Related papers: Binary Jumbled Indexing: Suffix tree histogram
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
The block tree [Belazzougui et al., J. Comput. Syst. Sci. '21] is a compressed representation of a length-$n$ text that supports access, rank, and select queries while requiring only $O(z\log\frac{n}{z})$ words of space, where $z$ is the…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Considering Grover's Search Algorithm (GSA) with the standard diffuser stage applied, we revisit the $3$-qubit unique String Detection Problem (SDP) and extend the algorithm to $4$-qubit SDP with multiple winners. We then investigate…
In this work, a new indexing technique of data streams called BSTree is proposed. This technique uses the method of data discretization, SAX [4], to reduce online the dimensionality of data streams. It draws on Btree to build the index and…
This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents some large data. A task can only be executed if all input and output data fit into memory, and a data can only…
The topic of this paper are integer programming models in which a subset of 0/1-variables encode a partitioning of a set of objects into disjoint subsets. Such models can be surprisingly hard to solve by branch-and-cut algorithms if the…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We…
We give two new approximation algorithms to compute the fractional hypertree width of an input hypergraph. The first algorithm takes as input $n$-vertex $m$-edge hypergraph $H$ of fractional hypertree width at most $\omega$, runs in…
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
A matching complex of a simple graph $G$ is a simplicial complex with faces given by the matchings of $G$. The topology of matching complexes is mysterious; there are few graphs for which the homotopy type is known. Marietti and Testa…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
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…
In Gapped String Indexing, the goal is to compactly represent a string $S$ of length $n$ such that for any query consisting of two strings $P_1$ and $P_2$, called patterns, and an integer interval $[\alpha, \beta]$, called gap range, we can…
In this paper we study a natural generalization of both {\sc $k$-Path} and {\sc $k$-Tree} problems, namely, the {\sc Subgraph Isomorphism} problem. In the {\sc Subgraph Isomorphism} problem we are given two graphs $F$ and $G$ on $k$ and $n$…
A labeled tree (or a trie) is a natural generalization of a string, which can also be seen as a compact representation of a set of strings. This paper considers the labeled tree indexing problem, and provides a number of new results on…
There are several data structures which can calculate the prefix sums of an array efficiently, while handling point updates on the array, such as Segment Trees and Binary Indexed Trees (BIT). Both these data structures can handle the these…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
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…