Related papers: Towards a Definitive Compressibility Measure for R…
We present a new on-line algorithm for computing the Lempel-Ziv factorization of a string that runs in $O(N\log N)$ time and uses only $O(N\log\sigma)$ bits of working space, where $N$ is the length of the string and $\sigma$ is the size of…
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 consider document listing on string collections, that is, finding in which strings a given pattern appears. In particular, we focus on repetitive collections: a collection of size $N$ over alphabet $[1,\sigma]$ is composed of $D$ copies…
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm…
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…
We present the first efficient averaging sampler that achieves asymptotically optimal randomness complexity and near-optimal sample complexity. For any $\delta < \varepsilon$ and any constant $\alpha > 0$, our sampler uses $m + O(\log (1 /…
Shannon Entropy has been extensively used for characterizing complexity of time series arising from chaotic dynamical systems and stochastic processes such as Markov chains. However, for short and noisy time series, Shannon entropy performs…
There is no single universally accepted definition of "Complexity". There are several perspectives on complexity and what constitutes complex behaviour or complex systems, as opposed to regular, predictable behaviour and simple systems. In…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of…
We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries:…
In this paper, we propose a novel approach to combine \emph{compact directed acyclic word graphs} (CDAWGs) and grammar-based compression. This leads us to an efficient self-index, called Linear-size CDAWGs (L-CDAWGs), which can be…
The compact directed acyclic word graph (CDAWG) of a string $T$ is an index occupying $O(\mathsf{e})$ space, where $\mathsf{e}$ is the number of right extensions of maximal repeats in $T$. For highly repetitive datasets, the measure…
The $r$-index (Gagie et al., JACM 2020) represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude. Its space usage, $\mathcal{O}(r)$ where $r$ is the number of…
A new framework is introduced for examining and evaluating the fundamental limits of lossless data compression, that emphasizes genuinely non-asymptotic results. The {\em sample complexity} of compressing a given source is defined as the…
We show that for any natural number $s$, there is a constant $\gamma$ and a subgraph-closed class having, for any natural $n$, at most $\gamma^n$ graphs on $n$ vertices up to isomorphism, but no adjacency labeling scheme with labels of size…
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…
We investigate the longest common substring problem for encoded sequences and its asymptotic behaviour. The main result is a strong law of large numbers for a re-scaled version of this quantity, which presents an explicit relation with the…
The LZ-End parsing [Kreft & Navarro, 2011] of an input string yields compression competitive with the popular Lempel-Ziv 77 scheme, but also allows for efficient random access. Kempa and Kosolobov showed that the parsing can be computed in…
We present a new data structure called the \emph{Compressed Random Access Memory} (CRAM) that can store a dynamic string $T$ of characters, e.g., representing the memory of a computer, in compressed form while achieving asymptotically…