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The investigation of allele frequency trajectories in populations evolving under controlled environmental pressures has become a popular approach to study evolutionary processes on the molecular level. Statistical models based on…
This article partakes of the PEGASE project the goal of which is a better understanding of the mechanisms explaining the behaviour of species living in a network of forest patches linked by ecological corridors (hedges for instance).…
Under the effect of strong genetic drift, it is highly probable to observe gene fixation or gene loss in a population, shown by infinite peaks on a coherently constructed potential energy landscape. It is then important to ask what such…
We show that the Eigen model and the asexual Wright-Fisher model can be obtained as different limit cases of a unique stochastic model. This derivation makes clear which are the exact differences between these two models. The two key…
This paper introduces a novel Bayesian approach for variable selection in high-dimensional and potentially sparse regression settings. Our method replaces the indicator variables in the traditional spike and slab prior with continuous,…
In this work we present a systematic mathematical approximation scheme that exposes the way that information, about the evolutionary forces of selection and random genetic drift, is encoded in gene-frequency trajectories. We determine…
The entropy rates of the Wright-Fisher process, the Moran process, and generalizations are computed and used to compare these processes and their dependence on standard evolutionary parameters. Entropy rates are measures of the variation…
Inference methods are often formulated as variational approximations: these approximations allow easy evaluation of statistics by marginalization or linear response, but these estimates can be inconsistent. We show that by introducing…
The proposed approach extends the confidence posterior distribution to the semi-parametric empirical Bayes setting. Whereas the Bayesian posterior is defined in terms of a prior distribution conditional on the observed data, the confidence…
The transition distribution of a sample taken from a Wright-Fisher diffusion with general small mutation rates is found using a coalescent approach. The approximation is equivalent to having at most one mutation in the coalescent tree of…
We present Adjacent Possible Exploration (APE), a selective fine-tuning method for adapting large language models that systematically explores parameter modifications while maintaining model stability. Inspired by evolutionary optimization…
The estimation of parameters in the frequency spectrum of a seasonally persistent stationary stochastic process is addressed. For seasonal persistence associated with a pole in the spectrum located away from frequency zero, a new…
Phenotypes of individuals in a population of organisms are not fixed. Phenotypic fluctuations, which describe temporal variation of the phenotype of an individual or individual-to-individual variation across a population, are present in…
We construct extensions of the pure-jump $\Lambda$-Wright-Fisher processes with frequency-dependent selection ($\Lambda$-WF processes with selection) beyond their first passage time at the boundary $1$. We show that they satisfy some…
The Welch-Satterthwaite t-test is one of the most prominent and often used statistical inference method in applications. The method is, however, not flexible with respect to adjustments for baseline values or other covariates, which may…
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…
Quantitative assessment of extinction risk requires confidence intervals (CIs) that remain informative with limited data. Their usefulness has long been debated because short observation spans can make uncertainty so large that population…
The spectral evolution model aims to characterize the growth of large networks (i.e., how they evolve as new edges are established) in terms of the eigenvalue decomposition of the adjacency matrices. It assumes that, while eigenvectors…
Natural populations often show enhanced genetic drift consistent with a strong skew in their offspring number distribution. The skew arises because the variability of family sizes is either inherently strong or amplified by population…
In this paper we develop and test algorithmic techniques to estimate genotypes fitnesses by analysis of observed daily frequency data monitoring the long-term evolution of bacterial populations. In particular, we develop a non-linear least…