Related papers: Arbitrary-length analogs to de Bruijn sequences
We present practical algorithms for generating universal cycles uniformly at random. In particular, we consider universal cycles for shorthand permutations, subsets and multiset permutations, weak orders, and orientable sequences.…
We introduce an algorithm for the uniform generation of infinite traces, i.e., infinite words up to commutation of some letters. The algorithm outputs on-the-fly approximations of a theoretical infinite trace, the latter being distributed…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…
Numerical characteristics of polynomial identities of left nilpotent algebras are examined. Previously, we came up with a construction which, given an infinite binary word, allowed us to build a two-step left nilpotent algebra with…
We consider random sub-graphs of a fixed graph $G=(V,E)$ with large minimum degree. We fix a positive integer $k$ and let $G_k$ be the random sub-graph where each $v\in V$ independently chooses $k$ random neighbors, making $kn$ edges in…
We study a construction published by Donald Knuth in 1965 yielding a completely uniformly distributed sequence of real numbers. Knuth's work is based on de Bruijn sequences of increasing orders and alphabet sizes, which grow exponentially…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image…
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…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
We relate binary words with a given number of subsequences to continued fractions of rational numbers with a given denominator. We deduce that there are binary strings of length $O(\log n \log \log n)$ with exactly $n$ subsequences; this…
The nature of the alignment with gaps corresponding to a longest common subsequence (LCS) of two independent iid random sequences drawn from a finite alphabet is investigated. It is shown that such an optimal alignment typically matches…
We show that the de Bruijn-Erd\H{o}s condition for the error term in their improvement of Fekete's Lemma is not only sufficient but also necessary in the following strong sense. Suppose that given a sequence $0\leq f(1)\leq f(2)\leq…
Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Two finite words $u$ and $v$ are $k$-binomially equivalent if, for each word $x$ of length at most $k$, $x$ appears the same number of times as a subsequence (i.e., as a scattered subword) of both $u$ and $v$. This notion generalizes…
Given a random text over a finite alphabet, we study the frequencies at which fixed-length words occur as subsequences. As the data size grows, the joint distribution of word counts exhibits a rich asymptotic structure. We investigate all…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
Let us call a sequence of numbers heapable if they can be sequentially inserted to form a binary tree with the heap property, where each insertion subsequent to the first occurs at a leaf of the tree, i.e. below a previously placed number.…