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Edge-labeled graphs are widely used to describe relationships between entities in a database. Given a query subgraph that represents an example of what the user is searching for, we study the problem of efficiently searching for similar…
The Subgraph Isomorphism problem is of considerable importance in computer science. We examine the problem when the pattern graph H is of bounded treewidth, as occurs in a variety of applications. This problem has a well-known algorithm via…
A graph $G$ contains a graph $H$ as an induced minor if $H$ can be obtained from $G$ by vertex deletions and edge contractions. The class of $H$-induced-minor-free graphs generalizes the class of $H$-minor-free graphs, but unlike…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
In this paper we show lower bounds for a certain large class of algorithms solving the Graph Isomorphism problem, even on expander graph instances. Spielman [25] shows an algorithm for isomorphism of strongly regular expander graphs that…
We consider the complexity of finding weighted homomorphisms from intersection graphs of curves (string graphs) with $n$ vertices to a fixed graph $H$. We provide a complete dichotomy for the problem: if $H$ has no two vertices sharing two…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
The transversal hypergraph problem is the task of enumerating the minimal hitting sets of a hypergraph. It is a long-standing open question whether this can be done in output-polynomial time. For hypergraphs whose solutions have bounded…
Graph pattern matching algorithms to handle million-scale dynamic graphs are widely used in many applications such as social network analytics and suspicious transaction detections from financial networks. On the other hand, the computation…
Suffix trees are an important data structure at the core of optimal solutions to many fundamental string problems, such as exact pattern matching, longest common substring, matching statistics, and longest repeated substring. Recent lines…
We initiate the study of computational problems on $k$-mers (strings of length $k$) in labeled graphs. As a starting point, we consider the problem of counting the number of distinct $k$-mers found on the walks of a graph. We establish that…
Computing the Euler genus of a graph is a fundamental problem in graph theory and topology. It has been shown to be NP-hard by [Thomassen '89] and a linear-time fixed-parameter algorithm has been obtained by [Mohar '99]. Despite extensive…
We present linear time {\it in-place} algorithms for several basic and fundamental graph problems including the well-known graph search methods (like depth-first search, breadth-first search, maximum cardinality search), connectivity…
A degenerate or indeterminate string on an alphabet $\Sigma$ is a sequence of non-empty subsets of $\Sigma$. Given a degenerate string $t$ of length $n$, we present a new method based on the Burrows--Wheeler transform for searching for a…
Graph pattern matching is a fundamental operation for the analysis and exploration ofdata graphs. In thispaper, we presenta novel approachfor efficiently finding homomorphic matches for hybrid graph patterns, where each pattern edge may be…
The $r$-th iterated line graph $L^{r}(G)$ of a graph $G$ is defined by: (i) $L^{0}(G) = G$ and (ii) $L^{r}(G) = L(L^{(r- 1)}(G))$ for $r > 0$, where $L(G)$ denotes the line graph of $G$. The Hamiltonian Index $h(G)$ of $G$ is the smallest…
For any particular class of graphs, algorithms for computational problems restricted to the class often rely on structural properties that depend on the specific problem at hand. This begs the question if a large set of such results can be…
We propose an efficient algorithm for graph matching based on similarity scores constructed from counting a certain family of weighted trees rooted at each vertex. For two Erd\H{o}s-R\'enyi graphs $\mathcal{G}(n,q)$ whose edges are…
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…