Parametrized Stochastic Grammars for RNA Secondary Structure Prediction

We propose a two-level stochastic context-free grammar (SCFG) architecture for parametrized stochastic modeling of a family of RNA sequences, including their secondary structure. A stochastic model of this type can be used for maximum a posteriori estimation of the secondary structure of any new sequence in the family. The proposed SCFG architecture models RNA subsequences comprising paired bases as stochastically weighted Dyck-language words, i.e., as weighted balanced-parenthesis expressions. The length of each run of unpaired bases, forming a loop or a bulge, is taken to have a phase-type distribution: that of the hitting time in a finite-state Markov chain. Without loss of generality, each such Markov chain can be taken to have a bounded complexity. The scheme yields an overall family SCFG with a manageable number of parameters.Comment: 5 pages, submitted to the 2007 Information Theory and Applications Workshop (ITA 2007

The set of realizations of a max-plus linear sequence is semi-polyhedral

We show that the set of realizations of a given dimension of a max-plus linear sequence is a finite union of polyhedral sets, which can be computed from any realization of the sequence. This yields an (expensive) algorithm to solve the max-plus minimal realization problem. These results are derived from general facts on rational expressions over idempotent commutative semirings: we show more generally that the set of values of the coefficients of a commutative rational expression in one letter that yield a given max-plus linear sequence is a semi-algebraic set in the max-plus sense. In particular, it is a finite union of polyhedral sets

Calibrating Generative Models: The Probabilistic Chomsky-Schützenberger Hierarchy

A probabilistic Chomsky–Schützenberger hierarchy of grammars is introduced and studied, with the aim of understanding the expressive power of generative models. We offer characterizations of the distributions definable at each level of the hierarchy, including probabilistic regular, context-free, (linear) indexed, context-sensitive, and unrestricted grammars, each corresponding to familiar probabilistic machine classes. Special attention is given to distributions on (unary notations for) positive integers. Unlike in the classical case where the "semi-linear" languages all collapse into the regular languages, using analytic tools adapted from the classical setting we show there is no collapse in the probabilistic hierarchy: more distributions become definable at each level. We also address related issues such as closure under probabilistic conditioning

Nonnegativity Problems for Matrix Semigroups

The matrix semigroup membership problem asks, given square matrices $M,M_1,\ldots,M_k$ of the same dimension, whether $M$ lies in the semigroup generated by $M_1,\ldots,M_k$. It is classical that this problem is undecidable in general but decidable in case $M_1,\ldots,M_k$ commute. In this paper we consider the problem of whether, given $M_1,\ldots,M_k$, the semigroup generated by $M_1,\ldots,M_k$ contains a non-negative matrix. We show that in case $M_1,\ldots,M_k$ commute, this problem is decidable subject to Schanuel's Conjecture. We show also that the problem is undecidable if the commutativity assumption is dropped. A key lemma in our decidability result is a procedure to determine, given a matrix $M$, whether the sequence of matrices $(M^n)_{n\geq 0}$ is ultimately nonnegative. This answers a problem posed by S. Akshay (arXiv:2205.09190). The latter result is in stark contrast to the notorious fact that it is not known how to determine effectively whether for any specific matrix index $(i,j)$ the sequence $(M^n)_{i,j}$ is ultimately nonnegative (which is a formulation of the Ultimate Positivity Problem for linear recurrence sequences)