Related papers: On the Hairpin Incompletion
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…
The hairpin completion is an operation on formal languages which is inspired by the hairpin formation in biochemistry. Hairpin formations occur naturally within DNA-computing. It has been known that the hairpin completion of a regular…
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…
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 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…
This thesis investigates three biologically inspired operations: prefix-suffix duplication, bounded prefix-suffix duplication, and prefix-suffix-square completion. Duplication, a common genetic mutation, involves repeating DNA sequences and…
In this article we undertake a study of extension complexity from the perspective of formal languages. We define a natural way to associate a family of polytopes with binary languages. This allows us to define the notion of extension…
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…
Indexed languages are a classical notion in formal language theory, which has attracted attention in recent decades due to its role in higher-order model checking: They are precisely the languages accepted by order-2 pushdown automata. The…
Techniques are developed for creating new and general language families of only semilinear languages, and for showing families only contain semilinear languages. It is shown that for language families L that are semilinear full trios, the…
The state complexity of basic operations on finite languages (considering complete DFAs) has been in studied the literature. In this paper we study the incomplete (deterministic) state and transition complexity on finite languages of…
We study the complexity of basic regular operations on languages represented by incomplete deterministic or nondeterministic automata, in which all states are final. Such languages are known to be prefix-closed. We get tight bounds on both…
Despite strong performance on a variety of tasks, neural sequence models trained with maximum likelihood have been shown to exhibit issues such as length bias and degenerate repetition. We study the related issue of receiving…
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…
Completion is a well-known transformation that captures the stable model semantics of logic programs by turning a program into a set of first-order definitions. Stable models are models of the completion, but not all models of the…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
The downward closure of a word language is the set of all (not necessarily contiguous) subwords of its members. It is well-known that the downward closure of any language is regular. While the downward closure appears to be a powerful…
A class of languages C is perfect if it is closed under Boolean operations and the emptiness problem is decidable. Perfect language classes are the basis for the automata-theoretic approach to model checking: a system is correct if the…