Computation and inference

Figure: Epidemic size predicted using Approximate Bayesian Computation (R. Eggo 2018).

This theme provides a space for the exploration of ideas for efficient computation, to learn new methodologies for inference and to share knowledge across CMMID.

In the CMMID we use mathematical and statistical tools to understand the dynamics and control of infection. Members use methods of inference to inform data based decisions which can account for large and/or complex data, models and questions. In addition, to deal with these complexities, there is a need for efficient computation. From methods to account for partial observation of cases and uncertainty in confirmation of cases, to tools for creating fast and reproducible code, challenges arise in both computation and inference that are common to many infectious disease research questions.

People

Amanda Minter (theme co-ordinator), Katherine Atkins, Lloyd Chapman, Sam Clifford, Roz Eggo, Akira Endo, Seb Funk, Alasdair Henderson, Adam Kucharski, Nicky McCreesh, Amy Pinsent, Kathleen O’Reilly, Tom Sumner, Naomi Walker, Nayantara Wijayanandana

Publications

• O’Reilly KM, Cori A, Durry E, Wadood MZ, Bosan A, Aylward RB, et al. (2015) A new method to estimate the coverage of mass vaccination campaigns against poliomyelitis from surveillance data. Am J Epidemiol.;182:961–970. pmid:26568569
• Kucharski AJ, Edmunds WJ (2015) Characterizing the transmission potential of zoonotic infections from minor outbreaks. PLOS Comput Biol 11(4):e1004154
• Kucharski AJ, Lessler J, Read JM, Zhu H, Jiang CQ et al. (2015) Estimating the life course of influenza A(H3N2) antibody responses from cross-sectional data. PLOS Biol 13(3):e1002082
• Kucharski AJ, Mills HL, Pinsent A, Fraser C, Van Kerkhove MD et al. (2014) Distinguishing between reservoir exposure and human-to-human transmission for emerging pathogens using case onset data. PLOS Curr. 7:6

Resources

Resources including recommended books/journals for those new and/or interested in computation and inference are listed below.

Computation

• Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists
  Visser MD, McMahon SM, Merow C, Dixon PM, Record S, et al. (2015) Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists. PLOS Computational Biology 11(3): e1004140. https://doi.org/10.1371/journal.pcbi.1004140

Markov Chain Monte Carlo

• Gelman A, Carlin JB, Stern HS, Rubin DB. Bayesian Data Analysis. 2nd ed.: Chapman & Hall/CRC; 2004
• Girolami M (2008) Bayesian inference for differential equations. Theoretical Computer Science 408: 4–16.
• A Bayesian Framework for Parameter Estimation in Dynamical Models
  Coelho FC, Codeço CT, Gomes MGM (2011) A Bayesian Framework for Parameter Estimation in Dynamical Models. PLOS ONE 6(5): e19616.https://doi.org/10.1371/journal.pone.0019616

Approximate Bayesian Computation

• Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf MPH. (2009). Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. R. Soc. Interface 6 187-202; DOI: 10.1098/rsif.2008.0172.
• Hartig, F. , Calabrese, J. M., Reineking, B. , Wiegand, T. and Huth, A. (2011), Statistical inference for stochastic simulation models – theory and application. Ecology Letters, 14: 816-827. doi:1111/j.1461-0248.2011.01640.x
• Sunnåker M, Busetto AG, Numminen E, Corander J, Foll M, et al. (2013) Approximate Bayesian Computation. PLOS Computational Biology 9(1): e1002803.https://doi.org/10.1371/journal.pcbi.1002803
• McKinley, Trevelyan J.; Vernon, Ian; Andrianakis, Ioannis; McCreesh, Nicky; Oakley, Jeremy E.; Nsubuga, Rebecca N.; Goldstein, Michael; White, Richard G. Approximate Bayesian Computation and Simulation-Based Inference for Complex Stochastic Epidemic Models. Statist. Sci. 33 (2018), no. 1, 4–18. doi:10.1214/17-STS618. https://projecteuclid.org/euclid.ss/1517562021

Comparison of MCMC and ABC

• McKinley, T., Cook, A. R. and Deardon, R. (2009). Inference in epidemic models without likelihoods.  J. Biostat.5.