Related papers: Spectral Geometry and Heat Kernels on Phylogenetic…
The work in this thesis concerns the investigation of eigenvalues of the Laplacian matrix, normalized Laplacian matrix, signless Laplacian matrix and distance signless Laplacian matrix of graphs. In Chapter 1, we present a brief…
We study finite-time spectral rigidity in reversible Markov chains via exact spectral relaxation dynamics. While the underlying identities follow classically from self-adjointness on $L^2(\pi)$, organizing the dynamics around the relaxation…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
Using methods from algebraic graph theory and convex optimization, we study the relationship between local structural features of a network and spectral properties of its Laplacian matrix. In particular, we derive expressions for the…
Tree embedding has been a fundamental method in algorithm design with wide applications. We focus on the efficiency of building tree embedding in various computational settings under high-dimensional Euclidean $\mathbb{R}^d$. We devise a…
Spectral methods that are based on eigenvectors and eigenvalues of discrete graph Laplacians, such as Diffusion Maps and Laplacian Eigenmaps are often used for manifold learning and non-linear dimensionality reduction. It was previously…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
Large language models are remarkably capable, yet how computation propagates through their layers remains poorly understood. A growing line of work treats depth as discrete time and the residual stream as a dynamical system, where each…
We investigate uniqueness issues that arise in $l^\infty$-optimization to linear spaces and Bergman fans of matroids. For linear spaces, we give a polyhedral decomposition of $\mathbb{R}^n$ based on the dimension of the set of…
We present a model for spectral theory of families of selfadjoint operators, and their corresponding unitary one-parameter groups (acting in Hilbert space.) The models allow for a scale of complexity, indexed by the natural numbers…
Understanding the emergence of biodiversity patterns in nature is a central problem in biology. Theoretical models of speciation have addressed this question in the macroecological scale, but little has been investigated in the…
We consider the Laplacian on a rooted metric tree graph with branching number $ K \geq 2 $ and random edge lengths given by independent and identically distributed bounded variables. Our main result is the stability of the absolutely…
Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…
Laplacian operators are classical objects that are fundamental in both pure and applied mathematics and are becoming increasingly prominent in modern computational and data science fields such as applied and computational topology and…
We introduce a one-parameter family of massive Laplacian operators $(\Delta^{m(k)})_{k\in[0,1)}$ defined on isoradial graphs, involving elliptic functions. We prove an explicit formula for the inverse of $\Delta^{m(k)}$, the massive Green…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
By a discrete torus we mean the Cayley graph associated to a finite product of finite cycle groups with generating set given by choosing a generator for each cyclic factor. In this article we study the spectral theory of the combinatorial…
We consider the heat semi-group generated by the Laplace operator on metric trees. Among our results we show how the behavior of the associated heat kernel depends on the geometry of the tree. As applications we establish new eigenvalue…
We study the asymptotic expansion of the determinant of the graph Laplacian associated to discretizations of a half-translation surface endowed with a flat unitary vector bundle. By doing so, over the discretizations, we relate the…