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The range-minimum query (RMQ) problem is a fundamental data structuring task with numerous applications. Despite the fact that succinct solutions with worst-case optimal $2n+o(n)$ bits of space and constant query time are known, it has been…
We consider succinct data structures for representing a set of $n$ horizontal line segments in the plane given in rank space to support \emph{segment access}, \emph{segment selection}, and \emph{segment rank} queries. A segment access query…
The Subset Sum problem, which asks whether a set of $n$ integers has a subset summing to a target $t$, is a fundamental NP-complete problem in cryptography and combinatorial optimization. The classical meet-in-the-middle (MIM) algorithm of…
Given a string $w$, another string $v$ is said to be a subsequence of $w$ if $v$ can be obtained from $w$ by removing some of its letters; on the other hand, $v$ is called an absent subsequence of $w$ if $v$ is not a subsequence of $w$. The…
Given a finite set satisfying condition $\mathcal{A}$, the subset selection problem asks, how large of a subset satisfying condition $\mathcal{B}$ can we find? We make progress on three instances of subset selection problems in planar point…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We give a new characterization of maximal repetitions (or runs) in strings based on Lyndon words. The characterization leads to a proof of what was known as the "runs" conjecture (Kolpakov \& Kucherov (FOCS '99)), which states that the…
Let $S$ be a string of length $n$. In this paper we introduce the notion of \emph{string attractor}: a subset of the string's positions $[1,n]$ such that every distinct substring of $S$ has an occurrence crossing one of the attractor's…
Many problems in bioinformatics are about finding strings that approximately represent a collection of given strings. We look at more general problems where some input strings can be classified as outliers. The Close to Most Strings problem…
We show that Closest Substring, one of the most important problems in the field of biological sequence analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This problem is…
For a static array A of n ordered objects, a range minimum query asks for the position of the minimum between two specified array indices. We show how to preprocess A into a scheme of size 2n+o(n) bits that allows to answer range minimum…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
We examine the amount of preprocessing needed for answering certain on-line queries as fast as possible. We start with the following basic problem. Suppose we are given a semigroup $(S,\circ )$. Let $s_1 ,\ldots, s_n$ be elements of $S$. We…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
Given a large data matrix $A\in\mathbb{R}^{n\times n}$, we consider the problem of determining whether its entries are i.i.d. with some known marginal distribution $A_{ij}\sim P_0$, or instead $A$ contains a principal submatrix $A_{{\sf…
Given $(a_1, \dots, a_n, t) \in \mathbb{Z}_{\geq 0}^{n + 1}$, the Subset Sum problem ($\mathsf{SSUM}$) is to decide whether there exists $S \subseteq [n]$ such that $\sum_{i \in S} a_i = t$. There is a close variant of the $\mathsf{SSUM}$,…
Data series similarity search is an important operation and at the core of several analysis tasks and applications related to data series collections. Despite the fact that data series indexes enable fast similarity search, all existing…
We study the density estimation problem defined as follows: given $k$ distributions $p_1, \ldots, p_k$ over a discrete domain $[n]$, as well as a collection of samples chosen from a ``query'' distribution $q$ over $[n]$, output $p_i$ that…