Related papers: Optimal Time and Space Construction of Suffix Arra…
In the Longest Common Factor with $k$ Mismatches (LCF$_k$) problem, we are given two strings $X$ and $Y$ of total length $n$, and we are asked to find a pair of maximal-length factors, one of $X$ and the other of $Y$, such that their…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
Simon's congruence $\sim_k$ is defined as follows: two words are $\sim_k$-equivalent if they have the same set of subsequences of length at most $k$. We propose an algorithm which computes, given two words $s$ and $t$, the largest $k$ for…
The retrieval problem is the problem of associating data with keys in a set. Formally, the data structure must store a function f: U ->{0,1}^r that has specified values on the elements of a given set S, a subset of U, |S|=n, but may have…
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,…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
A Longest Common Extension (LCE) query on a text $T$ of length $N$ asks for the length of the longest common prefix of suffixes starting at given two positions. We show that the signature encoding $\mathcal{G}$ of size $w = O(\min(z \log N…
We develop dynamic dictionaries on the word RAM that use asymptotically optimal space, up to constant factors, subject to insertions and deletions, and subject to supporting perfect-hashing queries and/or membership queries, each operation…
Given string $S[1..N]$ and integer $k$, the {\em suffix selection} problem is to determine the $k$th lexicographically smallest amongst the suffixes $S[i... N]$, $1 \leq i \leq N$. We study the suffix selection problem in the cache-aware…
The Karp-Rabin fingerprint of a string is a type of hash value that due to its strong properties has been used in many string algorithms. In this paper we show how to construct a data structure for a string $S$ of size $N$ compressed by a…
We present algorithms for length-constrained maximum sum segment and maximum density segment problems, in particular, and the problem of finding length-constrained heaviest segments, in general, for a sequence of real numbers. Given a…
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…
A longest repeat query on a string, motivated by its applications in many subfields including computational biology, asks for the longest repetitive substring(s) covering a particular string position (point query). In this paper, we extend…
In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\in\Sigma^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries…
Given a string $T$ of length $N$, the goal of grammar compression is to construct a small context-free grammar generating only $T$. Among existing grammar compression methods, RePair (recursive paring) [Larsson and Moffat, 1999] is notable…
Strings in the real world are often encoded with some level of uncertainty. In the character-level uncertainty model, an uncertain string $X$ of length $n$ on an alphabet $\Sigma$ is a sequence of $n$ probability distributions over…
We describe a matrix multiplication recognition algorithm for a subset of binary linear context-free rewriting systems (LCFRS) with running time $O(n^{\omega d})$ where $M(m) = O(m^{\omega})$ is the running time for $m \times m$ matrix…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
Random access to highly compressed strings -- represented by straight-line programs or Lempel-Ziv parses, for example -- is a well-studied topic. Random access to such strings in strongly sublogarithmic time is impossible in the worst case,…
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…