Clonal fitness inferred from time-series modelling of single-cell cancer genomes
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy
number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of …
number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of …
Statistical inference for stochastic differential equations
P Craigmile, R Herbei, G Liu… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Many scientific fields have experienced growth in the use of stochastic differential equations
(SDEs), also known as diffusion processes, to model scientific phenomena over time. SDEs …
(SDEs), also known as diffusion processes, to model scientific phenomena over time. SDEs …
Bayesian inference of natural selection from allele frequency time series
JG Schraiber, SN Evans, M Slatkin - Genetics, 2016 - academic.oup.com
The advent of accessible ancient DNA technology now allows the direct ascertainment of
allele frequencies in ancestral populations, thereby enabling the use of allele frequency time …
allele frequencies in ancestral populations, thereby enabling the use of allele frequency time …
Riemannian langevin algorithm for solving semidefinite programs
M Li, MA Erdogdu - Bernoulli, 2023 - projecteuclid.org
Riemannian Langevin algorithm for solving semidefinite programs Page 1 Bernoulli 29(4),
2023, 3093–3113 https://doi.org/10.3150/22-BEJ1576 Riemannian Langevin algorithm for …
2023, 3093–3113 https://doi.org/10.3150/22-BEJ1576 Riemannian Langevin algorithm for …
From denoising diffusions to denoising markov models
Denoising diffusions are state-of-the-art generative models exhibiting remarkable empirical
performance. They work by diffusing the data distribution into a Gaussian distribution and …
performance. They work by diffusing the data distribution into a Gaussian distribution and …
From denoising diffusions to denoising Markov models
Denoising diffusions are state-of-the-art generative models exhibiting remarkable empirical
performance. They work by diffusing the data distribution into a Gaussian distribution and …
performance. They work by diffusing the data distribution into a Gaussian distribution and …
Frequent asymmetric migrations suppress natural selection in spatially structured populations
Natural microbial populations often have complex spatial structures. This can impact their
evolution, in particular the ability of mutants to take over. While mutant fixation probabilities …
evolution, in particular the ability of mutants to take over. While mutant fixation probabilities …
Mutant fate in spatially structured populations on graphs: connecting models to experiments
A Abbara, L Pagani, C García-Pareja… - PLOS Computational …, 2024 - journals.plos.org
In nature, most microbial populations have complex spatial structures that can affect their
evolution. Evolutionary graph theory predicts that some spatial structures modelled by …
evolution. Evolutionary graph theory predicts that some spatial structures modelled by …
Bayesian inference of species trees using diffusion models
We describe a new and computationally efficient Bayesian methodology for inferring species
trees and demographics from unlinked binary markers. Likelihood calculations are carried …
trees and demographics from unlinked binary markers. Likelihood calculations are carried …
Poisson random fields for dynamic feature models
We present the Wright-Fisher Indian buffet process (WF-IBP), a probabilistic model for time-
dependent data assumed to have been generated by an unknown number of latent features …
dependent data assumed to have been generated by an unknown number of latent features …