Related papers: Wee LCP
The notions of synchronizing and partitioning sets are recently introduced variants of locally consistent parsings with great potential in problem-solving. In this paper we propose a deterministic algorithm that constructs for a given…
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…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches…
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 this paper we consider the basic variant where the pattern is…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
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…
We present two structural results concerning longest common prefixes of non-empty languages. First, we show that the longest common prefix of the language generated by a context-free grammar of size $N$ equals the longest common prefix of…
Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
We consider the problem of encoding a string of length $n$ from an integer alphabet of size $\sigma$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…
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…
A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can…
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 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…
A longest common extension (LCE) query on a string computes the length of the longest common suffix or prefix at two given positions. A dynamic LCE algorithm maintains a data structure that allows efficient LCE queries on a string that can…
We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…