Efficient Algorithms for Morphisms over Omega-Regular Languages

Morphisms to finite semigroups can be used for recognizing omega-regular languages. The so-called strongly recognizing morphisms can be seen as a deterministic computation model which provides minimal objects (known as the syntactic morphism) and a trivial complementation procedure. We give a quadratic-time algorithm for computing the syntactic morphism from any given strongly recognizing morphism, thereby showing that minimization is easy as well. In addition, we give algorithms for efficiently solving various decision problems for weakly recognizing morphisms. Weakly recognizing morphism are often smaller than their strongly recognizing counterparts. Finally, we describe the language operations needed for converting formulas in monadic second-order logic (MSO) into strongly recognizing morphisms, and we give some experimental results.Comment: Full version of a paper accepted to FSTTCS 201

Finite Automata for the Sub- and Superword Closure of CFLs: Descriptional and Computational Complexity

We answer two open questions by (Gruber, Holzer, Kutrib, 2009) on the state-complexity of representing sub- or superword closures of context-free grammars (CFGs): (1) We prove a (tight) upper bound of $2^{\mathcal{O}(n)}$ on the size of nondeterministic finite automata (NFAs) representing the subword closure of a CFG of size $n$. (2) We present a family of CFGs for which the minimal deterministic finite automata representing their subword closure matches the upper-bound of $2^{2^{\mathcal{O}(n)}}$ following from (1). Furthermore, we prove that the inequivalence problem for NFAs representing sub- or superword-closed languages is only NP-complete as opposed to PSPACE-complete for general NFAs. Finally, we extend our results into an approximation method to attack inequivalence problems for CFGs

Small NFAs from Regular Expressions: Some Experimental Results

Regular expressions (res), because of their succinctness and clear syntax, are the common choice to represent regular languages. However, efficient pattern matching or word recognition depend on the size of the equivalent nondeterministic finite automata (NFA). We present the implementation of several algorithms for constructing small epsilon-free NFAss from res within the FAdo system, and a comparison of regular expression measures and NFA sizes based on experimental results obtained from uniform random generated res. For this analysis, nonredundant res and reduced res in star normal form were considered.Comment: Proceedings of 6th Conference on Computability in Europe (CIE 2010), pages 194-203, Ponta Delgada, Azores, Portugal, June/July 201

Efficient Algorithms for Membership in Boolean Hierarchies of Regular Languages

The purpose of this paper is to provide efficient algorithms that decide membership for classes of several Boolean hierarchies for which efficiency (or even decidability) were previously not known. We develop new forbidden-chain characterizations for the single levels of these hierarchies and obtain the following results: - The classes of the Boolean hierarchy over level $\Sigma_1$ of the dot-depth hierarchy are decidable in $NL$ (previously only the decidability was known). The same remains true if predicates mod $d$ for fixed $d$ are allowed. - If modular predicates for arbitrary $d$ are allowed, then the classes of the Boolean hierarchy over level $\Sigma_1$ are decidable. - For the restricted case of a two-letter alphabet, the classes of the Boolean hierarchy over level $\Sigma_2$ of the Straubing-Th\'erien hierarchy are decidable in $NL$. This is the first decidability result for this hierarchy. - The membership problems for all mentioned Boolean-hierarchy classes are logspace many-one hard for $NL$. - The membership problems for quasi-aperiodic languages and for $d$-quasi-aperiodic languages are logspace many-one complete for $PSPACE$

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

Logics for Unranked Trees: An Overview

Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for expressing navigational properties, and some make it easy to relate complex properties of trees to the existence of tree automata for those properties. Furthermore, logics differ significantly in their model-checking properties, their automata models, and their behavior on ordered and unordered trees. In this paper we present a survey of logics for unranked trees