相关论文: Sparse Suffix Tree Construction with Small Space

Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…

In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…

Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…

The tree breadth ${\rm tb}(G)$ of a connected graph $G$ is the smallest non-negative integer $\rho$ such that $G$ has a tree decomposition whose bags all have radius at most $\rho$. We show that, given a connected graph $G$ of order $n$ and…

In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $\sigma$, and we are asked to find a longest string occurring as a fragment of both $S$ and…

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…

In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…

We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…

Suppose that we are given a string $s$ of length $n$ over an alphabet $\{0,1,\ldots,n^{O(1)}\}$ and $\delta$ is the string complexity of $s$, a known compression measure. We describe an index on $s$ with $O(\delta\log\frac{n}{\delta})$…

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…

Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…

We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…

We investigate whether an n-vertex instance (G,k) of Treewidth, asking whether the graph G has treewidth at most k, can efficiently be made sparse without changing its answer. By giving a special form of OR-cross-composition, we prove that…

The weighted ancestor problem on a rooted node-weighted tree $T$ is a generalization of the classic predecessor problem: construct a data structure for a set of integers that supports fast predecessor queries. Both problems are known to…

Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…

We consider the problem of finding, given two documents of total length $n$, a longest string occurring as a substring of both documents. This problem, known as the Longest Common Substring (LCS) problem, has a classic $O(n)$-time solution…

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…

Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…

We investigate the problem of determining a compact underspecified semantical representation for sentences that may be highly ambiguous. Due to combinatorial explosion, the naive method of building semantics for the different syntactic…

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…