32 citations · 123 across the 25 of their papers we have counts for
26 papers
Well-posedness for Wright--Fisher SPDEs with measurable drift
Jere Koskela, Oliver Tough
We prove weak existence and uniqueness in law of -valued solutions for a class of scalar stochastic heat equations with measurable drifts , driven…
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…
A debiased Bernoulli factory and unbiased estimation of a probability
Jere Koskela, Toni Karvonen, Krzysztof Łatuszyński +1
Given a known function and a random but almost surely finite number of independent, Ber-distributed random variables with unknown , we pr…
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…
Bayesian inference from time series of allele frequency data using exact simulation techniques
Jaromir Sant, Paul A. Jenkins, Jere Koskela +1
A central statistical problem in population genetics is to infer evolutionary and biological parameters such as the strength of natural selection and allele age from DNA samples ex…
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…
Jump stochastic differential equations for the characterisation of the Bragg peak in proton beam radiotherapy
Alastair Crossley, Karen Habermann, Emma Horton +3
Proton beam radiotherapy stands at the forefront of precision cancer treatment, leveraging the unique physical interactions of proton beams with human tissue to deliver minimal dos…
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…
Bayesian Inference of Reproduction Number from Epidemiological and Genetic Data Using Particle MCMC
Alicia Gill, Jere Koskela, Xavier Didelot +1
Inference of the reproduction number through time is of vital importance during an epidemic outbreak. Typically, epidemiologists tackle this using observed prevalence or incidence…
Excursion theory for the Wright-Fisher diffusion
Paul A. Jenkins, Jere Koskela, Victor M. Rivero +3
In this work, we develop excursion theory for the Wright--Fisher diffusion with mutation. Our construction is intermediate between the classical excursion theory where all excursio…
Bernoulli factories and duality in Wright-Fisher and Allen-Cahn models of population genetics
Jere Koskela, Krzysztof Łatuszyński, Dario Spanò
Mathematical models of genetic evolution often come in pairs, connected by a so-called duality relation. The most seminal example are the Wright-Fisher diffusion and the Kingman co…
EWF : simulating exact paths of the Wright--Fisher diffusion
Jaromir Sant, Paul A. Jenkins, Jere Koskela +1
The Wright--Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as…
Weak Convergence of Non-neutral Genealogies to Kingman's Coalescent
Suzie Brown, Paul A. Jenkins, Adam M. Johansen +1
Interacting particle systems undergoing repeated mutation and selection steps model genetic evolution, and also describe a broad class of sequential Monte Carlo methods. The geneal…
Diffusion Limits at Small Times for Coalescent Processes with Mutation and Selection
Philip A. Hanson, Paul A. Jenkins, Jere Koskela +1
The Ancestral Selection Graph (ASG) is an important genealogical process which extends the well-known Kingman coalescent to incorporate natural selection. We show that the number o…
Simple conditions for convergence of sequential Monte Carlo genealogies with applications
Suzie Brown, Paul A. Jenkins, Adam M. Johansen +1
We present simple conditions under which the limiting genealogical process associated with a class of interacting particle systems with non-neutral selection mechanisms, as the num…
Zig-zag sampling for discrete structures and non-reversible phylogenetic MCMC
Jere Koskela
We construct a zig-zag process targeting a posterior distribution defined on a hybrid state space consisting of both discrete and continuous variables. The construction does not re…
Convergence of Likelihood Ratios and Estimators for Selection in non-neutral Wright-Fisher Diffusions
Jaromir Sant, Paul A. Jenkins, Jere Koskela +1
A number of discrete time, finite population size models in genetics describing the dynamics of allele frequencies are known to converge (subject to suitable scaling) to a diffusio…
Statistical tools for seed bank detection
Jochen Blath, Eugenio Buzzoni, Jere Koskela +1
In this article, we derive statistical tools to analyze and distinguish the patterns of genetic variability produced by classical and recent population genetic models related to se…
Robust model selection between population growth and multiple merger coalescents
Jere Koskela, Maite Wilke Berenguer
We study the effect of biological confounders on the model selection problem between Kingman coalescents with population growth, and Xi-coalescents involving simultaneous multiple…
Asymptotic genealogies of interacting particle systems with an application to sequential Monte Carlo
Jere Koskela, Paul A. Jenkins, Adam M. Johansen +1
We study weighted particle systems in which new generations are resampled from current particles with probabilities proportional to their weights. This covers a broad class of sequ…
Multi-locus data distinguishes between population growth and multiple merger coalescents
Jere Koskela
We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models…
Inference and rare event simulation for stopped Markov processes via reverse-time sequential Monte Carlo
Jere Koskela, Dario Spano, Paul A. Jenkins
We present a sequential Monte Carlo algorithm for Markov chain trajectories with proposals constructed in reverse time, which is advantageous when paths are conditioned to end in a…
Bayesian non-parametric inference for -coalescents: consistency and a parametric method
Jere Koskela, Paul A. Jenkins, Dario Spanò
We investigate Bayesian non-parametric inference of the -measure of -coalescent processes with recurrent mutation, parametrised by probability measures on the unit interval.…