Related papers: Adaptive preferential sampling in phylodynamics
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
We consider a family of models describing the evolution under selection of a population whose dynamics can be related to the propagation of noisy traveling waves. For one particular model, that we shall call the exponential model, the…
We introduce a modified spatial $\Lambda$-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective…
Coalescence processes have received a lot of attention in the context of conditional branching processes with fixed population size and non-overlapping generations. Here we focus on similar problems in the context of the standard…
When two (possibly different in distribution) continuous-state branching processes with immigration are present, we study the relative frequency of one of them when the total mass is forced to be constant at a dense set of times. This leads…
Phylodynamics is used to estimate epidemic dynamics from phylogenetic trees or genomic sequences of pathogens, but the likelihood calculations needed can be challenging for complex models. We present a neural Bayes estimator (NBE) for key…
Wright-Fisher diffusions and their dual ancestral graphs occupy a central role in the study of allele frequency change and genealogical structure, and they provide expressions, explicit in some special cases but generally implicit, for the…
Epidemic models are used to analyze the progression or outcome of an epidemic under different control policies like vaccinations, quarantines, lockdowns, use of face-masks, pharmaceutical interventions, etc. When these models accurately…
An important problem in evolutionary genomics is to investigate whether a certain trait measured on each sample is associated with the sample phylogenetic tree. The phylogenetic tree represents the shared evolutionary history of the samples…
We introduce a new type of point process model to describe the incidence of contagious diseases. The model is a variant of the Hawkes self-exciting process and exhibits similar clustering but without the restriction that the component…
Let $K_n$ denote the number of types of a sample of size $n$ taken from an exchangeable coalescent process ($\Xi$-coalescent) with mutation. A distributional recursion for the sequence $(K_n)_{n\in{\mathbb N}}$ is derived. If the coalescent…
Spreading processes are conventionally monitored on a macroscopic level by counting the number of incidences over time. The spreading process can then be modeled either on the microscopic level, assuming an underlying interaction network,…
We define a Markov process on the partitions of $[n]=\{1,\ldots,n\}$ by drawing a sample in $[n]$ at each time of a Poisson process, by merging blocks that contain one of these points and by leaving all other blocks unchanged. This…
Kingman derived the Ewens sampling formula for random partitions describing the genetic variation in a neutral mutation model defined by a Poisson process of mutations along lines of descent governed by a simple coalescent process, and…
Conditional sampling distributions (CSDs), sometimes referred to as copying models, underlie numerous practical tools in population genomic analyses. Though an important application that has received much attention is the inference of…
Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known…
This paper provides an elementary, self-contained analysis of diffusion-based sampling methods for generative modeling. In contrast to existing approaches that rely on continuous-time processes and then discretize, our treatment works…
This paper deals with the stochastic modeling of a class of heterogeneous population in a random environment, called birth-death-swap. In addition to demographic events, swap events, i.e. moves between subgroups, occur in the population.…
We consider a model of a population in which individuals are sampled from different species. The Yule-Kingman nested coalescent describes the genealogy of the sample when each species merges with another randomly chosen species with a…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…