Related papers: The Tandem Duplication Distance Problem is hard ov…
Motivated by an application where we try to make proofs for Description Logic inferences smaller by rewriting, we consider the following decision problem, which we call the small term reachability problem: given a term rewriting system $R$,…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
We study random string-duplication systems, which we call P\'olya string models. These are motivated by DNA storage in living organisms, and certain random mutation processes that affect their genome. Unlike previous works that study the…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
One of the main problems encountered so far with recurrent neural networks is that they struggle to retain long-time information dependencies in their recurrent connections. Neural Turing Machines (NTMs) attempt to mitigate this issue by…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
In the era of high throughput DNA sequencing (HTS) technologies, calculating the edit distance (i.e., the minimum number of substitutions, insertions, and deletions between a pair of sequences) for billions of genomic sequences is the…
Indexing a set of strings for prefix search or membership queries is a fundamental task with many applications such as information retrieval or database systems. A classic abstract data type for modelling such an index is a trie. Due to the…
This paper studies two problems that are motivated by the novel recent approach of composite DNA that takes advantage of the DNA synthesis property which generates a huge number of copies for every synthesized strand. Under this paradigm,…
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…
Dimension reduction is a technique used to transform data from a high-dimensional space into a lower-dimensional space, aiming to retain as much of the original information as possible. This approach is crucial in many disciplines like…
Let $\Sigma$ be an alphabet. For two strings $X$, $Y$, and a constrained string $P$ over the alphabet $\Sigma$, the constrained longest common subsequence and substring problem for two strings $X$ and $Y$ with respect to $P$ is to find a…
We address the separability problem for straight-line string constraints. The separability problem for languages of a class C by a class S asks: given two languages A and B in C, does there exist a language I in S separating A and B (i.e.,…
DNA is a promising storage medium, but its stability and occurrence of Indel errors pose a significant challenge. The relative occurrence of Guanine(G) and Cytosine(C) in DNA is crucial for its longevity, and reverse complementary base…
$ \newcommand{\Z}{\mathbb{Z}} \newcommand{\eps}{\varepsilon} \newcommand{\cc}[1]{\mathsf{#1}} \newcommand{\NP}{\cc{NP}} \newcommand{\problem}[1]{\mathrm{#1}} \newcommand{\BDD}{\problem{BDD}} $Bounded Distance Decoding $\BDD_{p,\alpha}$ is…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…