Related papers: Determining species tree topologies from clade pro…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
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…
An early burst of speciation followed by a subsequent slowdown in the rate of diversification is commonly inferred from molecular phylogenies. This pattern is consistent with some verbal theory of ecological opportunity and adaptive…
We investigate at decision trees that incorporate both traditional queries based on one attribute and queries based on hypotheses about the values of all attributes. Such decision trees are similar to ones studied in exact learning, where…
Trees corresponding to $\Lambda$- and $\Xi$-$n$-coalescents can be both quite similar and fundamentally different compared to bifurcating tree models based on Kingman's $n$-coalescent. This has consequences for inference of a well-fitting…
Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…
The concept of trustworthy AI has gained widespread attention lately. One of the aspects relevant to trustworthy AI is robustness of ML models. In this study, we show how to probabilistically quantify robustness against naturally occurring…
Recently, there has been interest in extending long-known results about the multispecies coalescent tree to other models of gene trees. Results about the gene duplication and loss (GDL) tree have mathematical proofs, including species tree…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
In this paper, we characterize the structure and topological indices of a class of random spider trees (RSTs) such as degree-based Gini index, degree-based Hoover index, generalized Zagreb index and other indices associated with these. We…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
A learning algorithm is presented which given the structure of a causal tree, will estimate its link probabilities by sequential measurements on the leaves only. Internal nodes of the tree represent conceptual (hidden) variables…
Joint distributions over many variables are frequently modeled by decomposing them into products of simpler, lower-dimensional conditional distributions, such as in sparsely connected Bayesian networks. However, automatically learning such…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
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…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
Most current methods for inferring species-level phylogenies under the coalescent model assume that no gene flow occurs following speciation. While some studies have examined the impact of gene flow on estimation accuracy for certain…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…