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The spectrum of Markov generators encodes physical information beyond simple decay and oscillation, which reflects irreversibility and governs the structure of correlation functions. In this work, we prove an ellipse theorem that provides a…
Trees of finite cone type have appeared in various contexts. In particular, they come up as simplified models of regular tessellations of the hyperbolic plane. The spectral theory of the associated Laplacians can thus be seen as induced by…
The goal of this work is to decompose random populations with a genealogy in subfamilies of a given degree of kinship and to obtain a notion of infinitely divisible genealogies. We model the genealogical structure of a population by…
We prove the existence of the total length process for the genealogical tree of a population model with random size given by a quadratic stationary continuous-state branching processes. We also give, for the one-dimensional marginal, its…
The study of spectral properties of natural geometric elliptic partial differential operators acting on smooth sections of vector bundles over Riemannian manifolds is a central theme in global analysis, differential geometry and…
Reconstructing the tree of life from molecular sequences is a fundamental problem in computational biology. Modern data sets often contain a large number of genes, which can complicate the reconstruction problem due to the fact that…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Spectral analysis has long been recognized as a fundamental tool for studying the existence, uniqueness, and qualitative behavior of solutions to semilinear elliptic and parabolic equations, as well as their long-time dynamics. In modern…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
We introduce a theory of local kernels, which generalize the kernels used in the standard diffusion maps construction of nonparametric modeling. We prove that evaluating a local kernel on a data set gives a discrete representation of the…
The complete knowledge of Laplacian eigenvalues and eigenvectors of complex networks plays an outstanding role in understanding various dynamical processes running on them; however, determining analytically Laplacian eigenvalues and…
We study basic spectral features of graph Laplacians associated with a class of rooted trees which contains all regular trees. Trees in this class can be generated by substitution processes. Their spectra are shown to be purely absolutely…
Ultametrics are an important class of distances used in applications such as phylogenetics, clustering and classification theory. Ultrametrics are essentially distances that can be represented by an edge-weighted rooted tree so that all of…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…
We study the spectral Tur\'an problem for trees. To avoid limiting our perspective to specific families of trees, we parametrize trees in terms of their unique bipartition. We say $T \in \mathcal{T}_{m,l+1}^{\delta}$ if $T$ is a tree of…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
We investigate the genealogical structure of general critical or subcritical continuous-state branching processes. Analogously to the coding of a discrete tree by its contour function, this genealogical structure is coded by a real-valued…