3 papers
stat.ME2025
A primer on inference and prediction with epidemic renewal models and sequential Monte Carlo
Nicholas Steyn, Kris V. Parag, Robin N. Thompson +1
Renewal models are widely used in statistical epidemiology as semi-mechanistic models of disease transmission. While primarily used for estimating the instantaneous reproduction nu…
q-bio.PE2025
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…
q-bio.PE2025
Generalised Bayesian distance-based phylogenetics for the genomics era
Matthew J. Penn, Neil Scheidwasser, Mark P. Khurana +3
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conve…