arXiv subjects

Viet Chi Tran

Publications and source records attributed to Viet Chi Tran.

At least 37 records · Page 2Linked to original sources

arXiv2020

Inference with selection, varying population size and evolving population structure: Application of ABC to a forward-backward coalescent process with interactions

Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed \textit{a priori} known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interactions and asexual reproduction. We develop an inferential procedure for ecological, demographic and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. {This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging}. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated data from a toy model, and to real data by analyzing the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia human populations in order to test whether different social organizations show significantly different fertility.

q-bio.PE↗

arXiv2020

Statistical deconvolution of the free Fokker-Planck equation at fixed time

We are interested in reconstructing the initial condition of a non-linear partial differential equation (PDE), namely the Fokker-Planck equation, from the observation of a Dyson Brownian motion at a given time $t>0$. The Fokker-Planck equation describes the evolution of electrostatic repulsive particle systems, and can be seen as the large particle limit of correctly renormalized Dyson Brownian motions. The solution of the Fokker-Planck equation can be written as the free convolution of the initial condition and the semi-circular distribution. We propose a nonparametric estimator for the initial condition obtained by performing the free deconvolution via the subordination functions method. This statistical estimator is original as it involves the resolution of a fixed point equation, and a classical deconvolution by a Cauchy distribution. This is due to the fact that, in free probability, the analogue of the Fourier transform is the R-transform, related to the Cauchy transform. In past literature, there has been a focus on the estimation of the initial conditions of linear PDEs such as the heat equation, but to the best of our knowledge, this is the first time that the problem is tackled for a non-linear PDE. The convergence of the estimator is proved and the integrated mean square error is computed, providing rates of convergence similar to the ones known for non-parametric deconvolution methods. Finally, a simulation study illustrates the good performances of our estimator.

math.PR↗

arXiv2020

COVID-19 pandemic control: balancing detection policy and lockdown intervention under ICU sustainability

We consider here an extended SIR model, including several features of the recent COVID-19 outbreak: in particular the infected and recovered individuals can either be detected (+) or undetected (-) and we also integrate an intensive care unit (ICU) capacity. Our model enables a tractable quantitative analysis of the optimal policy for the control of the epidemic dynamics using both lockdown and detection intervention levers. With parametric specification based on literature on COVID-19, we investigate the sensitivities of various quantities on the optimal strategies, taking into account the subtle trade-off between the sanitary and the socio-economic cost of the pandemic, together with the limited capacity level of ICU. We identify the optimal lockdown policy as an intervention structured in 4 successive phases: First a quick and strong lockdown intervention to stop the exponential growth of the contagion; second a short transition phase to reduce the prevalence of the virus; third a long period with full ICU capacity and stable virus prevalence; finally a return to normal social interactions with disappearance of the virus. The optimal scenario hereby avoids the second wave of infection, provided the lockdown is released sufficiently slowly. We also provide optimal intervention measures with increasing ICU capacity, as well as optimization over the effort on detection of infectious and immune individuals. Whenever massive resources are introduced to detect infected individuals, the pressure on social distancing can be released, whereas the impact of detection of immune individuals reveals to be more moderate.

q-bio.PE↗

arXiv2020

The 2d-directed spanning forest converges to the Brownian web

The two-dimensional directed spanning forest (DSF) introduced by Baccelli and Bordenave is a planar directed forest whose vertex set is given by a homogeneous Poisson point process $\mathcal{N}$ on $\mathbb{R}^2$. If the DSF has direction $-e_y$, the ancestor $h(u)$ of a vertex $u \in \mathcal{N}$ is the nearest Poisson point (in the $L_2$ distance) having strictly larger $y$-coordinate. This construction induces complex geometrical dependencies. In this paper we show that the collection of DSF paths, properly scaled, converges in distribution to the Brownian web (BW). This verifies a conjecture made by Baccelli and Bordenave in 2007.

math.PR↗

arXiv2020

Renewal in Hawkes processes with self-excitation and inhibition

This paper investigates Hawkes processes on the positive real line exhibiting both self-excitation and inhibition. Each point of this point process impacts its future intensity by the addition of a signed reproduction function. The case of a nonnegative reproduction function corresponds to self-excitation, and has been widely investigated in the literature. In particular, there exists a cluster representation of the Hawkes process which allows to apply results known for Galton-Watson trees. In the present paper, we establish limit theorems for Hawkes process with signed reproduction functions by using renewal techniques. We notably prove exponential concentration inequalities, and thus extend results of Reynaud-Bouret and Roy (2007) which were proved for nonnegative reproduction functions using this cluster representation which is no longer valid in our case. An important step for this is to establish the existence of exponential moments for renewal times of M/G/infinity queues that appear naturally in our problem. These results have their own interest, independently of the original problem for the Hawkes processes.

math.PR↗

arXiv2020

Stochastic epidemics in a homogeneous community

These notes describe stochastic epidemics in a homogenous community. Our main concern is stochastic compartmental models (i.e. models where each individual belongs to a compartment, which stands for its status regarding the epidemic under study : S for susceptible, E for exposed, I for infectious, R for recovered) for the spread of an infectious disease. In the present notes we restrict ourselves to homogeneously mixed communities. We present our general model and study the early stage of the epidemic in chapter 1. Chapter 2 studies the particular case of Markov models, especially in the asymptotic of a large population, which leads to a law of large numbers and a central limit theorem. Chapter 3 considers the case of a closed population, and describes the final size of the epidemic (i.e. the total number of individuals who ever get infected). Chapter 4 considers models with a constant influx of susceptibles (either by birth, immigration of loss of immunity of recovered individuals), and exploits the CLT and Large Deviations to study how long it takes for the stochastic disturbances to stop an endemic situation which is stable for the deterministic epidemic model. The document ends with an Appendix which presents several mathematical notions which are used in these notes, as well as solutions to many of the exercises which are proposed in the various chapters.

math.PR↗

arXiv2020

Nonparametric adaptive estimation of order 1 Sobol indices in stochastic models, with an application to Epidemiology

Global sensitivity analysis is a set of methods aiming at quantifying the contribution of an uncertain input parameter of the model (or combination of parameters) on the variability of the response. We consider here the estimation of the Sobol indices of order 1 which are commonly-used indicators based on a decomposition of the output's variance. In a deterministic framework, when the same inputs always give the same outputs, these indices are usually estimated by replicated simulations of the model. In a stochastic framework, when the response given a set of input parameters is not unique due to randomness in the model, metamodels are often used to approximate the mean and dispersion of the response by deterministic functions. We propose a new non-parametric estimator without the need of defining a metamodel to estimate the Sobol indices of order 1. The estimator is based on warped wavelets and is adaptive in the regularity of the model. The convergence of the mean square error to zero, when the number of simulations of the model tend to infinity, is computed and an elbow effect is shown, depending on the regularity of the model. Applications in Epidemiology are carried to illustrate the use of non-parametric estimators.

math.ST↗

arXiv2019

Stochastic analysis of emergence of evolutionary cyclic behavior in population dynamics with transfer

Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a stochastic model for the evolution of a discrete population structured by a trait taking finitely many values, with density-dependent competition. Traits are vertically inherited unless a mutation occurs, and can also be horizontally transferred by unilateral conjugation with frequency dependent rate. Our goal is to analyze the trade-off between natural evolution to higher birth rates on one side, and transfer which drives the population towards lower birth rates on the other side. Simulations show that evolutionary outcomes include evolutionary suicide or cyclic re-emergence of small populations with well-adapted traits. We focus on a parameter scaling where individual mutations are rare but the global mutation rate tends to infinity. This implies that negligible sub-populations may have a strong contribution to evolution. Our main result quantifies the asymptotic dynamics of subpopulation sizes on a logarithmic scale. We characterize the possible evolutionary outcomes with explicit criteria on the model parameters. An important ingredient for the proofs lies in comparisons of the stochastic population process with linear or logistic birth-death processes with immigration. For the latter processes, we derive several results of independent interest.

math.PR↗

arXiv2019

Collision times of random walks and applications to the Brownian web

Convergence of directed forests, spanning on random subsets of lattices or on point processes, towards the Brownian web has made the subject of an abundant literature, a large part of which relies on a criterion proposed by Fontes, Isopi, Newman and Ravishankar (2004). One of their convergence condition, called (B2), states that the probability of the event that there exists three distinct paths for a time interval of length $t(>0)$, all starting within a segment of length $\varepsilon$, is of small order of $\varepsilon$. This condition is often verified by applying an FKG type correlation inequality together with a coalescing time tail estimate for two paths. For many models where paths have complex interactions, it is hard to establish FKG type inequalities. In this article, we show that for a non-crossing path model, with certain assumptions, a suitable upper bound on expected first collision time among three paths can be obtained directly using Lyapunov functions. This, in turn, provides an alternate verification of Condition (B2). We further show that in case of independent simple symmetric one dimensional random walks or in case of independent Brownian motions, the expected value can be computed explicitly. We apply this alternate method of verification of (B2) to several models in the basin of attraction of the Brownian web studied earlier in the literature ([S67], [H71], [FLT04]).

math.PR↗

arXiv2017

Stochastic dynamics for adaptation and evolution of microorganisms

We present a model for the dynamics of a population of bacteria with a continuum of traits, who compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait with possible mutations. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We consider a stochastic individual-based pure jump process taking values in the space of point measures, and whose jump events describe the individual reproduction, transfer and death mechanisms. In a large population scale, the stochastic process is proved to converge to the solution of a nonlinear integro-differential equation. When there are only two different traits and no mutation, this equation reduces to a non-standard two-dimensional dynamical system. We show how crucial the forms of the transfer rates are for the long-term behavior of its solutions. We describe the dynamics of invasion and fixation when one of the two traits is initially rare, and compute the invasion probabilities. Then, we study the process under the assumption of rare mutations. We prove that the stochastic process at the mutation time scale converges to a jump process which describes the successive invasions of successful mutants. We show that the horizontal transfer can have a major impact on the distribution of the successive mutational fixations, leading to dramatically different behaviors, from expected evolution scenarios to evolutionary suicide. Simulations are given to illustrate these phenomena.

math.PR↗

arXiv2017

Directed, cylindric and radial Brownian webs

The Brownian web (BW) is a collection of coalescing Brownian paths indexed by the plane. It appears in particular as continuous limit of various discrete models of directed forests of coalescing random walks and navigation schemes. Radial counterparts have been considered but global invariance principles are hard to establish. In this paper, we consider cylindrical forests which in some sense interpolate between the directed and radial forests: we keep the topology of the plane while still taking into account the angular component. We define in this way the cylindric Brownian web (CBW), which is locally similar to the planar BW but has several important macroscopic differences. For example, in the CBW, the coalescence time between two paths admits exponential moments and the CBW as its dual contain each a.s. a unique bi-infinite path. This pair of bi-infinite paths is distributed as a pair of reflected Brownian motions on the cylinder. Projecting the CBW on the radial plane, we obtain a radial Brownian web (RBW), i.e. a family of coalescing paths where under a natural parametrization, the angular coordinate of a trajectory is a Brownian motion. Recasting some of the discrete radial forests of the literature on the cylinder, we propose rescalings of these forests that converge to the CBW, and deduce the global convergence of the corresponding rescaled radial forests to the RBW. In particular, a modification of the radial model proposed in Coletti and Valencia is shown to converge to the CBW.

math.PR↗

arXiv2016

Inferring $R_0$ in emerging epidemics - the effect of common population structure is small

When controlling an emerging outbreak of an infectious disease it is essential to know the key epidemiological parameters, such as the basic reproduction number $R_0$ and the control effort required to prevent a large outbreak. These parameters are estimated from the observed incidence of new cases and information about the infectious contact structures of the population in which the disease spreads. However, the relevant infectious contact structures for new, emerging infections are often unknown or hard to obtain. Here we show that for many common true underlying heterogeneous contact structures, the simplification to neglect such structures and instead assume that all contacts are made homogeneously in the whole population, results in conservative estimates for $R_0$ and the required control effort. This means that robust control policies can be planned during the early stages of an outbreak, using such conservative estimates of the required control effort.

q-bio.PE↗

arXiv2015

The effect of competition and horizontal trait inheritance on invasion, fixation and polymorphism

Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present a modeling framework for the dynamics of two populations that compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We capture this feedback with a stochastic individual-based model, from which we derive a deterministic approximation for large populations. The interaction between horizontal transfer and competition makes possible the stable (or bi-stable) polymorphic maintenance of deleterious traits (including costly plasmids). When transfer rates are of a general density-dependent form, transfer stochasticity contributes strongly to population fluctuations. For an initially rare trait, we describe the probabilistic dynamics of invasion and fixation. Acceleration of fixation by HT is faster when competition is weak in the resident population. Thus, HT can have a major impact on the distribution of mutational effects that are fixed, and our model provides a basis for a general theory of the influence of HT on eco-evolutionary dynamics and adaptation.

q-bio.PE↗

arXiv2015

Impact of a treatment as prevention strategy on hepatitis C virus transmission and on morbidity in people who inject drugs

Background: Highly effective direct-acting antiviral (DAA) regimens (90% efficacy) are becoming available for hepatitis C virus (HCV) treatment. This therapeutic revolution leads us to consider possibility of eradicating the virus. However, for this, an effective cascade of care is required. Methods: In the context of the incoming DAAs, we used a dynamic individual-based model including a model of the people who inject drugs (PWID) social network to simulate the impact of improved testing, linkage to care, and adherence to treatment, and of modified treatment recommendation on the transmission and on the morbidity of HCV in PWID in France. Results: Under the current incidence and cascade of care, with treatment initiated at fibrosis stage $\ge$F2, the HCV prevalence decreased from 42.8% to 24.9% [95% confidence interval 24.8%--24.9%] after 10 years. Changing treatment initiation criteria to treat from F0 was the only intervention leading to a substantial additional decrease in the prevalence, which fell to 11.6% [11.6%--11.7%] at 10 years. Combining this change with improved testing, linkage to care, and adherence to treatment decreased HCV prevalence to 7% [7%--7.1%] at 10 years and avoided 15.3% [14.0%-16.6%] and 29.0% [27.9%--30.1%] of cirrhosis complications over 10 and 40 years respectively. Conclusion: A high decrease in viral transmission occurs only when treatment is initiated before liver disease progresses to severe stages, suggesting that systematic treatment in PWID, where incidence remains high, would be beneficial. However, eradication will be difficult to achieve.

q-bio.PE↗

arXiv2015

A statistical network analysis of the HIV/AIDS epidemics in Cuba

The Cuban contact-tracing detection system set up in 1986 allowed the reconstruction and analysis of the sexual network underlying the epidemic (5,389 vertices and 4,073 edges, giant component of 2,386 nodes and 3,168 edges), shedding light onto the spread of HIV and the role of contact-tracing. Clustering based on modularity optimization provides a better visualization and understanding of the network, in combination with the study of covariates. The graph has a globally low but heterogeneous density, with clusters of high intraconnectivity but low interconnectivity. Though descriptive, our results pave the way for incorporating structure when studying stochastic SIR epidemics spreading on social networks.

stat.AP↗

arXiv2015

Dynamic modelling of hepatitis C virus transmission among people who inject drugs: a methodological review

Equipment sharing among people who inject drugs (PWID) is a key risk factor in infection by hepatitis C virus (HCV). Both the effectiveness and cost-effectiveness of interventions aimed at reducing HCV transmission in this population (such as opioid substitution therapy, needle exchange programs or improved treatment) are difficult to evaluate using field surveys. Ethical issues and complicated access to the PWID population make it difficult to gather epidemiological data. In this context, mathematical modelling of HCV transmission is a useful alternative for comparing the cost and effectiveness of various interventions. Several models have been developed in the past few years. They are often based on strong hypotheses concerning the population structure. This review presents compartmental and individual-based models in order to underline their strengths and limits in the context of HCV infection among PWID. The final section discusses the main results of the papers.

stat.AP↗

arXiv2014

Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks

How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep.

math.PR↗

arXiv2013

On Computer-Intensive Simulation and Estimation Methods for Rare Event Analysis in Epidemic Models

This article focuses, in the context of epidemic models, on rare events that may possibly correspond to crisis situations from the perspective of Public Health. In general, no close analytic form for their occurrence probabilities is available and crude Monte-Carlo procedures fail. We show how recent intensive computer simulation techniques, such as interacting branching particle methods, can be used for estimation purposes, as well as for generating model paths that correspond to realizations of such events. Applications of these simulation-based methods to several epidemic models are also considered and discussed thoroughly.

stat.AP↗