Related papers: Uniformization stable Markov models and their Jord…

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…

These lecture notes introduce the statistical analysis of continuous-time generative models built from Markov dynamics. We begin with the stochastic-calculus foundations of score-based diffusion models, including time reversal, score…

We investigate the properties of uniform doubly stochastic random matrices, that is non-negative matrices conditioned to have their rows and columns sum to 1. The rescaled marginal distributions are shown to converge to exponential…

Integrating a product of linear forms over the unit simplex can be done in polynomial time if the number of variables n is fixed (V. Baldoni et al., 2011). In this note, we highlight that this problem is equivalent to obtaining the…

Many biological and medical questions can be modeled using time-to-event data in finite-state Markov chains, with the phase-type distribution describing intervals between events. We solve the inverse problem: given a phase-type…

When the process underlying DNA substitutions varies across evolutionary history, the standard Markov models underlying standard phylogenetic methods are mathematically inconsistent. The most prominent example is the general time reversible…

We prove that the probability substitution matrices obtained from a continuous-time Markov chain form a multiplicatively closed set if and only if the rate matrices associated to the chain form a linear space spanning a Lie algebra. The key…

This paper is devoted to the study of preservation of eigenvalues, Jordan structure and complementary invariant subspaces of structured matrices under structured perturbations. Perturbations and structure-preserving perturbations are…

Understanding and predicting how complex systems respond to external perturbations is a central challenge in nonequilibrium statistical physics. Here we consider continuous-time Markov networks, which we subject to perturbations along a…

We address a class of Markov jump linear systems that are characterized by the underlying Markov process being time-inhomogeneous with a priori unknown transition probabilities. Necessary and sufficient conditions for uniform stochastic…

Synchronizability of stable, output-coupled, identical, time-varying linear systems is studied. It is shown that if the observability grammian satisfies a persistence of excitation condition, then there exists a bounded, time-varying linear…

We consider Hidden Markov Models that emit sequences of observations that are drawn from continuous distributions. For example, such a model may emit a sequence of numbers, each of which is drawn from a uniform distribution, but the support…

McDonald and Paparella [Linear Algebra Appl. 498 (2016), 145--159] gave a necessary condition on the structure of Jordan chains of $h$-cyclic matrices. In this work, that necessary condition is shown to be sufficient. As a consequence, we…

Markov chains for probability distributions related to matrix product states and 1D Hamiltonians are introduced. With appropriate 'inverse temperature' schedules, these chains can be combined into a random approximation scheme for ground…

A special class of Jordan algebras over a field $F$ of characteristic zero is considered. Such an algebra consists of an $r$-dimensional subspace of the vector space of all square matrices of a fixed order $n$ over $F$. It contains the…

Characterizing whether a Markov process of discrete random variables has an homogeneous continuous-time realization is a hard problem. In practice, this problem reduces to deciding when a given Markov matrix can be written as the…

Let $M_n(R)$ be the algebra of all $n\times n$ matrices over a unital commutative ring $R$ with 6 invertible. We say that $A\in M_n(R)$ is a Jordan product determined point if for every $R$-module $X$ and every symmetric $R$-bilinear map…

We consider novel phylogenetic models with rate matrices that arise via the embedding of a progenitor model on a small number of character states, into a target model on a larger number of character states. Adapting representation-theoretic…

We derive a generalization of the Perron-Frobenius theorem to time-varying row-stochastic matrices as follows: using Kolmogorov's concept of absolute probability sequences, which are time-varying analogs of principal eigenvectors, we…

Inspired from non-equilibrium statistical physics models, a general framework enabling the definition and synthesis of stationary time series with a priori prescribed and controlled joint distributions is constructed. Its central feature…