Related papers: Spectral Geometry and Heat Kernels on Phylogenetic…
In our work we have reconsidered the old problem of diffusion at the boundary of ultrametric tree from a "number theoretic" point of view. Namely, we use the modular functions (in particular, the Dedekind eta-function) to construct the…
The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the…
We define two families of determinantal random spanning subgraphs of a finite connected graph, one supported by acyclic spanning subgraphs (spanning forests) with fixed number of connected components, the other by connected spanning…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
We generalize the definition and enumeration of spanning trees from the setting of graphs to that of arbitrary-dimensional simplicial complexes $\Delta$, extending an idea due to G. Kalai. We prove a simplicial version of the Matrix-Tree…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
We study a representation-theoretic refinement of the ordinary Laplacian spectrum of a graph. Given a graph $G$ on $n$ vertices, one may associate to it the element \[ X_G=\sum_{ij\in E(G)} (ij)\in \C[S_n]. \] The action of $X_G$ in…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
The scattering process on multiloop infinite p+1-valent graphs (generalized trees) is studied. These graphs are discrete spaces being quotients of the uniform tree over free acting discrete subgroups of the projective group $PGL(2, {\bf…
Let $R_T$ be the Ricci matrix of a finite tree $T$ introduced in \cite{BaiChengHua2026}, the largest eigenvalue $\lambda_{\max}(R_T)$ determines the sign of a discrete Einstein metric curvature on the tree. This paper investigates the…
Maximum likelihood estimators are used extensively to estimate unknown parameters of stochastic trait evolution models on phylogenetic trees. Although the MLE has been proven to converge to the true value in the independent-sample case, we…
Let $(X,d)$ be a proper ultrametric space. Given a measure $m$ on $X$ and a function $B \mapsto C(B)$ defined on the collection of all non-singleton balls $B$ of $X$, we consider the associated hierarchical Laplacian $L=L_{C}\,$. The…
The classical matrix-tree theorem relates the determinant of the combinatorial Laplacian on a graph to the number of spanning trees. We generalize this result to Laplacians on one- and two-dimensional vector bundles, giving a combinatorial…
We introduce a method of constructing a general Laakso space while calculating the spectrum and multiplicities of the Laplacian operator on it. Using this information, we found the leading term of the trace of the heat kernel of a Laakso…
This paper introduces a novel computational framework for modeling and analyzing the spatiotemporal shape variability of tree-like 4D structures whose shapes deform and evolve over time. Tree-like 3D objects, such as botanical trees and…
We generalize the notion of tight geodesics in the curve complex to tight trees. We then use tight trees to construct model geometries for certain surface bundles over graphs. This extends some aspects of the combinatorial model for doubly…
The rates-across-sites assumption in phylogenetic inference posits that the rate matrix governing the Markovian evolution of a character on an edge of the putative phylogenetic tree is the product of a character-specific scale factor and a…