Infinitely divisible nonnegative matrices, MM-matrices, and the embedding problem for finite state stationary Markov Chains

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 nonnegative roots is shown to be the closure of the set of matrices with matrix roots in $\mathcal{IM}$. The methods presented here employ nothing beyond basic matrix analysis, however it answers a question regarding $M$-matrices posed over 30 years ago and as an application, a new characterization of the set of all embeddable stochastic matrices is obtained as a corollary

Exact finite approximations of average-cost countable Markov Decision Processes

For a countable-state Markov decision process we introduce an embedding which produces a finite-state Markov decision process. The finite-state embedded process has the same optimal cost, and moreover, it has the same dynamics as the original process when restricting to the approximating set. The embedded process can be used as an approximation which, being finite, is more convenient for computation and implementation.Comment: Submitted to Automatic

Embeddability and rate identifiability of Kimura 2-parameter 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 nucleotide substitution. For these $4\times 4$ matrices, we fully characterize the set of embeddable K80 Markov matrices and the set of embeddable matrices for which rates are identifiable. In particular, we describe an open subset of embeddable matrices with non-identifiable rates. This set contains matrices with positive eigenvalues and also diagonal largest in column matrices, which might lead to consequences in parameter estimation in phylogenetics. Finally, we compute the relative volumes of embeddable K80 matrices and of embeddable matrices with identifiable rates. This study concludes the embedding problem for the more general model K81 and its submodels, which had been initiated by the last two authors in a separate work.Comment: 20 pages; 10 figure