Related papers: Embeddability of Kimura 3ST Markov matrices
Deciding whether a Markov matrix is embeddable (i.e. can be written as the exponential of a rate matrix) is an open problem even for $4\times 4$ matrices. We study the embedding problem and rate identifiability for the K80 model of…
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…
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…
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…
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…
In this paper, we consider mutations of skew-symmetrizable matrices of rank 3. Every skew-symmetrizable matrix corresponds to a weighted quiver, and we study the conditions when this quiver is always cyclic after applying mutations. In this…
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…
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…
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…
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…
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…
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…
Phylogenetic models have polynomial parametrization maps. For symmetric group-based models, Matsen studied the polynomial inequalities that characterize the joint probabilities in the image of these parametrizations. We employ this…
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…
In most stochastic models of molecular sequence evolution the probability of each possible pattern of homologous characters at a site is estimated numerically. However in the case of Kimura's three-substitution-types (K3ST) model, these…
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…
Markov matrices have an important role in the filed of stochastic processes. In this paper, we will show and prove a series of conclusions on Markov matrices and transformations rather than pay attention to stochastic processes although…
In this article we study in detail a family of random matrix ensembles which are obtained from random permutations matrices (chosen at random according to the Ewens measure of parameter $\theta>0$) by replacing the entries equal to one by…
In this paper, we determine representatives for the mutation classes of skew-symmetrizable 3x3 matrices and associated graphs using a natural minimality condition, generalizing and strengthening results of Beineke-Brustle-Hille and…
We give a precise definition of mutation of skew symmetrizable matrices over group rings and relate it to folding and mutation of quivers with symmetries. These matrices can have non-zero diagonal entries and we explain a mutation rule in…