Subshifts as Models for MSO Logic

We study the Monadic Second Order (MSO) Hierarchy over colourings of the discrete plane, and draw links between classes of formula and classes of subshifts. We give a characterization of existential MSO in terms of projections of tilings, and of universal sentences in terms of combinations of "pattern counting" subshifts. Conversely, we characterise logic fragments corresponding to various classes of subshifts (subshifts of finite type, sofic subshifts, all subshifts). Finally, we show by a separation result how the situation here is different from the case of tiling pictures studied earlier by Giammarresi et al.Comment: arXiv admin note: substantial text overlap with arXiv:0904.245

Enumeration Reducibility in Closure Spaces with Applications to Logic and Algebra

In many instances in first order logic or computable algebra, classical theorems show that many problems are undecidable for general structures, but become decidable if some rigidity is imposed on the structure. For example, the set of theorems in many finitely axiomatisable theories is nonrecursive, but the set of theorems for any finitely axiomatisable complete theory is recursive. Finitely presented groups might have an nonrecursive word problem, but finitely presented simple groups have a recursive word problem. In this article we introduce a topological framework based on closure spaces to show that many of these proofs can be obtained in a similar setting. We will show in particular that these statements can be generalized to cover arbitrary structures, with no finite or recursive presentation/axiomatization. This generalizes in particular work by Kuznetsov and others. Examples from first order logic and symbolic dynamics will be discussed at length

Subshifts, MSO Logic, and Collapsing Hierarchies

We use monadic second-order logic to define two-dimensional subshifts, or sets of colorings of the infinite plane. We present a natural family of quantifier alternation hierarchies, and show that they all collapse to the third level. In particular, this solves an open problem of [Jeandel & Theyssier 2013]. The results are in stark contrast with picture languages, where such hierarchies are usually infinite.Comment: 12 pages, 5 figures. To appear in conference proceedings of TCS 2014, published by Springe

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