Related papers: Patterns Within the Markov Tree
For fixed integers $D \geq 0$ and $c \geq 3$, we demonstrate how to use $2$-adic valuation trees of sequences to analyze Diophantine equations of the form $x^2+D=2^cy$ and $x^3+D=2^cy$, for $y$ odd. Further, we show for what values $D \in…
We study (plane) tree-valued Markov chains $(T_n,n \geq 1)$ with uniform backward dynamics and show that they can be obtained by sampling from a real tree. As non--plane trees, every such Markov chain is represented by a weighted real tree.…
We study infinite tree and ultrametric matrices, and their action on the boundary of the tree. For each tree matrix we show the existence of a symmetric random walk associated to it and we study its Green potential. We provide a…
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…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
Phylogenetic trees constitute an interesting class of objects for stochastic processes due to the non-standard nature of the space they inhabit. In particular, many statistical applications require the construction of Markov processes on…
We study the enumeration of spinal tree-child phylogenetic networks, a rigid family of tree-child networks in which all internal vertices lie on a single root--to--leaf path. We provide two complementary combinatorial frameworks. First, we…
Let $p$ be a prime and $a$ a quadratic non-residue $\bmod p$. Then the set of integral solutions of the diophantine equation $x_0^2 - ax_1^2 -px_2^2 + apx_3^2=1$ form a cocompact discrete subgroup $\Gamma_{p,a}\subset SL(2,\mathbb{R})$ and…
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 a natural $q$-deformation of the classical Markov numbers. This $q$-deformation is closely related to $q$-deformed rational numbers recently introduced by two of us. Both notions, those of $q$-rationals and $q$-Markov numbers,…
The general Markov plus invariable sites (GM+I) model of biological sequence evolution is a two-class model in which an unknown proportion of sites are not allowed to change, while the remainder undergo substitutions according to a Markov…
In 1990 West conjectured that there are $2(3n)!/((n+1)!(2n+1)!)$ two-stack sortable permutations on $n$ letters. This conjecture was proved analytically by Zeilberger in 1992. Later, Dulucq, Gire, and Guibert gave a combinatorial proof of…
This paper provides some new guidance in the construction of region graphs for Generalized Belief Propagation (GBP). We connect the problem of choosing the outer regions of a LoopStructured Region Graph (SRG) to that of finding a…
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…
Computational procedures for the stationary probability distribution, the group inverse of the Markovian kernel and the mean first passage times of an irreducible Markov chain, are developed using perturbations. The derivation of these…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
In the United States, regions are frequently divided into districts for the purpose of electing representatives. How the districts are drawn can affect who's elected, and drawing districts to give an advantage to a certain group is known as…
We develop a unified spectral framework for finite ultrametric phylogenetic trees, grounding the analysis of phylogenetic structure in operator theory and stochastic dynamics in the finite setting. For a given finite ultrametric measure…
Diophantine triples taking values in recurrence sequences have recently been studied quite a lot. In particular the question was raised whether or not there are finitely many Diophantine triples in the Tribonacci sequence. We answer this…
Recursive formulas are derived for the number of solutions of linear and quadratic Diophantine equations with positive coefficients. This result is further extended to general non-linear additive Diophantine equations. It is shown that all…