Related papers: Split probabilities and species tree inference und…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…
As genomic scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process are essential for the testing and evaluation of new inference methods. However, the simulators themselves must be…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
We consider three bivariate polynomial invariants $P$, $A$, and $S$ for rooted trees, as well as a trivariate polynomial invariant $M$. These invariants are motivated by random destruction processes such as the random cutting model or site…
One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…
Coloured probability tree models are statistical models coding conditional independence between events depicted in a tree graph. They are more general than the very important class of context-specific Bayesian networks. In this paper, we…
The most popular approach for analyzing survival data is the Cox regression model. The Cox model may, however, be misspecified, and its proportionality assumption may not always be fulfilled. An alternative approach for survival prediction…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Gene genealogies are frequently studied by measuring properties such as their height ($H$), length ($L$), sum of external branches ($E$), sum of internal branches ($I$), and mean of their two basal branches ($B$), and the coalescence times…
Internet mapping projects generally consist in sampling the network from a limited set of sources by using traceroute probes. This methodology, akin to the merging of spanning trees from the different sources to a set of destinations, leads…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
We study the fundamental question of how likely it is that two randomly chosen trees are isomorphic to each other for different models of random trees. We show that the probability decays exponentially for rooted labeled trees as well as…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories…
A cluster tree provides a highly-interpretable summary of a density function by representing the hierarchy of its high-density clusters. It is estimated using the empirical tree, which is the cluster tree constructed from a density…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…