Related papers: Arbitrary-length analogs to de Bruijn sequences
We consider a type of long-range percolation problem on the positive integers, motivated by earlier work of others on the appearance of (in)finite words within a site percolation model. The main issue is whether a given infinite binary word…
We show that any $n$-bit string can be recovered with high probability from $\exp(\widetilde{O}(n^{1/5}))$ independent random subsequences.
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
In this paper, the construction of finite-length binary sequences whose nonlinear complexity is not less than half of the length is investigated. By characterizing the structure of the sequences, an algorithm is proposed to generate all…
Squares (fragments of the form $xx$, for some string $x$) are arguably the most natural type of repetition in strings. The basic algorithmic question concerning squares is to check if a given string of length $n$ is square-free, that is,…
We present two variations of Duval's algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for…
The discrepancy of a binary string refers to the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. We provide an investigation of the discrepancy of…
A repetition free Longest Common Subsequence (LCS) of two sequences x and y is an LCS of x and y where each symbol may appear at most once. Let R denote the length of a repetition free LCS of two sequences of n symbols each one chosen…
A reformulation of the path length of binary search trees is given in terms of permutations, allowing to extend the definition to the instance of words, where the letters are obtained by independent geometric random variables (with…
We consider in this paper the possibility of embedding a quantum search algorithm within a classical binary search framework. The result appears promising: taking full advantage of quantum parallelism, we show that it may actually be…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
Brandenburg and (implicitly) Dejean introduced the concept of repetition threshold: the smallest real number alpha such that there exists an infinite word over a k-letter alphabet that avoids beta-powers for all beta>alpha. We generalize…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
We investigate the order of the variance of the optimal alignments score of two independent iid binary random words having the same length. The letters are equiprobable, but the scoring function is such that one letter has a larger score…
Since human randomness production has been studied and widely used to assess executive functions (especially inhibition), many measures have been suggested to assess the degree to which a sequence is random-like. However, each of them…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
We introduce the notion of de Bruijn entropy of an Eulerian quiver and show how the corresponding relative entropy can be applied to practical string similarity problems. This approach explicitly links the combinatorial and…
We present an algorithm which computes the $D^{th}$ term of a sequence satisfying a linear recurrence relation of order $d$ over a field $K$ in $O( \mathsf{M}(\bar d)\log(D) + \mathsf{M}(d)\log(d))$ operations in $K$, where $\bar d \leq d$…
Negative avoiding sequences of span $n$ are periodic sequences of elements from $\mathbb{Z}_k$ for some $k$ with the property that no $n$-tuple occurs more than once in a period and if an $n$-tuple does occur then its negative does not.…
The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…