Related papers: Descriptional Complexity of Semi-Simple Splicing S…
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…
The string splicing was introduced by Tom Head which stands as an abstract model for the DNA recombination under the influence of restriction enzymes. The complex chemical process of three dimensional molecules in three dimensional space…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…
Theory of splicing is an abstract model of the recombinant behaviour of DNAs. In a splicing system, two strings to be spliced are taken from the same set and the splicing rule is from another set. Here we propose a generalised splicing (GS)…
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…
We introduce program splicing, a programming methodology that aims to automate the commonly used workflow of copying, pasting, and modifying code available online. Here, the programmer starts by writing a "draft" that mixes unfinished code,…
In this paper, we prove decidability properties and new results on the position of the family of languages generated by (circular) splicing systems within the Chomsky hierarchy. The two main results of the paper are the following. First, we…
Text Simplification improves the readability of sentences through several rewriting transformations, such as lexical paraphrasing, deletion, and splitting. Current simplification systems are predominantly sequence-to-sequence models that…
Sentence splitting is a major simplification operator. Here we present a simple and efficient splitting algorithm based on an automatic semantic parser. After splitting, the text is amenable for further fine-tuned simplification operations.…
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…
A central strategy of synthetic biology is to understand the basic processes of living creatures through engineering organisms using the same building blocks. Biological machines described in terms of parts can be studied by computer…
RNA co-transcriptionality is the process where RNA sequences are spliced while being transcribed from DNA templates. This process holds potential as a key tool for molecular programming. Co-transcriptional folding has been shown to be…
In this paper, we associate the idea of derivation languages with flat splicing systems and compare the families of derivation languages (Szilard and control languages) of these systems with the family of languages in Chomsky hierarchy. We…
The Split and Rephrase (SPRP) task, which consists in splitting complex sentences into a sequence of shorter grammatical sentences, while preserving the original meaning, can facilitate the processing of complex texts for humans and…
Inference algorithms in probabilistic programming languages (PPLs) can be thought of as interpreters, since an inference algorithm traverses a model given evidence to answer a query. As with interpreters, we can improve the efficiency of…
Bioinformatics encompass storing, analyzing and interpreting the biological data. Most of the challenges for Machine Learning methods like Cellular Automata is to furnish the functional information with the corresponding biological…
It is known that the majority of the human genome consists of repeated sequences. Furthermore, it is believed that a significant part of the rest of the genome also originated from repeated sequences and has mutated to its current form. In…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
We propose a new sentence simplification task (Split-and-Rephrase) where the aim is to split a complex sentence into a meaning preserving sequence of shorter sentences. Like sentence simplification, splitting-and-rephrasing has the…
Compounding is a highly productive word-formation process in some languages that is often problematic for natural language processing applications. In this paper, we investigate whether distributional semantics in the form of word…