相关论文: It Is NL-complete to Decide Whether a Hairpin Comp…
The hairpin completion is an operation on formal languages that has been inspired by the hairpin formation in DNA biochemistry and by DNA computing. In this paper we investigate the hairpin completion of regular languages. It is well known…
The (bounded) hairpin completion and its iterated versions are operations on formal lan- guages which have been inspired by the hairpin formation in DNA-biochemistry. The paper answers two questions asked in the literature about the…
Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive…
Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced and…
Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand $w = x\alpha y \calpha$, and outputs $w' = x \alpha y \bar{\alpha} \bar{x}$, where $\bar{x}$ denotes the Watson-Crick complement…
The aim of this paper is to design the polynomial construction of a finite recognizer for hairpin completions of regular languages. This is achieved by considering completions as new expression operators and by applying derivation…
Hairpin completion, derived from the hairpin formation observed in DNA biochemistry, is an operation applied to strings, particularly useful in DNA computing. Conceptually, a right hairpin completion operation transforms a string $S$ into…
Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly thereafter, it was proven that the languages…
We investigate regular realizability (RR) problems, which are the problems of verifying whether intersection of a regular language -- the input of the problem -- and fixed language called filter is non-empty. We consider two kind of…
In this paper, we consider the satisfiability problem for string logic with equations, regular membership and Presburger constraints over length functions. The difficulty comes from multiple occurrences of string variables making…
Motivated by work on bio-operations on DNA strings, we consider an outfix-guided insertion operation that can be viewed as a generalization of the overlap assembly operation on strings studied previously. As the main result we construct a…
State-of-the-art deep-learning-based approaches to Natural Language Processing (NLP) are credited with various capabilities that involve reasoning with natural language texts. In this paper we carry out a large-scale empirical study…
We report some further developments regarding the language theory of higher-dimensional automata (HDAs). Regular languages of HDAs are sets of finite interval partially ordered multisets (pomsets) with interfaces. We show a pumping lemma…
Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a…
Given a finite alphabet $\Sigma$ and a deterministic finite automaton on $\Sigma$, the problem of determining whether the language recognized by the automaton contains any pangram is \NP-complete. Various other language classes and problems…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Hybrid logic with binders is an expressive specification language. Its satisfiability problem is undecidable in general. If frames are restricted to N or general linear orders, then satisfiability is known to be decidable, but of…
We study the problem of deciding whether a given language is directed. A language $L$ is \emph{directed} if every pair of words in $L$ have a common (scattered) superword in $L$. Deciding directedness is a fundamental problem in connection…
Results of computational complexity exist for a wide range of phrase structure-based grammar formalisms, while there is an apparent lack of such results for dependency-based formalisms. We here adapt a result on the complexity of…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…