Related papers: Revisiting an equivalence between maximum parsimon…
Given a pair of graphs with the same number of vertices, the inexact graph matching problem consists in finding a correspondence between the vertices of these graphs that minimizes the total number of induced edge disagreements. We study…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
Maximum likelihood estimation is a fundamental optimization problem in statistics. We study this problem on manifolds of matrices with bounded rank. These represent mixtures of distributions of two independent discrete random variables. We…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Surprisal theory posits that the processing difficulty of a word is determined by its predictability in context, offering a potential link between human sentence processing and next-word predictions from language models. While language…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Time-homogeneous Markov chains are often used as disease progression models in studies of cost-effectiveness and optimal decision-making. Maximum likelihood estimation of these models can be challenging when data are collected at a time…
Recently maximum pseudo-likelihood (MPL) inference method has been successfully applied to statistical physics models with intractable likelihoods. We use information theory to derive a relation between the pseudo-likelihood and likelihood…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Most statistical models for pairwise comparisons, including the Bradley-Terry (BT) and Thurstone models and many extensions, make a relatively strong assumption of stochastic transitivity. This assumption imposes the existence of an…
Modern data sets in various domains often include units that were sampled non-randomly from the population and have a latent correlation structure. Here we investigate a common form of this setting, where every unit is associated with a…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
The $\lambda$-exponential family generalizes the standard exponential family via a generalized convex duality motivated by optimal transport. It is the constant-curvature analogue of the exponential family from the information-geometric…
There are various parametric models for analyzing pairwise comparison data, including the Bradley-Terry-Luce (BTL) and Thurstone models, but their reliance on strong parametric assumptions is limiting. In this work, we study a flexible…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
For supercritical multitype branching processes in continuous time, we investigate the evolution of types along those lineages that survive up to some time t. We establish almost-sure convergence theorems for both time and population…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary `Tree of Life'. This approach recognises that extinction not only removes species but…