Related papers: Nested tree space: a geometric framework for co-ph…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
The structure of topological spaces is analysed here through the lenses of fibrous preorders. Each topological space has an associated fibrous preorder and those fibrous preorders which return a topological space are called spacial. A…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Merge trees are a type of graph-based topological summary that tracks the evolution of connected components in the sublevel sets of scalar functions. They enjoy widespread applications in data analysis and scientific visualization. In this…
We compare the structures and methods in the theory of causal fermion systems with generalized trace dynamics and non-commutative geometry. Although the three theories differ on many aspects, they agree in that the geometric structure to be…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
Bayesian networks faithfully represent the symmetric conditional independences existing between the components of a random vector. Staged trees are an extension of Bayesian networks for categorical random vectors whose graph represents…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
In a supercritical branching particle system, the trimmed tree consists of those particles which have descendants at all times. We develop this concept in the superprocess setting. For a class of continuous superprocesses with Feller…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Staged trees are a relatively recent class of probabilistic graphical models that extend Bayesian networks to formally and graphically account for non-symmetric patterns of dependence. Machine learning algorithms to learn them from data…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks as they contain both directed as well as undirected edges. While…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
$\Delta$-spaces have been defined by a natural generalization of a classical notion of $\Delta$-sets of reals to Tychonoff topological spaces; moreover, the class $\Delta$ of all $\Delta$-spaces consists precisely of those $X$ for which the…
Several structure-learning algorithms for staged trees, asymmetric extensions of Bayesian networks, have been proposed. However, these either do not scale efficiently as the number of variables considered increases, a priori restrict the…