相关论文: Identifiability of 2-tree mixtures for group-based…
The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
The theory of complex trees is introduced as a new approach to study a broad class of self-similar sets. Systems of equations encoded by complex trees tip-to-tip equivalence relations are used to obtain one-parameter families of connected…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
The $\text{NJ}_{st}$ method was proposed by Liu and Yu to infer a species tree topology from unrooted topological gene trees. While its statistical consistency under the multispecies coalescent model was established only for a 4-taxon tree,…
The study of neuronal morphology is important not only for its potential relationship with neuronal dynamics, but also as a means to classify diverse types of cells and compare than among species, organs, and conditions. In the present…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Repetitions within a given genealogical tree provides some information about the degree of consanguineity of a population. They can be analyzed with techniques usually employed in statistical physics when dealing with fixed point…
We define a class of probability distributions that we call simplicial mixture models, inspired by simplicial complexes from algebraic topology. The parameters of these distributions represent their topology and we show that it is possible…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
This work focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A particular example that is the focus of our work is the phylogenetic tree, with nodes often representing biological…
Recent research has established sufficient conditions for finite mixture models to be identifiable from grouped observations. These conditions allow the mixture components to be nonparametric and have substantial (or even total) overlap.…
Many real-world networks known as attributed networks contain two types of information: topology information and node attributes. It is a challenging task on how to use these two types of information to explore structural regularities. In…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
Phenomenological models are highly effective tools for forecasting disease dynamics using real world data, particularly in scenarios where detailed knowledge of disease mechanisms is limited. However, their reliability depends on the model…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…