Related papers: MONI can find k-MEMs
We describe the first self-indexes able to count and locate pattern occurrences in optimal time within a space bounded by the size of the most popular dictionary compressors. To achieve this result we combine several recent findings,…
Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…
Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…
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…
We study the maximum multiplicity $\mathcal{M}(k,n)$ of a simple transposition $s_k=(k \: k+1)$ in a reduced word for the longest permutation $w_0=n \: n-1 \: \cdots \: 2 \: 1$, a problem closely related to much previous work on sorting…
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 search query consists of several words. In a proximity full-text search, we want to find documents that contain these words near each other. This task requires much time when the query consists of high-frequently occurring words. If we…
This paper proposes an efficient and novel method to address range search on multidimensional points in $\theta(t)$ time, where $t$ is the number of points reported in $\Re^k$ space. This is accomplished by introducing a new data structure,…
We study the complexity of a fundamental algorithm for fairly allocating indivisible items, the round-robin algorithm. For $n$ agents and $m$ items, we show that the algorithm can be implemented in time $O(nm\log(m/n))$ in the worst case.…
We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
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…
In the subset sum problem we are given n positive integers along with a target integer t. A solution is a subset of these integers summing to t. In this short note we show that for a given subset sum instance there is a proof of size…
A substring $u$ of a string $T$ is said to be a repeat if $u$ occurs at least twice in $T$. An occurrence $[i..j]$ of a repeat $u$ in $T$ is said to be a net occurrence if each of the substrings $aub = T[i-1..j+1]$, $au = T[i-1..j+1]$, and…
Brown et al.\ (2025) described a pre-processing step, called $k$-mer based breaking (KeBaB), that speeds up searching for long maximal exact matches (MEMs) between a pattern $P$ and an indexed repetitive text $T$. KeBaB produces a set of…
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
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…