceutical interventions (NPIs) to reduce COVID-19 mortality and healthcare demand. https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf [last accessed 07/04/2020]

Gov.UK (2020) Scientific Advisory Group for Emergencies (SAGE): Coronavirus response. https://www.gov.uk/government/groups/scientific-advisory-group-for-emergencies-sage-coronavirus-covid-19-response [last accessed 07/04/2020]

Moss S (2020) “SIMSOC Discussion: How can disease models be made useful? “, Posted by Scott Moss, 22 March 2020 10:26 [last accessed 07/04/2020]

Squazzoni F, Polhill JG, Edmonds B, Ahrweiler P, Antosz P, Scholz G, Borit M, Verhagen H, Giardini F, Gilbert N (2020) Computational models that matter during a global pandemic outbreak: A call to action, Journal of Artificial Societies and Social Simulation, 23 (2) 10

SSC2019 (2019) Social simulation conference programme 2019. https://ssc2019.uni-mainz.de/files/2019/09/ssc19_final.pdf [last accessed 07/04/2020]

van Boven M, Klinkenberg D, Pen I, Weissing FJ, Heesterbeek H (2008) Self-interest versus group-interest in antiviral control. PLoS One. 3(2)

Venkatesan S, Nguyen-Van-Tam JS, Siebers PO (2019) A novel framework for evaluating the impact of individual decision-making on public health outcomes and its potential application to study antiviral treatment collection during an influenza pandemic. PLoS One. 14(10)

Verelst F, Willem L, Beutels P (2016) Behavioural change models for infectious disease transmission: A systematic review (2010–2015). Journal of The Royal Society Interface. 13(125)


Siebers, P-O. and Venkatesan, S. (2020) Get out of your silos and work together. Review of Artificial Societies and Social Simulation, 8th April 2020. https://rofasss.org/2020/0408/get-out-of-your-silos