Polynomial Time Algorithms for Multi-Type Branching Processes and Stochastic Context-Free Grammars

We show that one can approximate the least fixed point solution for a multivariate system of monotone probabilistic polynomial equations in time polynomial in both the encoding size of the system of equations and in log(1/\epsilon), where \epsilon > 0 is the desired additive error bound of the solution. (The model of computation is the standard Turing machine model.) We use this result to resolve several open problems regarding the computational complexity of computing key quantities associated with some classic and heavily studied stochastic processes, including multi-type branching processes and stochastic context-free grammars

Structure preserving transformations on non-left-recursive grammars

We will be concerned with grammar covers, The first part of this paper presents a general framework for covers. The second part introduces a transformation from nonleft-recursive grammars to grammars in Greibach normal form. An investigation of the structure preserving properties of this transformation, which serves also as an illustration of our framework for covers, is presented

From left-regular to Greibach normal form grammars

Each context-free grammar can be transformed to a context-free grammar in Greibach normal form, that is, a context-free grammar where each right-hand side of a prorfuction begins with a terminal symbol and the remainder of the right-hand side consists of nonterminal symbols. In this short paper we show that for a left-regular grammar G we can obtain a right-regular grammar G’ (which is by definition in Greibach normal form) which left-to-right covers G (in this case left parses of G’ can be mapped by a homomorphism on right parses of G. Moreover, it is possible to obtain a context-free grammar G” in Greibach normal form which right covers the left-regular grammar G (in this case right parses of G” are mapped on right parses of G)

Genomics and proteomics: a signal processor's tour

The theory and methods of signal processing are becoming increasingly important in molecular biology. Digital filtering techniques, transform domain methods, and Markov models have played important roles in gene identification, biological sequence analysis, and alignment. This paper contains a brief review of molecular biology, followed by a review of the applications of signal processing theory. This includes the problem of gene finding using digital filtering, and the use of transform domain methods in the study of protein binding spots. The relatively new topic of noncoding genes, and the associated problem of identifying ncRNA buried in DNA sequences are also described. This includes a discussion of hidden Markov models and context free grammars. Several new directions in genomic signal processing are briefly outlined in the end

Grammars with two-sided contexts

In a recent paper (M. Barash, A. Okhotin, "Defining contexts in context-free grammars", LATA 2012), the authors introduced an extension of the context-free grammars equipped with an operator for referring to the left context of the substring being defined. This paper proposes a more general model, in which context specifications may be two-sided, that is, both the left and the right contexts can be specified by the corresponding operators. The paper gives the definitions and establishes the basic theory of such grammars, leading to a normal form and a parsing algorithm working in time O(n^4), where n is the length of the input string.Comment: In Proceedings AFL 2014, arXiv:1405.527

Type-driven semantic interpretation and feature dependencies in R-LFG

Once one has enriched LFG's formal machinery with the linear logic mechanisms needed for semantic interpretation as proposed by Dalrymple et. al., it is natural to ask whether these make any existing components of LFG redundant. As Dalrymple and her colleagues note, LFG's f-structure completeness and coherence constraints fall out as a by-product of the linear logic machinery they propose for semantic interpretation, thus making those f-structure mechanisms redundant. Given that linear logic machinery or something like it is independently needed for semantic interpretation, it seems reasonable to explore the extent to which it is capable of handling feature structure constraints as well. R-LFG represents the extreme position that all linguistically required feature structure dependencies can be captured by the resource-accounting machinery of a linear or similiar logic independently needed for semantic interpretation, making LFG's unification machinery redundant. The goal is to show that LFG linguistic analyses can be expressed as clearly and perspicuously using the smaller set of mechanisms of R-LFG as they can using the much larger set of unification-based mechanisms in LFG: if this is the case then we will have shown that positing these extra f-structure mechanisms is not linguistically warranted.Comment: 30 pages, to appear in the the ``Glue Language'' volume edited by Dalrymple, uses tree-dvips, ipa, epic, eepic, fullnam

Certified Context-Free Parsing: A formalisation of Valiant's Algorithm in Agda

Valiant (1975) has developed an algorithm for recognition of context free languages. As of today, it remains the algorithm with the best asymptotic complexity for this purpose. In this paper, we present an algebraic specification, implementation, and proof of correctness of a generalisation of Valiant's algorithm. The generalisation can be used for recognition, parsing or generic calculation of the transitive closure of upper triangular matrices. The proof is certified by the Agda proof assistant. The certification is representative of state-of-the-art methods for specification and proofs in proof assistants based on type-theory. As such, this paper can be read as a tutorial for the Agda system

An Efficient Probabilistic Context-Free Parsing Algorithm that Computes Prefix Probabilities

We describe an extension of Earley's parser for stochastic context-free grammars that computes the following quantities given a stochastic context-free grammar and an input string: a) probabilities of successive prefixes being generated by the grammar; b) probabilities of substrings being generated by the nonterminals, including the entire string being generated by the grammar; c) most likely (Viterbi) parse of the string; d) posterior expected number of applications of each grammar production, as required for reestimating rule probabilities. (a) and (b) are computed incrementally in a single left-to-right pass over the input. Our algorithm compares favorably to standard bottom-up parsing methods for SCFGs in that it works efficiently on sparse grammars by making use of Earley's top-down control structure. It can process any context-free rule format without conversion to some normal form, and combines computations for (a) through (d) in a single algorithm. Finally, the algorithm has simple extensions for processing partially bracketed inputs, and for finding partial parses and their likelihoods on ungrammatical inputs.Comment: 45 pages. Slightly shortened version to appear in Computational Linguistics 2