Related papers: In-Place Sparse Suffix Sorting
Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP…
We present sorting algorithms that represent the fastest known techniques for a wide range of input sizes, input distributions, data types, and machines. A part of the speed advantage is due to the feature to work in-place. Previously, the…
Here we study the complexity of string problems as a function of the size of a program that generates input. We consider straight-line programs (SLP), since all algorithms on SLP-generated strings could be applied to processing…
We provide a sparse version of the bounded degree SOS hierarchy BSOS [7] for polynomial optimization problems. It permits to treat large scale problems which satisfy a structured sparsity pattern. When the sparsity pattern satisfies the…
Semidefinite programs (SDPs) often arise in relaxations of some NP-hard problems, and if the solution of the SDP obeys certain rank constraints, the relaxation will be tight. Decomposition methods based on chordal sparsity have already been…
Given a sequence of integers, we want to find a longest increasing subsequence of the sequence. It is known that this problem can be solved in $O(n \log n)$ time and space. Our goal in this paper is to reduce the space consumption while…
The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix…
Suppose we want to seek the longest common subsequences (LCSs) of two strings as informative patterns that explain the relationship between the strings. The dynamic programming algorithm gives us a table from which all LCSs can be extracted…
We give the first Congested Clique algorithm that computes a sparse hopset with polylogarithmic hopbound in polylogarithmic time. Given a graph $G=(V,E)$, a $(\beta,\epsilon)$-hopset $H$ with "hopbound" $\beta$, is a set of edges added to…
The stable principal component pursuit (SPCP) problem is a non-smooth convex optimization problem, the solution of which has been shown both in theory and in practice to enable one to recover the low rank and sparse components of a matrix…
The advent of "next-generation" DNA sequencing (NGS) technologies has meant that collections of hundreds of millions of DNA sequences are now commonplace in bioinformatics. Knowing the longest common prefix array (LCP) of such a collection…
The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…
One specific subset of quantum algorithms is Grovers Ordered Search Problem (OSP), the quantum counterpart of the classical binary search algorithm, which utilizes oracle functions to produce a specified value within an ordered database.…
LZ77-based compression schemes compress the input text by replacing factors in the text with an encoded reference to a previous occurrence formed by the couple (length, offset). For a given factor, the smallest is the offset, the smallest…
We study a generalized framework for structured sparsity. It extends the well-known methods of Lasso and Group Lasso by incorporating additional constraints on the variables as part of a convex optimization problem. This framework provides…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
The Cartesian-tree pattern matching is a recently introduced scheme of pattern matching that detects fragments in a sequential data stream which have a similar structure as a query pattern. Formally, Cartesian-tree pattern matching seeks…
Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…
A large number of computational and scientific methods commonly require decomposing a sparse matrix into triangular factors as LU decomposition. A common problem faced during this decomposition is that even though the given matrix may be…