Related papers: String Consensus Problems with Swaps and Substitut…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
Given a graph where every vertex has exactly one labeled token, how can we most quickly execute a given permutation on the tokens? In (sequential) token swapping, the goal is to use the shortest possible sequence of swaps, each of which…
A classical measure of string comparison is given by the longest common subsequence (LCS) problem on a pair of strings. We consider its generalisation, called the semi-local LCS problem, which arises naturally in many string-related…
In many applications, it is necessary to determine the similarity of two strings. A widely-used notion of string similarity is the edit distance: the minimum number of insertions, deletions, and substitutions required to transform one…
Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
We consider two variants of the classical Stable Roommates problem with Incomplete (but strictly ordered) preference lists SRI that are degree constrained, i.e., preference lists are of bounded length. The first variant, EGAL d-SRI,…
Distributed abstract programs are a novel class of distributed optimization problems where (i) the number of variables is much smaller than the number of constraints and (ii) each constraint is associated to a network node. Abstract…
In this article, we study the problem of finding the longest common separable pattern between several permutations. We give a polynomial-time algorithm when the number of input permutations is fixed and show that the problem is NP-hard for…
In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
In this paper, we investigate problems which are dual to the unification problem, namely the Fixed Point (FP) problem, Common Term (CT) problem and the Common Equation (CE) problem for string rewriting systems. Our main motivation is…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
In the Maximum Duo-Preservation String Mapping problem we are given two strings and wish to map the letters of the former to the letters of the latter so as to maximise the number of duos. A duo is a pair of consecutive letters that is…
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…
The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…
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…