Related papers: Suffixient Sets

A set $S \subseteq V$ of the graph $G = (V, E)$ is called a $[1, 2]$-set of $G$ if any vertex which is not in $S$ has at least one but no more than two neighbors in $S$. A set $S \subseteq V$ is called a $[1, 2]$-total set of $G$ if any…

Let $\T_{n}$ be the set of rooted labeled trees on $\set{0,...,n}$. A maximal decreasing subtree of a rooted labeled tree is defined by the maximal subtree from the root with all edges being decreasing. In this paper, we study a new…

We revisit the classic border tree data structure [Gu, Farach, Beigel, SODA 1994] that answers the following prefix-suffix queries on a string $T$ of length $n$ over an integer alphabet $\Sigma=[0,\sigma)$: for any $i,j \in [0,n)$ return…

We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…

Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…

The suffix array is a classic full-text index, combining effectiveness with simplicity. We discuss three approaches aiming to improve its efficiency even more: changes to the navigation, data layout and adding extra data. In short, we show…

A dynamic coloring of the vertices of a graph $G$ starts with an initial subset $S$ of colored vertices, with all remaining vertices being non-colored. At each discrete time interval, a colored vertex with exactly one non-colored neighbor…

A substring $u$ of a string $T$ is said to be a repeat if $u$ occurs at least twice in $T$. An occurrence $[i..j]$ of a repeat $u$ in $T$ is said to be a net occurrence if each of the substrings $aub = T[i-1..j+1]$, $au = T[i-1..j+1]$, and…

A subset of vertices $F$ in a graph $G$ is called a \emph{dissociation set} if the induced subgraph $G[F]$ of $G$ has maximum degree at most 1. A \emph{maximal dissociation set} of $G$ is a dissociation set which is not a proper subset of…

We consider construction of the suffix tree and the directed acyclic word graph (DAWG) indexing data structures for a collection $\mathcal{T}$ of texts, where a new symbol may be appended to any text in $\mathcal{T} = \{T_1, \ldots, T_K\}$,…

An automorphism on a graph $G$ is a bijective mapping on the vertex set $V(G)$, which preserves the relation of adjacency between any two vertices of $G$. An automorphism $g$ fixes a vertex $v$ if $g$ maps $v$ onto itself. The stabilizer of…

The choice dictionary is introduced as a data structure that can be initialized with a parameter $n\in\mathbb{N}=\{1,2,\ldots\}$ and subsequently maintains an initially empty subset $S$ of $\{1,\ldots,n\}$ under insertion, deletion,…

We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n /…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

Let A be a finite alphabet and f: A^* --> A^* be a morphism with an iterative fixed point f^\omega(\alpha), where \alpha{} is in A. Consider the subshift (X, T), where X is the shift orbit closure of f^\omega(\alpha) and T: X --> X is the…

A good edge-labelling of a simple, finite graph is a labelling of its edges with real numbers such that, for every ordered pair of vertices (u,v), there is at most one nondecreasing path from u to v. In this paper we prove that any graph on…

The observed frequency of the longest proper prefix, the longest proper suffix, and the longest infix of a word $w$ in a given sequence $x$ can be used for classifying $w$ as avoided or overabundant. The definitions used for the expectation…

We deal with the problem of maintaining the suffix tree indexing structure for a fully-online collection of multiple strings, where a new character can be prepended to any string in the collection at any time. The only previously known…

Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…

Let $\Sigma$ and $\Pi$ be disjoint alphabets, respectively called the static alphabet and the parameterized alphabet. Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to parameterized match (p-match) if there exists a…