Related papers: MONI can find k-MEMs
In this paper, we explore worst-case solutions for the problems of single and multiple matching on strings in the word RAM model with word length w. In the first problem, we have to build a data structure based on a pattern p of length m…
We give a quantum algorithm to find the index y in a table T of size N such that in time O(c sqrt N), T[y] is minimum with probability at least 1-1/2^c.
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
In this paper we present an algorithm to compute the Lyndon array of a string $T$ of length $n$ as a byproduct of the inversion of the Burrows-Wheeler transform of $T$. Our algorithm runs in linear time using only a stack in addition to the…
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…
Intervals have been generated in many applications (e.g., temporal databases), and they are often associated with weights, such as prices. This paper addresses the problem of processing top-k weighted stabbing queries on interval data.…
Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
We consider the family of $\Phi$-Subset problems, where the input consists of an instance $I$ of size $N$ over a universe $U_I$ of size $n$ and the task is to check whether the universe contains a subset with property $\Phi$ (e.g., $\Phi$…
In a previous paper we generalized the Knuth-Morris-Pratt (KMP) pattern matching algorithm and defined a non-conventional kind of RAM, the MP--RAMs (RAMS equipped with extra operations), and designed an O(n) on-line algorithm for solving…
We present space efficient Monte Carlo algorithms that solve Subset Sum and Knapsack instances with $n$ items using $O^*(2^{0.86n})$ time and polynomial space, where the $O^*(\cdot)$ notation suppresses factors polynomial in the input size.…
Natural language understanding tasks such as open-domain question answering often require retrieving and assimilating factual information from multiple sources. We propose to address this problem by integrating a semi-parametric…
The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high…
Time series play a fundamental role in many domains, capturing a plethora of information about the underlying data-generating processes. When a process generates multiple synchronized signals we are faced with multidimensional time series.…
We study the task of learning latent-variable models. A common algorithmic technique for this task is the method of moments. Unfortunately, moment-based approaches are hampered by the fact that the moment tensors of super-constant degree…
The present letter proposes a modification in the well known Grover's search algorithm, which searches a database of $N$ unsorted items in $O(\sqrt{N/M})$ steps, where $M$ represents the number of solutions to the search problem.…
We revisit the complexity of one of the most basic problems in pattern matching. In the k-mismatch problem we must compute the Hamming distance between a pattern of length m and every m-length substring of a text of length n, as long as…
We study theta-joins in general and join predicates with conjunctions and disjunctions of inequalities in particular, focusing on ranked enumeration where the answers are returned incrementally in an order dictated by a given ranking…
The minimizer of a word of size $k$ (a $k$-mer) is defined as its smallest substring of size $m$ (with $m\leq k$), according to some ordering on $m$-mers. minimizers have been used in bioinformatics -- notably -- to partition sequencing…