Related papers: Embeddability and rate identifiability of Kimura 2…
We study model embeddability, which is a variation of the famous embedding problem in probability theory, when apart from the requirement that the Markov matrix is the matrix exponential of a rate matrix, we additionally ask that the rate…
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…
A Markov matrix is embeddable if it can represent a homogeneous continuous-time Markov process. It is well known that if a Markov matrix has real and pairwise-different eigenvalues, then the embeddability can be determined by checking…
In this note, we characterize the embeddability of generic Kimura 3ST Markov matrices in terms of their eigenvalues. As a consequence, we are able to compute the volume of such matrices relative to the volume of all Markov matrices within…
The embedding problem of Markov matrices in Markov semigroups is a classic problem that regained a lot of impetus and activities through recent needs in phylogeny and population genetics. Here, we give an account for dimensions $d\leqslant…
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…
The classical embeddability problem asks whether a given stochastic matrix $T$, describing transition probabilities of a $d$-level system, can arise from the underlying homogeneous continuous-time Markov process. Here, we investigate the…
This paper explicitly details the relation between $M$-matrices, nonnegative roots of nonnegative matrices, and the embedding problem for finite-state stationary Markov chains. The set of nonsingular nonnegative matrices with arbitrary…
The embedding problem for Markov chains is a famous problem in probability theory and only partial results are available up till now. In this paper, we propose a variant of the embedding problem called the reversible embedding problem which…
We computationally resolve an open problem concerning the expressibility of $4 \times 4$ full-rank matrices as Hadamard products of two rank-2 matrices. Through exhaustive search over $\mathbb{F}_2$, we identify 5,304 counterexamples among…
The representation problem of finite-dimensional Markov matrices in Markov semigroups is revisited, with emphasis on concrete criteria for matrix subclasses of theoretical or practical relevance, such as equal-input, circulant, symmetric or…
We give an account of some results, both old and new, about any $n\times n$ Markov matrix that is embeddable in a one-parameter Markov semigroup. These include the fact that its eigenvalues must lie in a certain region in the unit ball. We…
We discuss the relationship between quaternion algebras and quadratic forms with a focus on computational aspects. Our basic motivating problem is to determine if a given algebra of rank 4 over a commutative ring R embeds in the 2x2-matrix…
For an indecomposable $3\times 3$ stochastic matrix (i.e., 1-step transition probability matrix) with coinciding negative eigenvalues, a new necessary and sufficient condition of the imbedding problem for time homogeneous Markov chains is…
The parameters of a linear compartment model are usually estimated from experimental input-output data. A problem arises when infinitely many parameter values can yield the same result; such a model is called unidentifiable. In this case,…
In this paper, we discuss the embedding problem for centrosymmetric matrices, which are higher order generalizations of the matrices occurring in Strand Symmetric Models. These models capture the substitution symmetries arising from the…
Exact methods for exponentiation of matrices of dimension $N$ can be computationally expensive in terms of execution time ($N^{3}$) and memory requirements ($N^{2}$) not to mention numerical precision issues. A type of matrix often…
The practically important classes of equal-input and of monotone Markov matrices are revisited, with special focus on embeddability, infinite divisibility, and mutual relations. Several uniqueness results for the classic Markov embedding…
The embeddability of reversible Markov matrices into time-homogeneous Markov semigroups is revisited, with some focus on simplifications and extensions. In particular, we do not demand irreducibility and consider weakly reversible matrices…
This article studies two notions of generalized matroid representations motivated by algorithmic information theory and cryptographic secret sharing. The first (entropic representability) involves discrete random variables, while the second…