84 citations · 221 across the 24 of their papers we have counts for
6 papers · 1 filter
Leaping through tree space: continuous phylogenetic inference for rooted and unrooted trees
Matthew J Penn, Neil Scheidwasser, Joseph Penn +3
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogen…
Phylo2Vec: a vector representation for binary trees
Matthew J Penn, Neil Scheidwasser, Mark P Khurana +3
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes i…
Intrinsic Randomness in Epidemic Modelling Beyond Statistical Uncertainty
Matthew J. Penn, Daniel J. Laydon, Joseph Penn +7
Uncertainty can be classified as either aleatoric (intrinsic randomness) or epistemic (imperfect knowledge of parameters). The majority of frameworks assessing infectious disease r…
Unifying incidence and prevalence under a time-varying general branching process
Mikko S. Pakkanen, Xenia Miscouridou, Matthew J. Penn +5
Renewal equations are a popular approach used in modelling the number of new infections, i.e., incidence, in an outbreak. We develop a stochastic model of an outbreak based on a ti…
Inference of COVID-19 epidemiological distributions from Brazilian hospital data
Iwona Hawryluk, Thomas A. Mellan, Henrique H. Hoeltgebaum +8
Knowing COVID-19 epidemiological distributions, such as the time from patient admission to death, is directly relevant to effective primary and secondary care planning, and moreove…
On the derivation of the renewal equation from an age-dependent branching process: an epidemic modelling perspective
Swapnil Mishra, Tresnia Berah, Thomas A. Mellan +6
Renewal processes are a popular approach used in modelling infectious disease outbreaks. In a renewal process, previous infections give rise to future infections. However, while th…