arXiv subjects

Jordi Roca-Lacostena

Publications and source records attributed to Jordi Roca-Lacostena.

7 recordsLinked to original sources

arXiv2022

Embeddability of centrosymmetric matrices capturing the double-helix structure in natural and synthetic DNA

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 double helix structure of the DNA. Deciding whether a transition matrix is embeddable or not enables us to know if the observed substitution probabilities are consistent with a homogeneous continuous time substitution model, such as the Kimura models, the Jukes-Cantor model or the general time-reversible model. On the other hand, the generalization to higher order matrices is motivated by the setting of synthetic biology, which works with different sizes of genetic alphabets.

q-bio.PE↗

arXiv2021

The embedding problem for Markov matrices

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 exponential of some rate matrix (a Markov generator). This is an old question known in the literature as the embedding problem (Elfving37), which has been only solved for matrices of size $2\times 2$ or $3\times 3$. In this paper, we address this problem and related questions and obtain results in two different lines. First, for matrices of any size, we give a bound on the number of Markov generators in terms of the spectrum of the Markov matrix. Based on this, we establish a criterion for deciding whether a generic Markov matrix (different eigenvalues) is embeddable and propose an algorithm that lists all its Markov generators. Then, motivated and inspired by recent results on substitution models of DNA, we focus in the $4\times 4$ case and completely solve the embedding problem for any Markov matrix. The solution in this case is more concise as the embeddability is given in terms of a single condition.

math.PR↗

arXiv2020

An open set of $4\times4$ embeddable matrices whose principal logarithm is not a Markov generator

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 whether its principal logarithm is a rate matrix or not. The same holds for Markov matrices close enough to the identity matrix or that rule a Markov process subjected to certain restrictions. In this paper we prove that this criterion cannot be generalized and we provide open sets of Markov matrices that are embeddable and whose principal logarithm is a not a rate matrix.

math.PR↗

arXiv2019

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.

q-bio.PE↗

arXiv2019

Embeddability of Kimura 3ST Markov matrices

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 model. We also provide examples showing that, in general, mutation rates are not identifiable from substitution probabilities. These examples also illustrate that symmetries between mutation probabilities do not necessarily arise from symmetries between the corresponding mutation rates.

q-bio.PE↗

arXiv2015

Sufficient and necessary conditions for Dynamic Programming in Valuation-Based Systems

Valuation algebras abstract a large number of formalisms for automated reasoning and enable the definition of generic inference procedures. Many of these formalisms provide some notion of solution. Typical examples are satisfying assignments in constraint systems, models in logics or solutions to linear equation systems. Many widely used dynamic programming algorithms for optimization problems rely on low treewidth decompositions and can be understood as particular cases of a single algorithmic scheme for finding solutions in a valuation algebra. The most encompassing description of this algorithmic scheme to date has been proposed by Pouly and Kohlas together with sufficient conditions for its correctness. Unfortunately, the formalization relies on a theorem for which we provide counterexamples. In spite of that, the mainline of Pouly and Kohlas' theory is correct, although some of the necessary conditions have to be revised. In this paper we analyze the impact that the counter-examples have on the theory, and rebuild the theory providing correct sufficient conditions for the algorithms. Furthermore, we also provide necessary conditions for the algorithms, allowing for a sharper characterization of when the algorithmic scheme can be applied.

cs.AI↗

arXiv2014

Even more generic solution construction in Valuation-Based Systems

Valuation algebras abstract a large number of formalisms for automated reasoning and enable the definition of generic inference procedures. Many of these formalisms provide some notions of solutions. Typical examples are satisfying assignments in constraint systems, models in logics or solutions to linear equation systems. Recently, formal requirements for the presence of solutions and a generic algorithm for solution construction based on the results of a previously executed inference scheme have been proposed in the literature. Unfortunately, the formalization of Pouly and Kohlas relies on a theorem for which we provide a counter example. In spite of that, the mainline of the theory described is correct, although some of the necessary conditions to apply some of the algorithms have to be revised. To fix the theory, we generalize some of their definitions and provide correct sufficient conditions for the algorithms. As a result, we get a more general and corrected version of the already existing theory.

cs.AI↗