相关论文: Lyndon Array Construction during Burrows-Wheeler I…
We present a simple and fast algorithm for computing the $N$-th term of a given linearly recurrent sequence. Our new algorithm uses $O(\mathsf{M}(d) \log N)$ arithmetic operations, where $d$ is the order of the recurrence, and…
Recently, several works have shown that natural modifications of the classical conditional gradient method (aka Frank-Wolfe algorithm) for constrained convex optimization, provably converge with a linear rate when: i) the feasible set is a…
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse…
Indexing highly repetitive strings (i.e., strings with many repetitions) for fast queries has become a central research topic in string processing, because it has a wide variety of applications in bioinformatics and natural language…
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…
We evaluate the influence of different alphabet orderings on the Lyndon factorization of a string. Experiments with Pizza & Chili datasets show that for most alphabet reorderings, the number of Lyndon factors is usually small, and the…
Let $\mathcal{P}$ be the surface of a convex polyhedron with $n$ vertices. We consider the two-point shortest path query problem for $\mathcal{P}$: Constructing a data structure so that given any two query points $s$ and $t$ on…
Algorithms are given for determining $L_\infty$ isotonic regression of weighted data. For a linear order, grid in multidimensional space, or tree, of $n$ vertices, optimal algorithms are given, taking $\Theta(n)$ time. These improve upon…
We present an algorithm to compute the Jordan chain of a nearly defective matrix with a $2\times2$ Jordan block. The algorithm is based on an inverse-iteration procedure and only needs information about the invariant subspace corresponding…
We give a simple and efficient algorithm for adaptively counting inversions in a sequence of $n$ integers. Our algorithm runs in $O(n + n \sqrt{\lg{(Inv/n)}})$ time in the word-RAM model of computation, where $Inv$ is the number of…
In memory-constrained algorithms we have read-only access to the input, and the number of additional variables is limited. In this paper we introduce the compressed stack technique, a method that allows to transform algorithms whose space…
Information extraction from textual data, where the query is represented by a finite transducer and the task is to enumerate all results without repetition, and its extension to the weighted case, where each output element has a weight and…
Given a string on an integer alphabet, we present an algorithm that computes the set of all distinct squares belonging to this string in time linear to the string length. As an application, we show how to compute the tree topology of the…
Suffix trees are key and efficient data structure for solving string problems. A suffix tree is a compressed trie containing all the suffixes of a given text of length $n$ with a linear construction cost. In this work, we introduce an…
The suffix array $SA[1..n]$ of a text $T$ of length $n$ is a permutation of $\{1,\ldots,n\}$ describing the lexicographical ordering of suffixes of $T$, and it is considered to be among of the most important data structures in string…
Recovering the digital input of a time-discrete linear system from its (noisy) output is a significant challenge in the fields of data transmission, deconvolution, channel equalization, and inverse modeling. A variety of algorithms have…
Two important similarity measures between sequences are the longest common subsequence (LCS) and the dynamic time warping distance (DTWD). The computations of these measures for two given sequences are central tasks in a variety of…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…