Senior Research Software Engineer
PhD Student

I work on math models of disease transmission and ML-based surrogates for inference and optimisation, my areas of interest include: time-series prediction, transformers for time-series, Approximate Bayesian Inference, differential equations, differentiable agent based models, optimal control and JAX development.

I also work with global health researchers in the Department for Infectious Disease Epidemiology to inform malaria elimination strategies - how, where and when should resources be invested to most effectively reduce the global case burden and eventually eradicate Plasmodium parasites, and implement spatial and temporal disease models.

Projects

• Differentiable ABMs - Researching
• Global Health Policy Optimisation - Interested
• Machine Learning and Global Health Workshop (ICLR 2023) - Co-organiser and Fundraiser

Software

• individual - an R framework for individual (or agent) based modelling
• malariasimulation - an agent based model of malaria transmission
• fastms - A package, written in tensorflow, for training and testing seq2seq surrogates of the above malaria model
• mox (WIP) - A JAX library for developing seq2seq surrogates
• dux (WIP) - A JAX library for differentiating stochastic models

Publications

Challenger, J. D., van Beek, S. W., Ter Heine, R., van der Boor, S. C., Charles, G. D., Smit, M. J., … Others. (2023). Modeling the Impact of a Highly Potent Plasmodium falciparum Transmission-Blocking Monoclonal Antibody in Areas of Seasonal Malaria Transmission. The Journal of Infectious Diseases, jiad101.

Schmit, N., Topazian, H. M., Pianella, M., Charles, G. D., Winskill, P., White, M., … Ghani, A. C. (2023). Resource allocation strategies to achieve malaria eradication. MedRxiv, 2023–2004.

Topazian, H. M., Schmit, N., Gerard-Ursin, I., Charles, G. D., Thompson, H., Ghani, A. C., & Winskill, P. (2023). Modelling the relative cost-effectiveness of the RTS, S/AS01 malaria vaccine compared to investment in vector control or chemoprophylaxis. Vaccine, 41(20), 3215–3223.

Charles, G., Wolock, T. M., Winskill, P., Ghani, A., Bhatt, S., & Flaxman, S. (2022). Seq2Seq Surrogates of Epidemic Models to Facilitate Bayesian Inference. ArXiv Preprint ArXiv:2209. 09617.

Hogan, A. B., Wu, S. L., Doohan, P., Watson, O. J., Winskill, P., Charles, G., … Others. (2022). The value of vaccine booster doses to mitigate the global impact of the Omicron SARS-CoV-2 variant. MedRxiv, 2022–2001.

Olivera Mesa, D., Hogan, A. B., Watson, O. J., Charles, G. D., Hauck, K., Ghani, A. C., & Winskill, P. (2022). Modelling the impact of vaccine hesitancy in prolonging the need for Non-Pharmaceutical Interventions to control the COVID-19 pandemic. Communications Medicine, 2(1), 14.

Charles, G. D., & Wu, S. L. (2021). individual: An R package for individual-based epidemiological models. Journal of Open Source Software, 6(66), 3539.

Mesa, D. O., Hogan, A., Watson, O., Charles, G., Hauck, K., Ghani, A. C., & Winskill, P. (2021). Quantifying the impact of vaccine hesitancy in prolonging the need for Non-Pharmaceutical Interventions to control the COVID-19 pandemic.