Related papers: Spectral Geometry and Heat Kernels on Phylogenetic…
Mutations of genetic sequences are often accompanied by their recombinations, known as phylogenetic networks. These networks are typically reconstructed from coalescent processes that may arise from optimal merging or fitting together a…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
We propose a new space of phylogenetic trees which we call wald space. The motivation is to develop a space suitable for statistical analysis of phylogenies, but with a geometry based on more biologically principled assumptions than…
A framework for coherent pattern extraction and prediction of observables of measure-preserving, ergodic dynamical systems with both atomic and continuous spectral components is developed. It is based on an approximation of the generator of…
We give a formula relating the $L^2$-isoperimetric profile to the spectral distribution of the Laplace operator associated to a finitely generated group $\Gamma$ or a Riemannian manifold with a cocompact, isometric $\Gamma$-action. As a…
The celebrated Cheeger's Inequality establishes a bound on the edge expansion of a graph via its spectrum. This inequality is central to a rich spectral theory of graphs, based on studying the eigenvalues and eigenvectors of the adjacency…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We analyze the spectral clustering procedure for identifying coarse structure in a data set $x_1, \dots, x_n$, and in particular study the geometry of graph Laplacian embeddings which form the basis for spectral clustering algorithms. More…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Tree structured graphical models are powerful at expressing long range or hierarchical dependency among many variables, and have been widely applied in different areas of computer science and statistics. However, existing methods for…
Spectral functions play a central role in the characterization of a wide range of physical systems, including strongly interacting quantum field theories and many-body systems. Their non-perturbative determination from Euclidean correlation…
Kirchoff's matrix tree theorem of 1847 connects the number of spanning trees of a graph to the spectral determinant of the discrete Laplacian [22]. Recently an analogue was obtained for quantum graphs relating the number of spanning trees…
We study a variety of problems in the spectral theory of automorphic forms using entirely analytic techniques such as Selberg trace formula, asymptotics of Whittaker functions and behavior of heat kernels. Error terms for Weyl's law and an…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
We study the spectra of quantum trees of finite cone type. These are quantum graphs whose geometry has a certain homogeneity, and which carry a finite set of edge lengths, coupling constants and potentials on the edges. We show the spectrum…
The aim of the present article is to give an overview of spectral theory on metric graphs guided by spectral geometry on discrete graphs and manifolds. We present the basic concept of metric graphs and natural Laplacians acting on it and…
Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…
The recent development of spectral method has been praised for its high-order convergence in simulating complex physical problems. The combination of embedded boundary method and spectral method becomes a mainstream way to tackle…
By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil…