Related papers: Data Structure Lower Bounds on Random Access to Gr…

We show that if DTIME[2^{O(n)}] is not included in DSPACE[2^{o(n)}], then, for every set B in PSPACE, all strings x in B of length n can be represented by a string compressed(x) of length at most log (|B^{=n}|) + O(log n), such that a…

Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…

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…

Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…

Given two positions $i$ and $j$ in a string $T$ of length $N$, a longest common extension (LCE) query asks for the length of the longest common prefix between suffixes beginning at $i$ and $j$. A compressed LCE data structure is a data…

We consider the top tree compression scheme introduced by Bille et al. [ICALP 2013] and construct an infinite family of trees on $n$ nodes labeled from an alphabet of size $\sigma$, for which the size of the top DAG is…

We describe how, given a text $T [1..n]$ and a positive constant $\epsilon$, we can build a simple $O (z \log n)$-space index, where $z$ is the number of phrases in the LZ77 parse of $T$, such that later, given a pattern $P [1..m]$, in $O…

We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…

Let a text $T[1..n]$ be the only string generated by a context-free grammar with $g$ (terminal and nonterminal) symbols, and of size $G$ (measured as the sum of the lengths of the right-hand sides of the rules). Such a grammar, called a…

We consider the problem of finding repetitive structures and inherent patterns in a given string $\s{s}$ of length $n$ over a finite totally ordered alphabet. A border $\s{u}$ of a string $\s{s}$ is both a prefix and a suffix of $\s{s}$…

We present a data structure that stores a sequence $s[1..n]$ over alphabet $[1..\sigma]$ in $n\Ho(s) + o(n)(\Ho(s){+}1)$ bits, where $\Ho(s)$ is the zero-order entropy of $s$. This structure supports the queries \access, \rank\ and \select,…

We consider a fundamental problem in data structures, static predecessor searching: Given a subset S of size n from the universe [m], store S so that queries of the form "What is the predecessor of x in S?" can be answered efficiently. We…

We introduce a compressed suffix array representation that, on a text $T$ of length $n$ over an alphabet of size $\sigma$, can be built in $O(n)$ deterministic time, within $O(n\log\sigma)$ bits of working space, and counts the number of…

We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…

Unlike in statistical compression, where Shannon's entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures…

We overcome two major bottlenecks in the study of low rank approximation by assuming the low rank factors themselves are sparse. Specifically, (1) for low rank approximation with spectral norm error, we show how to improve the best known…

We consider the problem of representing, in a compressed format, a bit-vector $S$ of $m$ bits with $n$ 1s, supporting the following operations, where $b \in \{0, 1 \}$: $rank_b(S,i)$ returns the number of occurrences of bit $b$ in the…

Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…

We consider the classic Set Cover problem in the data stream model. For $n$ elements and $m$ sets ($m\geq n$) we give a $O(1/\delta)$-pass algorithm with a strongly sub-linear $\tilde{O}(mn^{\delta})$ space and logarithmic approximation…

This paper investigates the size in bits of the LZ77 encoding, which is the most popular and efficient variant of the Lempel-Ziv encodings used in data compression. We prove that, for a wide natural class of variable-length encoders for…