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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 $q$…
Indexing a set of strings for prefix search or membership queries is a fundamental task with many applications such as information retrieval or database systems. A classic abstract data type for modelling such an index is a trie. Due to the…
We investigate the variance of the length of the longest common subsequences of two independent random words of size $n$, where the letters of one word are i.i.d. uniformly drawn from $\{\alpha_1, \alpha_2, \cdots, \alpha_m\}$, while the…
An abundance of real-world problems manifest as covering edges and/or vertices of a graph with cliques that are optimized for some objectives. We consider different structural parameters of graph, and design fixed-parameter tractable…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
In this note, we first introduce a new problem called the longest common subsequence and substring problem. Let $X$ and $Y$ be two strings over an alphabet $\Sigma$. The longest common subsequence and substring problem for $X$ and $Y$ is to…
The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three…
The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
Lekkerkerker and Boland characterized the minimal forbidden induced subgraphs for the class of interval graphs. We give a linear-time algorithm to find one in any graph that is not an interval graph. Tucker characterized the minimal…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…
Computation on compressed strings is one of the key approaches to processing massive data sets. We consider local subsequence recognition problems on strings compressed by straight-line programs (SLP), which is closely related to…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
Linear rules have played an increasing role in structural proof theory in recent years. It has been observed that the set of all sound linear inference rules in Boolean logic is already coNP-complete, i.e. that every Boolean tautology can…
Consider two random strings having the same length and generated by an iid sequence taking its values uniformly in a fixed finite alphabet. Artificially place a long constant block into one of the strings, where a constant block is a…
A natural probabilistic model for motif discovery has been used to experimentally test the quality of motif discovery programs. In this model, there are $k$ background sequences, and each character in a background sequence is a random…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
We study the problems of finding a shortest synchronizing word and its length for a given prefix code. This is done in two different settings: when the code is defined by an arbitrary decoder recognizing its star and when the code is…