Decompositions of Grammar Constraints

A wide range of constraints can be compactly specified using automata or formal languages. In a sequence of recent papers, we have shown that an effective means to reason with such specifications is to decompose them into primitive constraints. We can then, for instance, use state of the art SAT solvers and profit from their advanced features like fast unit propagation, clause learning, and conflict-based search heuristics. This approach holds promise for solving combinatorial problems in scheduling, rostering, and configuration, as well as problems in more diverse areas like bioinformatics, software testing and natural language processing. In addition, decomposition may be an effective method to propagate other global constraints.Comment: Proceedings of the Twenty-Third AAAI Conference on Artificial Intelligenc

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

Introduction

This chapter will motivate why it is useful to consider the topic of derivations and filtering in more detail. We will argue against the popular belief that the minimalist program and optimality theory are incompatible theories in that the former places the explanatory burden on the generative device (the computational system) whereas the latter places it on the fi ltering device (the OT evaluator). Although this belief may be correct in as far as it describes existing tendencies, we will argue that minimalist and optimality theoretic approaches normally adopt more or less the same global architecture of grammar: both assume that a generator defines a set S of potentially well-formed expressions that can be generated on the basis of a given input and that there is an evaluator that selects the expressions from S that are actually grammatical in a given language L. For this reason, we believe that it has a high priority to investigate the role of the two components in more detail in the hope that this will provide a better understanding of the differences and similarities between the two approaches. We will conclude this introduction with a brief review of the studies collected in this book.

TDL--- A Type Description Language for Constraint-Based Grammars

This paper presents \tdl, a typed feature-based representation language and inference system. Type definitions in \tdl\ consist of type and feature constraints over the boolean connectives. \tdl\ supports open- and closed-world reasoning over types and allows for partitions and incompatible types. Working with partially as well as with fully expanded types is possible. Efficient reasoning in \tdl\ is accomplished through specialized modules.Comment: Will Appear in Proc. COLING-9

Best-First Surface Realization

Current work in surface realization concentrates on the use of general, abstract algorithms that interpret large, reversible grammars. Only little attention has been paid so far to the many small and simple applications that require coverage of a small sublanguage at different degrees of sophistication. The system TG/2 described in this paper can be smoothly integrated with deep generation processes, it integrates canned text, templates, and context-free rules into a single formalism, it allows for both textual and tabular output, and it can be parameterized according to linguistic preferences. These features are based on suitably restricted production system techniques and on a generic backtracking regime.Comment: 10 pages, LaTeX source, one EPS figur

Concurrent Lexicalized Dependency Parsing: The ParseTalk Model

A grammar model for concurrent, object-oriented natural language parsing is introduced. Complete lexical distribution of grammatical knowledge is achieved building upon the head-oriented notions of valency and dependency, while inheritance mechanisms are used to capture lexical generalizations. The underlying concurrent computation model relies upon the actor paradigm. We consider message passing protocols for establishing dependency relations and ambiguity handling.Comment: 90kB, 7pages Postscrip

A Graph Grammar for Modelling RNA Folding

We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the global behaviour resembles the one of a self-adaptive system. Each RNA configuration is a graph and the evolution of configurations is constrained by precise rules that can be described by a graph grammar.Comment: In Proceedings GaM 2016, arXiv:1612.0105

Robust Processing of Natural Language

Previous approaches to robustness in natural language processing usually treat deviant input by relaxing grammatical constraints whenever a successful analysis cannot be provided by ``normal'' means. This schema implies, that error detection always comes prior to error handling, a behaviour which hardly can compete with its human model, where many erroneous situations are treated without even noticing them. The paper analyses the necessary preconditions for achieving a higher degree of robustness in natural language processing and suggests a quite different approach based on a procedure for structural disambiguation. It not only offers the possibility to cope with robustness issues in a more natural way but eventually might be suited to accommodate quite different aspects of robust behaviour within a single framework.Comment: 16 pages, LaTeX, uses pstricks.sty, pstricks.tex, pstricks.pro, pst-node.sty, pst-node.tex, pst-node.pro. To appear in: Proc. KI-95, 19th German Conference on Artificial Intelligence, Bielefeld (Germany), Lecture Notes in Computer Science, Springer 199