相关论文: Space-Efficient Computation of the LCP Array from …
Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit…
Let $T$ be a string of length $n$ over an integer alphabet of size $\sigma$. In the word RAM model, $T$ can be represented in $O(n /\log_\sigma n)$ space. We show that a representation of all covers of $T$ can be computed in the optimal…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
We present the first $\mathrm{o}(n)$-space polynomial-time algorithm for computing the length of a longest common subsequence. Given two strings of length $n$, the algorithm runs in $\mathrm{O}(n^{3})$ time with $\mathrm{O}\left(\frac{n…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
In this paper, we revisit the much studied LCS problem for two given sequences. Based on the algorithm of Iliopoulos and Rahman for solving the LCS problem, we have suggested 3 new improved algorithms. We first reformulate the problem in a…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
The move structure represents a permutation $\pi$ of $[0,n)$ as a covering set of $O(r)$ disjoint intervals (contiguous subsets of $[0,n)$), where $r$ is the minimum number of intervals whose values permute together. Formally, $r = 1 +…
We prove that for every integer $n > 0$ and for every alphabet $\Sigma_k$ of size $k \geq 3$, there exists a necklace of length $n$ whose Burrows-Wheeler Transform (BWT) is completely unclustered, i.e., it consists of exactly $n$ runs with…
We present the first worst-case linear time algorithm that directly computes the parameterized suffix and LCP arrays for constant sized alphabets. Previous algorithms either required quadratic time or the parameterized suffix tree to be…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…
The compact directed acyclic word graph (CDAWG) of a string $T$ of length $n$ takes space proportional just to the number $e$ of right extensions of the maximal repeats of $T$, and it is thus an appealing index for highly repetitive…
We consider the problem of maintaining a collection of strings while efficiently supporting splits and concatenations on them, as well as comparing two substrings, and computing the longest common prefix between two suffixes. This problem…
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…
The boom of genomic sequencing makes compression of set of sequences inescapable. This underlies the need for multi-string indexing data structures that helps compressing the data. The most prominent example of such data structures is the…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
In this paper we consider the problem of computing the longest common abelian factor (LCAF) between two given strings. We present a simple $O(\sigma~ n^2)$ time algorithm, where $n$ is the length of the strings and $\sigma$ is the alphabet…
Enumerating characteristic substrings (e.g., maximal repeats, minimal unique substrings, and minimal absent words) in a given string has been an important research topic because there are a wide variety of applications in various areas such…