arXiv subjects

Martina Favero

Publications and source records attributed to Martina Favero.

9 recordsLinked to original sources

arXiv2026

Identifiability in epidemic models with prior immunity and under-reporting

Identifiability is the property in mathematical modelling that determines if model parameters can be uniquely estimated from data. For infectious disease models, failure to ensure identifiability can lead to misleading parameter estimates and unreliable policy recommendations. We examine the identifiability of a modified SIR model that accounts for under-reporting and pre-existing immunity in the population. We provide a mathematical proof of the unidentifiability of jointly estimating three parameters: the fraction under-reporting, the proportion of the population with prior immunity, and the community transmission rate, when only reported case data are available. We then show, analytically and with a simulation study, that the identifiability of all three parameters is achieved if the reported incidence is complemented with sample survey data of prior immunity or prevalence during the outbreak. Our results show the limitations of parameter inference in partially observed epidemics and the importance of identifiability analysis when developing and applying models for public health decision making.

stat.ME↗

arXiv2026

Large-sample analysis of cost functionals for inference under the coalescent

The coalescent is a foundational model of latent genealogical trees under neutral evolution, but suffers from intractable sampling probabilities. Methods for approximating these sampling probabilities either introduce bias or fail to scale to large sample sizes. We show that a class of cost functionals of the coalescent with recurrent mutation and a finite number of alleles converge to tractable processes in the infinite-sample limit. A particular choice of costs yields insight about importance sampling methods, which are a classical tool for coalescent sampling probability approximation. These insights reveal that the behaviour of coalescent importance sampling algorithms differs markedly from standard sequential importance samplers, with or without resampling. We conduct a simulation study to verify that our asymptotics are accurate for algorithms with finite (and moderate) sample sizes. Our results constitute the first theoretical description of large-sample importance sampling algorithms for the coalescent, provide heuristics for the a priori optimisation of computational effort, and identify settings where resampling is harmful for algorithm performance. We observe strikingly different behaviour for importance sampling methods under the infinite sites model of mutation, which is regarded as a good and more tractable approximation of finite alleles mutation in most respects.

math.ST↗

arXiv2025

Sideward contact tracing in an epidemic model with mixing groups

We consider a stochastic epidemic model with sideward contact tracing. We assume that infection is driven by interactions within mixing events (gatherings of two or more individuals). Once an infective is diagnosed, each individual who was infected at the same event as the diagnosed individual is contact traced with some given probability. Assuming few initial infectives in a large population, the early phase of the epidemic is approximated by a branching process with sibling dependencies. To address the challenges given by the dependencies, we consider sibling groups (individuals who become infected at the same event) as macro-individuals and define a macro-branching process. This allows us to derive an expression for the effective macro-reproduction number which corresponds to the effective individual reproduction number and represents a threshold for the behaviour of the epidemic. Through numerical examples, we show how the reproduction number varies with the distribution of the mixing event size, the mean size, the rate of diagnosis and the tracing probability.

q-bio.PE↗

arXiv2025

A dual process for the coupled Wright-Fisher diffusion

The coupled Wright-Fisher diffusion is a multi-dimensional Wright-Fisher diffusion for multi-locus and multi-allelic genetic frequencies, expressed as the strong solution to a system of stochastic differential equations that are coupled in the drift, where the pairwise interaction among loci is modelled by an inter-locus selection. In this paper, an ancestral process, which is dual to the coupled Wright-Fisher diffusion, is derived. The dual process corresponds to the block counting process of coupled ancestral selection graphs, one for each locus. Jumps of the dual process arise from coalescence, mutation, single-branching, which occur at one locus at the time, and double-branching, which occur simultaneously at two loci. The coalescence and mutation rates have the typical structure of the transition rates of the Kingman coalescent process. The single-branching rate not only contains the one-locus selection parameters in a form that generalises the rates of an ancestral selection graph, but it also contains the two-locus selection parameters to include the effect of the pairwise interaction on the single loci. The double-branching rate reflects the particular structure of pairwise selection interactions of the coupled Wright-Fisher diffusion. Moreover, in the special case of two loci, two alleles, with selection and parent independent mutation, the stationary density for the coupled Wright-Fisher diffusion and the transition rates of the dual process are obtained in an explicit form.

math.PR↗

arXiv2025

Weak convergence of the scaled jump chain and number of mutations of the Kingman coalescent

The Kingman coalescent is a fundamental process in population genetics modelling the ancestry of a sample of individuals backwards in time. In this paper, in a large-sample-size regime, we study asymptotic properties of the coalescent under neutrality and a general finite-alleles mutation scheme, i.e. including both parent independent and parent dependent mutation. In particular, we consider a sequence of Markov chains that is related to the coalescent and consists of block-counting and mutation-counting components. We show that these components, suitably scaled, converge weakly to deterministic components and Poisson processes with varying intensities, respectively. Along the way, we develop a novel approach, based on a change of measure, to generalise the convergence result from the parent independent to the parent dependent mutation setting, in which several crucial quantities are not known explicitly.

math.PR↗

arXiv2025

Sampling probabilities, diffusions, ancestral graphs, and duality under strong selection

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 sampling probability, a crucial quantity in inference. Under a finite-allele mutation model, with possibly parent-dependent mutation, we consider the asymptotic regime where the selective advantage of one allele grows to infinity, while the other parameters remain fixed. In this regime, we show that the Wright-Fisher diffusion can be approximated either by a Gaussian process or by a process whose components are independent continuous-state branching processes with immigration, aligning with analogous results for Wright-Fisher models but employing different methods. While the first process becomes degenerate at stationarity, the latter does not and provides a simple, analytic approximation for the leading term of the sampling probability. Furthermore, using another approach based on a recursion formula, we characterise all remaining terms to provide a full asymptotic expansion for the sampling probability. Finally, we study the asymptotic behaviour of the rates of the block-counting process of the conditional ancestral selection graph and establish an asymptotic duality relationship between this and the diffusion.

math.PR↗

arXiv2022

Modelling preventive measures and their effect on generation times in emerging epidemics

We present a stochastic epidemic model to study the effect of various preventive measures, such as uniform reduction of contacts and transmission, vaccination, isolation, screening and contact tracing, on a disease outbreak in a homogeneously mixing community. The model is based on an infectivity process, which we define through stochastic contact and infectiousness processes, so that each individual has an independent infectivity profile. In particular, we monitor variations of the reproduction number and of the distribution of generation times. We show that some interventions, i.e. uniform reduction and vaccination, affect the former while leaving the latter unchanged, whereas other interventions, i.e. isolation, screening and contact tracing, affect both quantities. We provide a theoretical analysis of the variation of these quantities, and we show that, in practice, the variation of the generation time distribution can be significant and that it can cause biases in the estimation of reproduction numbers. The framework, because of its general nature, captures the properties of many infectious diseases, but particular emphasis is on COVID-19, for which numerical results are provided.

q-bio.PE↗

arXiv2022

Asymptotic behaviour of sampling and transition probabilities in coalescent models under selection and parent dependent mutations

The results in this paper provide new information on asymptotic properties of classical models: the neutral Kingman coalescent under a general finite-alleles, parent-dependent mutation mechanism, and its generalisation, the ancestral selection graph. Several relevant quantities related to these fundamental models are not explicitly known when mutations are parent dependent. Examples include the probability that a sample taken from a population has a certain type configuration, and the transition probabilities of their block counting jump chains. In this paper, asymptotic results are derived for these quantities, as the sample size goes to infinity. It is shown that the sampling probabilities decay polynomially in the sample size with multiplying constant depending on the stationary density of the Wright-Fisher diffusion and that the transition probabilities converge to the limit of frequencies of types in the sample.

math.PR↗

arXiv2020

Estimates of the proportion of SARS-CoV-2 infected individuals in Sweden

In this paper a Bayesian SEIR model is studied to estimate the proportion of the population infected with SARS-CoV-2, the virus responsible for COVID-19. To capture heterogeneity in the population and the effect of interventions to reduce the rate of epidemic spread, the model uses a time-varying contact rate, whose logarithm has a Gaussian process prior. A Poisson point process is used to model the occurrence of deaths due to COVID-19 and the model is calibrated using data of daily death counts in combination with a snapshot of the the proportion of individuals with an active infection, performed in Stockholm in late March. The methodology is applied to regions in Sweden. The results show that the estimated proportion of the population who has been infected is around 13.5% in Stockholm, by 2020-05-15, and ranges between 2.5% - 15.6% in the other investigated regions. In Stockholm where the peak of daily death counts is likely behind us, parameter uncertainty does not heavily influence the expected daily number of deaths, nor the expected cumulative number of deaths. It does, however, impact the estimated cumulative number of infected individuals. In the other regions, where random sampling of the number of active infections is not available, parameter sharing is used to improve estimates, but the parameter uncertainty remains substantial.

q-bio.PE↗