Related papers: Selection and Coalescence in a Finite State Model
We introduce a low dimensional function of the site frequency spectrum that is tailor-made for distinguishing coalescent models with multiple mergers from Kingman coalescent models with population growth, and use this function to construct…
One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…
Strong positive feedback is considered a necessary condition to observe abrupt shifts of ecosystems. A few previous studies have shown that demographic noise -- arising from the probabilistic and discrete nature of birth and death processes…
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…
In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…
Disordered materials under an imposed forcing can display creep and aging effects, accompanied by intermittent, spatially heterogeneous dynamics. We propose a unifying microscopic description of these phenomena, based on the notion that as…
The problem of subgroups is ubiquitous in scientific research (ex. disease heterogeneity, spatial distributions in ecology...), and piecewise regression is one way to deal with this phenomenon. Morse-Smale regression offers a way to…
In these expository notes, we describe some features of the multiplicative coalescent and its connection with random graphs and minimum spanning trees. We use Pitman's proof of Cayley's formula, which proceeds via a calculation of the…
Coalescent theory combined with statistical modeling allows us to estimate effective population size fluctuations from molecular sequences of individuals sampled from a population of interest. When sequences are sampled serially through…
We present convincing empirical evidence for an effective and general strategy for building accurate small models. Such models are attractive for interpretability and also find use in resource-constrained environments. The strategy is to…
We address the problem of incremental sequence classification, where predictions are updated as new elements in the sequence are revealed. Drawing on temporal-difference learning from reinforcement learning, we identify a…
A probability model is presented for the dynamics of mutation-selection balance in a haploid infinite-population infinite-sites setting sufficiently general to cover mutation-driven changes in full age-specific demographic schedules. The…
Decision trees and random forest remain highly competitive for classification on medium-sized, standard datasets due to their robustness, minimal preprocessing requirements, and interpretability. However, a single tree suffers from high…
Identifiability of evolutionary tree models has been a recent topic of discussion and some models have been shown to be non-identifiable. A coalescent-based rooted population tree model, originally proposed by Nielsen et al. 1998 [2], has…
In a 1996 paper, See$\beta$elberg, Trautmann and Thorn modified Gillespie's (1975) Monte Carlo algorithm which is used to stochastically simulate the collision and coalescence process. Their modification reduces the storage requirements of…
We investigate the computational hardness of spin-glass instances on a square lattice, generated via a recently introduced tunable and scalable approach for planting solutions. The method relies on partitioning the problem graph into…
We propose a new algorithm to do posterior sampling of Kingman's coalescent, based upon the Particle Markov Chain Monte Carlo methodology. Specifically, the algorithm is an instantiation of the Particle Gibbs Sampling method, which…
A stochastic system of particles is considered in which the sizes of the particles increase by successive binary mergers with the constraint that each coagulation event involves a particle with minimal size. Convergence of a suitably…
Monte Carlo optimizations of Number Partitioning and of Diophantine approximations are microscopic realizations of `Trap Model' dynamics. This offers a fresh look at the physics behind this model, and points at other situations in which it…
We investigate the genealogy of a sample of $k\geq1$ particles chosen uniformly without replacement from a population alive at large times in a critical discrete-time Galton-Watson process in a varying environment (GWVE). We will show that…