Related papers: The Labeled Direct Product Optimally Solves String…
Given a connected, undirected graph whose edges are labelled (or coloured), the minimum labelling spanning tree (MLST) problem seeks a spanning tree whose edges have the smallest number of distinct labels (or colours). In recent work, the…
We investigate string graphs through the lens of graph product structure theory, which describes complicated graphs as subgraphs of strong products of simpler building blocks. A graph $G$ is called a string graph if its vertices can be…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the given pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation…
The LCP array is an important tool in stringology, allowing to speed up pattern matching algorithms and enabling compact representations of the suffix tree. Recently, Conte et al. [DCC 2023] and Cotumaccio et al. [SPIRE 2023] extended the…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
Exact pattern matching in labeled graphs is the problem of searching paths of a graph $G=(V,E)$ that spell the same string as the pattern $P[1..m]$. This basic problem can be found at the heart of more complex operations on variation graphs…
Pattern matching queries on strings can be solved in linear time by Knuth-Morris-Pratt (KMP) algorithm. In 1973, Weiner introduced the suffix tree of a string [FOCS 1973] and showed that the seemingly more difficult problem of computing…
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,…
This paper studies constructive heuristics for the minimum labelling spanning tree (MLST) problem. The purpose is to find a spanning tree that uses edges that are as similar as possible. Given an undirected labeled connected graph (i.e.,…
A labelled, undirected graph is a graph whose edges have assigned labels, from a specific set. Given a labelled, undirected graph, the well-known minimum labelling spanning tree problem is aimed at finding the spanning tree of the graph…
In the String Matching in Labeled Graphs (SMLG) problem, we need to determine whether a pattern string appears on a given labeled graph or a given automaton. Under the Orthogonal Vectors hypothesis, the SMLG problem cannot be solved in…
We investigate the problem of sequentially predicting the binary labels on the nodes of an arbitrary weighted graph. We show that, under a suitable parametrization of the problem, the optimal number of prediction mistakes can be…
We introduce the minimum labelling spanning bi-connected subgraph problem (MLSBP) replacing connectivity by bi-connectivity in the well known minimum labelling spanning tree problem (MLSTP). A graph is bi-connected if, for every two…
Graph algorithms are widely used for decision making and knowledge discovery. To ensure their effectiveness, it is essential that their output remains stable even when subjected to small perturbations to the input because frequent output…
Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…
In this paper we describe an extension of the Variable Neighbourhood Search (VNS) which integrates the basic VNS with other complementary approaches from machine learning, statistics and experimental algorithmic, in order to produce…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…
We give an algorithm for finding the arboricity of a weighted, undirected graph, defined as the minimum number of spanning forests that cover all edges of the graph, in $\sqrt{n} m^{1+o(1)}$ time. This improves on the previous best bound of…
We propose a convex-concave programming approach for the labeled weighted graph matching problem. The convex-concave programming formulation is obtained by rewriting the weighted graph matching problem as a least-square problem on the set…