Related papers: A proposal to a generalised splicing with a self a…
The problem of detecting and measuring the repetitiveness of one-dimensional strings has been extensively studied in data compression and text indexing. Our understanding of these issues has been significantly improved by the introduction…
In 2004, Klavins et al. introduced the use of graph grammars to describe -- and to program -- systems of self-assembly. It turns out that these graph grammars are a "dual notion" of a graph rewriting characterization of distributed systems…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Self-assembly is a fundamental process by which supramolecular species form spontaneously from their components. This process is ubiquitous throughout the life chemistry and is central to biological information processing. Algorithms for…
We introduce bonding grammars, a graph grammar formalism developed to model DNA computation by means of graph transformations. It is a modification of fusion grammars introduced by Kreowski, Kuske and Lye in 2017. Bonding is a graph…
In this letter we present a very general method to extract information from a generic string of characters, e.g. a text, a DNA sequence or a time series. Based on data-compression techniques, its key point is the computation of a suitable…
This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be…
Self-assembly is a process found everywhere in the Nature. In particular, it is known that DNA self-assembly is Turing universal. Thus one can do arbitrary computations or build nano-structures using DNA self-assembly. In order to…
This Ph.D. thesis collects results obtained investigating two different aspects of modern unifying theories. In the first part I summarized results achieved investigating simplicial aspects of string dualities. Exploiting Boundary Conformal…
Generalization to new domains not seen during training is one of the long-standing challenges in deploying neural networks in real-world applications. Existing generalization techniques either necessitate external images for augmentation,…
RNA-sequencing has revolutionized biomedical research and, in particular, our ability to study gene alternative splicing. The problem has important implications for human health, as alternative splicing may be involved in malfunctions at…
Within biology, it is of interest to construct DNA complexes of a certain shape. These complexes can be represented through graph theory, using edges to model strands of DNA joined at junctions, represented by vertices. Because guided…
Our goal is to develop a general strategy to decompose a random variable $X$ into multiple independent random variables, without sacrificing any information about unknown parameters. A recent paper showed that for some well-known natural…
With the recent advancements in deep learning, neural solvers have gained promising results in solving math word problems. However, these SOTA solvers only generate binary expression trees that contain basic arithmetic operators and do not…
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…
We propose a new generator for the generalized inverse Gaussian (GIG) distribution by decomposing the density of GIG into two components. The first component is a truncated inverse Gamma density, in order to sample from which we improve the…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
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,…
Large Language Models (LLMs) have shown remarkable capabilities across tasks, yet they often require additional prompting techniques when facing complex problems. While approaches like self-correction and response selection have emerged as…
Formal models for gene assembly in ciliates have been developed, in particular the string pointer reduction system (SPRS) and the graph pointer reduction system (GPRS). The reduction graph is a valuable tool within the SPRS, revealing much…