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Tresnia Berah

Publications and source records attributed to Tresnia Berah.

6 recordsLinked to original sources

Selection principles for quasi-stationary distributions and reinforcement processes

Let $P$ be a sub-Markov matrix on a finite set $S$, representing the transition probabilities of a Markov chain on \(S\) absorbed at a cemetery point $\partial\notin S$. We consider a reinforced process \((X_n,μ_n)\) defined as follows: $(X_n)$ behaves like a chain with kernel $P$ until it dies, and when it dies at time $n$, it is instantaneously ``resurrected'' at a point sampled according to its weighted past occupation measure $$ μ_n = \frac{1}{W_n} \left( w_0μ_0+\sum_{k=1}^n w_kδ_{X_k} \right), \qquad W_n=\sum_{k=0}^n w_k, $$ where the positive weights $w_k$ satisfy certain technical assumptions, a typical example being given by $w_k = k^q$, with $q\geq -1$. When $P$ is irreducible, the behaviour of $(μ_n)$ is well understood \cite{AFP}, \cite{bansaye2022non}: it converges almost surely toward the unique quasi-stationary distribution (QSD) of $P$. The purpose of this paper is to investigate the general situation where $P$ is not irreducible. Under generic assumptions on $P$, there are finitely many QSDs. We prove that the asymptotic selection depends on the summability of the inverse cumulative weights $1/W_n$. If $$ \sum_{n\geq 0}\frac1{W_n}=\infty, $$ then $(μ_n)$ almost surely converges toward the QSD associated with the largest Perron value. If instead $$ \sum_{n\geq0}\frac1{W_n}<\infty, $$ then each QSD is selected with positive probability. In particular, for polynomial weights $w_0=1$ and $w_k=k^q$, $k\geq1$, this gives almost sure selection of the QSD with largest Perron value for $-1\leq q\leq 0$, whereas each quasi-stationary distribution is selected with positive probability for $q>0$.

math.PR↗

Strong law of large numbers and L log L condition for supercritical branching processes

We consider branching processes for structured populations: each individual is characterized by a type or trait which belongs to a general measurable state space. We focus on the supercritical recurrent case, where the population may survive and grow and the trait distribution converges. The branching process is then expected to be driven by the positive triplet of first eigenvalue problem of the first moment semigroup. Under the assumption of convergence of the renormalized semigroup in weighted total variation norm, we prove strong convergence of the normalized empirical measure and non-degeneracy of the limiting martingale. Convergence is obtained under an Llog L condition which provides a Kesten-Stigum result in infinite dimension and relaxes the uniform convergence assumption of the renormalized first moment semigroup required in the work of Asmussen and Hering in 1976. The techniques of proofs combine families of martingales and contraction of semigroups and the truncation procedure of Asmussen and Hering. We also obtain L^1 convergence of the renormalized empirical measure and contribute to unifying different results in the literature. These results greatly extend the class of examples where a law of large numbers applies, as we illustrate it with absorbed branching diffusion, the house of cards model and some growth-fragmentation processes.

math.PR↗

Unifying incidence and prevalence under a time-varying general branching process

Renewal equations are a popular approach used in modelling the number of new infections, i.e., incidence, in an outbreak. We develop a stochastic model of an outbreak based on a time-varying variant of the Crump-Mode-Jagers branching process. This model accommodates a time-varying reproduction number and a time-varying distribution for the generation interval. We then derive renewal-like integral equations for incidence, cumulative incidence and prevalence under this model. We show that the equations for incidence and prevalence are consistent with the so-called back-calculation relationship. We analyse two particular cases of these integral equations, one that arises from a Bellman-Harris process and one that arises from an inhomogeneous Poisson process model of transmission. We also show that the incidence integral equations that arise from both of these specific models agree with the renewal equation used ubiquitously in infectious disease modelling. We present a numerical discretisation scheme to solve these equations, and use this scheme to estimate rates of transmission from serological prevalence of SARS-CoV-2 in the UK and historical incidence data on Influenza, Measles, SARS and Smallpox.

q-bio.PE↗

$π$VAE: a stochastic process prior for Bayesian deep learning with MCMC

Stochastic processes provide a mathematically elegant way model complex data. In theory, they provide flexible priors over function classes that can encode a wide range of interesting assumptions. In practice, however, efficient inference by optimisation or marginalisation is difficult, a problem further exacerbated with big data and high dimensional input spaces. We propose a novel variational autoencoder (VAE) called the prior encoding variational autoencoder ($π$VAE). The $π$VAE is finitely exchangeable and Kolmogorov consistent, and thus is a continuous stochastic process. We use $π$VAE to learn low dimensional embeddings of function classes. We show that our framework can accurately learn expressive function classes such as Gaussian processes, but also properties of functions to enable statistical inference (such as the integral of a log Gaussian process). For popular tasks, such as spatial interpolation, $π$VAE achieves state-of-the-art performance both in terms of accuracy and computational efficiency. Perhaps most usefully, we demonstrate that the low dimensional independently distributed latent space representation learnt provides an elegant and scalable means of performing Bayesian inference for stochastic processes within probabilistic programming languages such as Stan.

cs.LG↗

On the derivation of the renewal equation from an age-dependent branching process: an epidemic modelling perspective

Renewal processes are a popular approach used in modelling infectious disease outbreaks. In a renewal process, previous infections give rise to future infections. However, while this formulation seems sensible, its application to infectious disease can be difficult to justify from first principles. It has been shown from the seminal work of Bellman and Harris that the renewal equation arises as the expectation of an age-dependent branching process. In this paper we provide a detailed derivation of the original Bellman Harris process. We introduce generalisations, that allow for time-varying reproduction numbers and the accounting of exogenous events, such as importations. We show how inference on the renewal equation is easy to accomplish within a Bayesian hierarchical framework. Using off the shelf MCMC packages, we fit to South Korea COVID-19 case data to estimate reproduction numbers and importations. Our derivation provides the mathematical fundamentals and assumptions underpinning the use of the renewal equation for modelling outbreaks.

q-bio.PE↗

Estimating the number of infections and the impact of non-pharmaceutical interventions on COVID-19 in European countries: technical description update

Following the emergence of a novel coronavirus (SARS-CoV-2) and its spread outside of China, Europe has experienced large epidemics. In response, many European countries have implemented unprecedented non-pharmaceutical interventions including case isolation, the closure of schools and universities, banning of mass gatherings and/or public events, and most recently, wide-scale social distancing including local and national lockdowns. In this technical update, we extend a semi-mechanistic Bayesian hierarchical model that infers the impact of these interventions and estimates the number of infections over time. Our methods assume that changes in the reproductive number - a measure of transmission - are an immediate response to these interventions being implemented rather than broader gradual changes in behaviour. Our model estimates these changes by calculating backwards from temporal data on observed to estimate the number of infections and rate of transmission that occurred several weeks prior, allowing for a probabilistic time lag between infection and death. In this update we extend our original model [Flaxman, Mishra, Gandy et al 2020, Report #13, Imperial College London] to include (a) population saturation effects, (b) prior uncertainty on the infection fatality ratio, (c) a more balanced prior on intervention effects and (d) partial pooling of the lockdown intervention covariate. We also (e) included another 3 countries (Greece, the Netherlands and Portugal). The model code is available at https://github.com/ImperialCollegeLondon/covid19model/ We are now reporting the results of our updated model online at https://mrc-ide.github.io/covid19estimates/ We estimated parameters jointly for all M=14 countries in a single hierarchical model. Inference is performed in the probabilistic programming language Stan using an adaptive Hamiltonian Monte Carlo (HMC) sampler.

stat.AP↗