9 papers
Genealogical processes of sequential Monte Carlo methods and other non-neutral population models under rapid mutation
Jere Koskela, Paul A. Jenkins, Adam M. Johansen +1
We show that genealogical trees arising from a broad class of non-neutral models of population evolution converge to the Kingman coalescent under a suitable rescaling of time. As w…
SDE-based Monte Carlo dose calculation for proton therapy validated against Geant4
Christopher B. C. Dean, Maria L. Pérez-Lara, Emma Horton +3
Objective: To assess the accuracy and computational performance of a stochastic differential equation (SDE)--based model for proton beam dose calculation by benchmarking against Ge…
Large-sample analysis of cost functionals for inference under the coalescent
Martina Favero, Jere Koskela
The coalescent is a foundational model of latent genealogical trees under neutral evolution, but suffers from intractable sampling probabilities. Methods for approximating these sa…
A debiased Bernoulli factory and unbiased estimation of a probability
Jere Koskela, Toni Karvonen, Krzysztof ÅatuszyÅski +1
Given a known function and a random but almost surely finite number of independent, Ber-distributed random variables with unknown , w…
Asymptotic guarantees for Bayesian phylogenetic tree reconstruction
Alisa Kirichenko, Luke J. Kelly, Jere Koskela
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA…
Multi-type -coalescents from structured population models with bottlenecks
Marta Dai Pra, Alison Etheridge, Jere Koskela +1
We introduce an individual-based model for structured populations undergoing demographic bottlenecks, i.e. drastic reductions in population size that last many generations and can…