Related papers: Exact and efficient phylodynamic simulation from a…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
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…
Cell segmentation and tracking allow us to extract a plethora of cell attributes from bacterial time-lapse cell movies, thus promoting computational modeling and simulation of biological processes down to the single-cell level. However, to…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Fault tree analysis is a well-known technique in reliability engineering and risk assessment, which supports decision-making processes and the management of complex systems. Traditionally, fault tree (FT) models are built manually together…
We consider the problem of estimating a large causal polytree from a relatively small i.i.d. sample. This is motivated by the problem of determining causal structure when the number of variables is very large compared to the sample size,…
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…
The constant rate birth--death process is a popular null model for speciation and extinction. If one removes extinct and non-sampled lineages, this process induces `reconstructed trees' which describe the relationship between extant…
We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have $n$ extant species today, we look at the tree distribution of the reconstructed trees-- i.e. the trees…
The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Datasets can be biased due to societal inequities, human biases, under-representation of minorities, etc. Our goal is to certify that models produced by a learning algorithm are pointwise-robust to potential dataset biases. This is a…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
Almost all fields of science rely upon statistical inference to estimate unknown parameters in theoretical and computational models. While the performance of modern computer hardware continues to grow, the computational requirements for the…
Sequential importance sampling algorithms have been defined to estimate likelihoods in models of ancestral population processes. However, these algorithms are based on features of the models with constant population size, and become…
The controlled branching process is a generalization of the classical Bienaym\'e-Galton-Watson branching process. It is a useful model for describing the evolution of populations in which the population size at each generation needs to be…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…