Related papers: Spectral Geometry and Heat Kernels on Phylogenetic…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
Given a rooted tree $T$ with vertices $u_1,u_2,\ldots,u_n$, the level matrix $L(T)$ of $T$ is the $n \times n$ matrix for which the $(i,j)$-th entry is the absolute difference of the distances from the root to $v_i$ and $v_j$. This matrix…
We study the matrices Q_k of in-forests of a weighted digraph G and their connections with the Laplacian matrix L of G. The (i,j) entry of Q_k is the total weight of spanning converging forests (in-forests) with k arcs such that i belongs…
We study the spectral convergence of a symmetrized Graph Laplacian matrix induced by a Gaussian kernel evaluated on pairs of embedded data, sampled from a manifold with boundary, a sub-manifold of $\mathbb{R}^m$. Specifically, we deduce the…
The spectral analysis of the electromagnetic field on the background of a infinitely thin flat plasma layer is carried out. This model is loosely imitating a single base plane from graphite and it is of interest for theoretical studies of…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
We propose the first comprehensive approach for modeling and analyzing the spatiotemporal shape variability in tree-like 4D objects, i.e., 3D objects whose shapes bend, stretch, and change in their branching structure over time as they…
We establish an exact analytic relation between random spanning forests and the heat-kernel partition function. This identity enables estimation of partition functions, energies, and the Von Neumann entropy by Wilson sampling of forests,…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
Background. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set $L$ is known to be solvable in linear time.…
Building trees to represent or to fit distances is a critical component of phylogenetic analysis, metric embeddings, approximation algorithms, geometric graph neural nets, and the analysis of hierarchical data. Much of the previous…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
In this paper, we present an alternative method for the spectral analysis of a univariate, strictly stationary time series $\{Y_t\}_{t\in \mathbb {Z}}$. We define a "new" spectrum as the Fourier transform of the differences between copulas…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Quantum graphs have attracted attention from mathematicians for some time. A quantum graph is defined by having a Laplacian on each edge of a metric graph and imposing boundary conditions at the vertices to get an eigenvalue problem. A…
This article proposes a framework for the study of periodic maps $T$ from a (typically finite) set $X$ to itself when the set $X$ is equipped with one or more real- or complex-valued functions. The main idea, inspired by the time-evolution…
Nested (or reconciled) phylogenetic trees model co-evolutionary systems in which one evolutionary history is embedded within another. We introduce a geometric framework for such systems by defining $\sigma$-space, a moduli space of fully…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…