Related papers: Spectral Geometry and Heat Kernels on Phylogenetic…
Let $L$ be a fixed branch -- that is, an irreducible germ of curve -- on a normal surface singularity $X$. If $A,B$ are two other branches, define $u_L(A,B) := \dfrac{(L \cdot A) \: (L \cdot B)}{A \cdot B}$, where $A \cdot B$ denotes the…
Let $S$ be a normal complex analytic surface singularity. We say that $S$ is arborescent if the dual graph of any resolution of it is a tree. Whenever $A,B$ are distinct branches on $S$, we denote by $A \cdot B$ their intersection number in…
A central issue in the study of polymer physics is to understand the relation between the geometrical properties of macromolecules and various dynamics, most of which are encoded in the Laplacian spectra of a related graph describing the…
We investigate spectral properties of Kirchhoff Laplacians on radially symmetric antitrees. This class of metric graphs enjoys a rich group of symmetries, which enables us to obtain a decomposition of the corresponding Laplacian into the…
Phylogenetic trees are the fundamental mathematical representation of evolutionary processes in biology. They are also objects of interest in pure mathematics, such as algebraic geometry and combinatorics, due to their discrete geometry.…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
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.…
A generalized Fourier analysis on arbitrary graphs calls for a detailed knowledge of the eigenvectors of the graph Laplacian. Using the symmetries of the Cayley tree, we recursively construct the family of eigenvectors with exponentially…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…
The eigenvalues of the normalized Laplacian matrix of a network plays an important role in its structural and dynamical aspects associated with the network. In this paper, we study the spectra and their applications of normalized Laplacian…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
We present examples of rooted tree graphs for which the Laplacian has singular continuous spectral measures. For some of these examples we further establish fractional Hausdorff dimensions. The singular continuous components, in these…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
This paper investigates spectral properties of the deformed Laplacian matrix, which merges the Laplacian and signless Laplacian matrices of a graph through a one-parameter family of matrices. We present general results on the eigenvalues of…
The mating of trees approach to Schramm-Loewner evolution (SLE) in the random geometry of Liouville quantum gravity (LQG) has been recently developed by Duplantier-Miller-Sheffield (2014). In this paper we consider the mating of trees…
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the same tree topologies. Such incongruence between gene trees…
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…
Hierarchical tree structures are common in many real-world systems, from tree roots and branches to neuronal dendrites and biologically inspired artificial neural networks, as well as in technological networks for organizing and searching…