Related papers: String Rearrangement Inequalities and a Total Orde…
A fundamental concern in linguistics has been to understand how languages change, such as in relation to word order. Since the order of words in a sentence (i.e. the relative placement of Subject, Object, and Verb) is readily identifiable…
In-place associative integer sorting technique was proposed for integer lists which requires only constant amount of additional memory replacing bucket sort, distribution counting sort and address calculation sort family of algorithms.…
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 evaluate the influence of different alphabet orderings on the Lyndon factorization of a string. Experiments with Pizza & Chili datasets show that for most alphabet reorderings, the number of Lyndon factors is usually small, and the…
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…
This paper addresses the online exact string matching problem which consists in finding all occurrences of a given pattern p in a text t. It is an extensively studied problem in computer science, mainly due to its direct applications to…
Alignments, i.e., position-wise comparisons of two or more strings or ordered lists are of utmost practical importance in computational biology and a host of other fields, including historical linguistics and emerging areas of research in…
Simon's congruence $\sim_k$ is defined as follows: two words are $\sim_k$-equivalent if they have the same set of subsequences of length at most $k$. We propose an algorithm which computes, given two words $s$ and $t$, the largest $k$ for…
In this paper we present a really simple linear-time algorithm constructing a context-free grammar of size O(g log (N/g)) for the input string, where N is the size of the input string and g the size of the optimal grammar generating this…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…
This dissertation focuses on two fundamental sorting problems: string sorting and suffix sorting. The first part considers parallel string sorting on shared-memory multi-core machines, the second part external memory suffix sorting using…
It is known that an ordinal is the order type of the lexicographic ordering of a regular language if and only if it is less than omega^omega. We design a polynomial time algorithm that constructs, for each well-ordered regular language L…
A synchronizing word of a deterministic finite complete automaton is a word whose action maps every state to a single one. Finding a shortest or a short synchronizing word is a central computational problem in the theory of synchronizing…
A string $S[1,n]$ is a power (or tandem repeat) of order $k$ and period $n/k$ if it can decomposed into $k$ consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their…
A subsequence of a word $w$ is a word $u$ such that $u = w[i_1] w[i_2] , \dots w[i_{|u|}]$, for some set of indices $1 \leq i_1 < i_2 < \dots < i_k \leq |w|$. A word $w$ is $k$-subsequence universal over an alphabet $\Sigma$ if every word…
Given a pattern string $P$ of length $n$ consisting of $\delta$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $\Sigma$ of size $\Delta$, the {\em exact string…
Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…
We give efficient algorithms for ranking Lyndon words of length $n$ over an alphabet of size $\sigma$. The rank of a Lyndon word is its position in the sequence of lexicographically ordered Lyndon words of the same length. The outputs are…