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

Separating Dependency from Constituency in a Tree Rewriting System

In this paper we present a new tree-rewriting formalism called Link-Sharing Tree Adjoining Grammar (LSTAG) which is a variant of synchronous TAGs. Using LSTAG we define an approach towards coordination where linguistic dependency is distinguished from the notion of constituency. Such an approach towards coordination that explicitly distinguishes dependencies from constituency gives a better formal understanding of its representation when compared to previous approaches that use tree-rewriting systems which conflate the two issues.Comment: 7 pages, 6 Postscript figures, uses fullname.st

Tree transducers, L systems, and two-way machines

A relationship between parallel rewriting systems and two-way machines is investigated. Restrictions on the “copying power” of these devices endow them with rich structuring and give insight into the issues of determinism, parallelism, and copying. Among the parallel rewriting systems considered are the top-down tree transducer; the generalized syntax-directed translation scheme and the ETOL system, and among the two-way machines are the tree-walking automaton, the two-way finite-state transducer, and (generalizations of) the one-way checking stack automaton. The. relationship of these devices to macro grammars is also considered. An effort is made .to provide a systematic survey of a number of existing results

Application of shape grammar theory to underground rail station design and passenger evacuation

This paper outlines the development of a computer design environment that generates station ‘reference’ plans for analysis by designers at the project feasibility stage. The developed program uses the theoretical concept of shape grammar, based upon principles of recognition and replacement of a particular shape to enable the generation of station layouts. The developed novel shape grammar rules produce multiple plans of accurately sized infrastructure faster than by traditional means. A finite set of station infrastructure elements and a finite set of connection possibilities for them, directed by regulations and the logical processes of station usage, allows for increasingly complex composite shapes to be automatically produced, some of which are credible station layouts at ‘reference’ block plan level. The proposed method of generating shape grammar plans is aligned to London Underground standards, in particular to the Station Planning Standards and Guidelines 5th edition (SPSG5 2007) and the BS-7974 fire safety engineering process. Quantitative testing is via existing evacuation modelling software. The prototype system, named SGEvac, has both the scope and potential for redevelopment to any other country’s design legislation

Probabilistic Parsing Strategies

We present new results on the relation between purely symbolic context-free parsing strategies and their probabilistic counter-parts. Such parsing strategies are seen as constructions of push-down devices from grammars. We show that preservation of probability distribution is possible under two conditions, viz. the correct-prefix property and the property of strong predictiveness. These results generalize existing results in the literature that were obtained by considering parsing strategies in isolation. From our general results we also derive negative results on so-called generalized LR parsing.Comment: 36 pages, 1 figur

Flexible RNA design under structure and sequence constraints using formal languages

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical applications in biology, additional constraints must be taken into account, such as the presence/absence of regulatory motifs, either at a specific location or anywhere in the sequence. In this study, we investigate the design of RNA sequences from their targeted secondary structure, given these additional sequence constraints. To this purpose, we develop a general framework based on concepts of language theory, namely context-free grammars and finite automata. We efficiently combine a comprehensive set of constraints into a unifying context-free grammar of moderate size. From there, we use generic generic algorithms to perform a (weighted) random generation, or an exhaustive enumeration, of candidate sequences. The resulting method, whose complexity scales linearly with the length of the RNA, was implemented as a standalone program. The resulting software was embedded into a publicly available dedicated web server. The applicability demonstrated of the method on a concrete case study dedicated to Exon Splicing Enhancers, in which our approach was successfully used in the design of \emph{in vitro} experiments.Comment: ACM BCB 2013 - ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (2013