Related papers: Substring Complexity in Sublinear Space

We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…

Specifying a computational problem requires fixing encodings for input and output: encoding graphs as adjacency matrices, characters as integers, integers as bit strings, and vice versa. For such discrete data, the actual encoding is…

We show that the compressed suffix array and the compressed suffix tree of a string $T$ can be built in $O(n)$ deterministic time using $O(n\log\sigma)$ bits of space, where $n$ is the string length and $\sigma$ is the alphabet size.…

We consider a linear stochastic bandit problem where the dimension $K$ of the unknown parameter $\theta$ is larger than the sampling budget $n$. In such cases, it is in general impossible to derive sub-linear regret bounds since usual…

In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…

In the decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), the task is to list the $k$-error occurrences of $P$ in…

Real-world data typically contain repeated and periodic patterns. This suggests that they can be effectively represented and compressed using only a few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.). However, distance…

We study the classic set cover problem from the perspective of sub-linear algorithms. Given access to a collection of $m$ sets over $n$ elements in the query model, we show that sub-linear algorithms derived from existing techniques have…

The longest common substring problem consists in finding a longest string that appears as a (contiguous) substring of two input strings. We consider the dynamic variant of this problem, in which we are to maintain two dynamic strings $S$…

This paper introduces an objective metric for evaluating a parsing scheme. It is based on Shannon's original work with letter sequences, which can be extended to part-of-speech tag sequences. It is shown that this regular language is an…

Given a string $S$ of length $N$ on a fixed alphabet of $\sigma$ symbols, a grammar compressor produces a context-free grammar $G$ of size $n$ that generates $S$ and only $S$. In this paper we describe data structures to support the…

Entropy quantifies the number of bits required to store objects under certain given assumptions. While this is a well established concept for strings, in the context of tries the state-of-the-art regarding entropies is less developed. The…

We discuss further our proposed modification of the Susskind-Horowitz-Polchinski scenario in which black hole entropy goes over to string entropy as one scales the string length scale up and the string coupling constant down, keeping…

Following (Kolpakov et al., 2013; Gawrychowski and Manea, 2015), we continue the study of {\em $\alpha$-gapped repeats} in strings, defined as factors $uvu$ with $|uv|\leq \alpha |u|$. Our main result is the $O(\alpha n)$ bound on the…

The basic problem of semantic compression is to minimize the length of a message while preserving its meaning. This differs from classical notions of compression in that the distortion is not measured directly at the level of bits, but…

Estimating the second frequency moment $F_2$ of a data stream up to a $(1 \pm \varepsilon)$ factor is a central problem in the streaming literature. For errors $\varepsilon > \Omega(1/\sqrt{n})$, the tight bound…

Tensor network contractions are widely used in statistical physics, quantum computing, and computer science. We introduce a method to efficiently approximate tensor network contractions using low-rank approximations, where each intermediate…

We study the problem of deriving compressibility measures for Piecewise Linear Approximations (PLAs), i.e., error-bounded approximations of a set of two-dimensional increasing data points using a sequence of segments. Such approximations…

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…

Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…