Related papers: Extending de Bruijn sequences to larger alphabets
We introduce De Bruijn Graph Neural Networks (DBGNNs), a novel time-aware graph neural network architecture for time-resolved data on dynamic graphs. Our approach accounts for temporal-topological patterns that unfold in the causal topology…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
We define generalized de Bruijn words as those words having a Burrows-Wheeler transform that is a concatenation of permutations of the alphabet. We show that generalized de Bruijn words are in 1-to-1 correspondence with Hamiltonian cycles…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
Sequence assembly from short reads is an important problem in biology. It is known that solving the sequence assembly problem exactly on a bi-directed de Bruijn graph or a string graph is intractable. However finding a Shortest Double…
It is well known that Sturmian sequences are the aperiodic sequences that are balanced over a 2-letter alphabet. They are also characterized by their complexity: they have exactly $(n+1)$ factors of length $n$. One possible generalization…
Most of the literature on spanners focuses on building the graph from scratch. This paper instead focuses on adding edges to improve an existing graph. A major open problem in this field is: given a graph embedded in a metric space, and a…
Sidon sequences and their generalizations have found during the years and especially recently various applications in coding theory. One of the most important applications of these sequences is in the connection of synchronization patterns.…
We construct (k+-1)-regular graphs which provide sequences of expanders by adding or substracting appropriate 1-factors from given sequences of k-regular graphs. We compute numerical examples in a few cases for which the given sequences are…
We consider a symbolic coding of linear trajectories in the regular octagon with opposite sides identified (and more generally in regular 2n-gons). Each infinite trajectory gives a cutting sequence corresponding to the sequence of sides…
Longest common extension queries (often called longest common prefix queries) constitute a fundamental building block in multiple string algorithms, for example computing runs and approximate pattern matching. We show that a sequence of $q$…
A sequence $S=s_{1}s_{2}..._{n}$ is \emph{nonrepetitive} if no two adjacent blocks of $S$ are identical. In 1906 Thue proved that there exist arbitrarily long nonrepetitive sequences over 3-element set of symbols. We study a generalization…
The linear complexity of a sequence has been used as an important measure of keystream strength, hence designing a sequence which possesses high linear complexity and $k$-error linear complexity is a hot topic in cryptography and…
The problem is considered of arranging symbols around a cycle, in such a way that distances between different instances of a same symbol be as uniformly distributed as possible. A sequence of moments is defined for cycles, similarly to the…
In this article we introduce a definition of k-uniform thresholds hypergraphs through a binary sequence, a natural extension of the classical definition for thresholds graphs. We characterize some of its eigenvalues and multiplicities by…
The classical way of extending an $[n, k, d]$ linear code $\C$ is to add an overall parity-check coordinate to each codeword of the linear code $\C$. This extended code, denoted by $\overline{\C}(-\bone)$ and called the standardly extended…
The linear complexity and the $k$-error linear complexity of a binary sequence are important security measures for key stream strength. By studying binary sequences with the minimum Hamming weight, a new tool named as hypercube theory is…
We introduce two-dimensional toroidal arrays that are a variant of the de Bruijn tori. We call them nested perfect toroidal arrays. Instead of asking that every array of a given size has exactly one occurrence, we partition the positions in…
We propose a novel construction for the well-known prefer-max De Bruijn sequence, based on the cycle joining technique. We further show that the construction implies known results from the literature in a straightforward manner. First, it…
Given a set of $t$ words of length $n$ over a $k$-letter alphabet, it is proved that there exists a common subsequence among two of them of length at least $\frac{n}{k}+cn^{1-1/(t-k-2)}$, for some $c>0$ depending on $k$ and $t$. This is…