Related papers: Hadamard Phylogenetic Methods and the n-taxon proc…
Branching processes are a class of continuous-time Markov chains (CTMCs) prevalent for modeling stochastic population dynamics in ecology, biology, epidemiology, and many other fields. The transient or finite-time behavior of these systems…
Markov branching systems form a fundamental class of stochastic models that are extensively applied in biology, physics, finance, and other domains. These systems are distinguished by their continuous-time evolution and inherent branching…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…
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…
Handwritten Mathematical Expression Recognition (HMER) has extensive applications in automated grading and office automation. However, existing sequence-based decoding methods, which directly predict $\LaTeX$ sequences, struggle to…
We present a symbolic decomposition of the Pearson chi-square statistic with unequal cell probabilities, by presenting Hadamard-type matrices whose columns are eigenvectors of the variance-covariance matrix of the cell counts. All of the…
This paper investigates the use of quasigroups, Hadamard transforms and Number Theoretic Transforms for use in sequence randomization. This can also be used to generate hash functions for sequence encryption.
We propose an analytic approach for the steady-state dynamics of Markov processes on locally tree-like graphs. It is based on time-translation invariant probability distributions for edge trajectories, which we encode in terms of infinite…
The P\'olya tree (PT) process is a general-purpose Bayesian nonparametric model that has found wide application in a range of inference problems. It has a simple analytic form and the posterior computation boils down to beta-binomial…
Despite substantial progress in non-equilibrium physics, steady-state (s.s.) probabilities remain intractable to analysis. For a Markov process, s.s. probabilities can be expressed in terms of transition rates using the Matrix-Tree theorem…
A general method to construct recombinant tree approximations for stochastic volatility models is developed and applied to the Heston model for stock price dynamics. In this application, the resulting approximation is a four tuple Markov…
In this paper we study several problems concerning the number of homomorphisms of trees. We give an algorithm for the number of homomorphisms from a tree to any graph by the Transfer-matrix method. By using this algorithm and some…
The paper deals with a new class of random walks strictly connected with the Pareto distribution. We consider stochastic processes in the sense of generalized convolution or weak generalized convolution following the idea given in [1]. The…
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…
Bottom-Up Hidden Tree Markov Model is a highly expressive model for tree-structured data. Unfortunately, it cannot be used in practice due to the intractable size of its state-transition matrix. We propose a new approximation which lies on…
The Hubbard model is an important tool to understand the electrical properties of various materials. More specifically, on the honeycomb lattice it is used to describe graphene predicting a quantum phase transition from a semimetal to a…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…