Related papers: Loopless Algorithms to Generate Maximum Length Gra…
The most well-known Gray code of permutations is plain changes. It was discovered in the 1600s by bell-ringers who wished to order the permutations of [n] by swaps (e.g., 123, 132, 312, 321, 231, 213 for n = 3). In other words, plain…
A prefix normal word is a binary word with the property that no substring has more $1$s than the prefix of the same length. By proving that the set of prefix normal words is a bubble language, we can exhaustively list all prefix normal…
Given a countable set X (usually taken to be the natural numbers or integers), an infinite permutation, \pi, of X is a linear ordering of X. This paper investigates the combinatorial complexity of infinite permutations on the natural…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
Let $LA_{n}(\tau)$ be the length of the longest alternating subsequence of a uniform random permutation $\tau\in[n]$. Classical probabilistic arguments are used to rederive the asymptotic mean, variance and limiting law of $LA_{n}(\tau)$.…
Motivated by a historical combinatorial problem that resembles the well-known Josephus problem, we investigate circular partition algorithms and formulate problems in deterministic finite automata with practical algorithms. The historical…
Let ${\boldsymbol A}\in{\mathbb R}^{n\times n}$ be a symmetric random matrix with independent and identically distributed Gaussian entries above the diagonal. We consider the problem of maximizing $\langle{\boldsymbol \sigma},{\boldsymbol…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
Can a list of binary strings be ordered so that consecutive strings differ in a single bit? Can a list of permutations be ordered so that consecutive permutations differ by a swap? Can a list of non-crossing set partitions be ordered so…
In the k-mappability problem, we are given a string x of length n and integers m and k, and we are asked to count, for each length-m factor y of x, the number of other factors of length m of x that are at Hamming distance at most k from y.…
A universal cycle (u-cycle) for permutations of length $n$ is a cyclic word, any size $n$ window of which is order-isomorphic to exactly one permutation of length $n$, and all permutations of length $n$ are covered. It is known that…
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…
We demonstrate a direct mapping of max k-SAT problems (and weighted max k-SAT) to a Chimera graph, which is the non-planar hardware graph of the devices built by D-Wave Systems Inc. We further show that this mapping can be used to map a…
The paper contains a proof of the conjecture of M. Klin and D. Maru$\breve{\rm s}$i$\breve{\rm c}$ that an automorphism group of a transitive graph contains a permutation, decomposed in cycles of the same length. The proof is based on the…
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in…
We study the problem of designing a data structure that reports the positions of the distinct $\tau$-majorities within any range of an array $A[1,n]$, without storing $A$. A $\tau$-majority in a range $A[i,j]$, for $0<\tau< 1$, is an…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…
Snake-in-the-box code is a Gray code which is capable of detecting a single error. Gray codes are important in the context of the rank modulation scheme which was suggested recently for representing information in flash memories. For a Gray…
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,…
In this paper we study the adaptive prefix coding problem in cases where the size of the input alphabet is large. We present an online prefix coding algorithm that uses $O(\sigma^{1 / \lambda + \epsilon}) $ bits of space for any constants…