相关论文: A renewal theory approach to IBD sharing
When a beneficial mutation occurs in a population, the new, favored allele may spread to the entire population. This process is known as a selective sweep. Suppose we sample $n$ individuals at the end of a selective sweep. If we focus on a…
Spatial patterning is common in ecological systems and has been extensively studied via different modeling approaches. Individual-based models (IBMs) accurately describe nonlinear interactions at the organism level and the stochastic…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
Source-sink systems are metapopulations of habitat patches with different, and possibly temporally varying, habitat qualities, which are commonly used in ecology to study the fate of spatially extended natural populations. We propose new…
We show that evolutionary computation can be implemented as standard Markov-chain Monte-Carlo (MCMC) sampling. With some care, `genetic algorithms' can be constructed that are reversible Markov chains that satisfy detailed balance; it…
Attribution methods are primarily designed to study input component contributions to individual model predictions. However, some research applications require a summary of attribution patterns across the entire dataset to facilitate the…
Consider a haploid population which has evolved through an exchangeable reproduction dynamics, and in which all individuals alive at time $t$ have a most recent common ancestor (MRCA) who lived at time $A_t$, say. As time goes on, not only…
We consider parameter estimation in a regression model corresponding to an iid sequence of censored observations of a finite state modulated renewal process. The model assumes a similar form as in Cox regression except that the baseline…
Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…
We define a doubly infinite, monotone labeling of Bienayme-Galton-Watson (BGW) genealogies. The genealogy of the current generation backwards in time is uniquely determined by the coalescent point process $(A_i; i\ge 1)$, where $A_i$ is the…
The Moran model with recombination is considered, which describes the evolution of the genetic composition of a population under recombination and resampling. There are $n$ sites (or loci), a finite number of letters (or alleles) at every…
The generalized Fibonacci recurrence $g_n=g_{n-k}+g_{n-m}$ was recently used to demonstrate the theoretically optimal nature of limited senescence in morphologically symmetrically dividing bacteria. Here, we study this recurrence from a…
We review the theory of regenerative processes, which are processes that can be intuitively seen as comprising of i.i.d.\ cycles. Although we focus on the classical definition, we present a more general definition that allows for some form…
Inspired by the combination of feedforward and iterative computations in the virtual cortex, and taking advantage of the ability of denoising autoencoders to estimate the score of a joint distribution, we propose a novel approach to…
It is our intention to provide via fractional calculus a generalization of the pure and compound Poisson processes, which are known to play a fundamental role in renewal theory, without and with reward, respectively. We first recall the…
Structural and appearance changes in brain imaging over time are crucial indicators of neurodevelopment and neurodegeneration. The rapid advancement of large-scale generative models provides a promising backbone for modeling these complex…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…
We study a stochastic model based on a modified fragmentation of a finite interval. The mechanism consists in cutting the interval at a random location and substituting a unique fragment on the right of the cut to regenerate and preserve…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
Dropout represents a typical issue to be addressed when dealing with longitudinal studies. If the mechanism leading to missing information is non-ignorable, inference based on the observed data only may be severely biased. A frequent…