Related papers: Linear-size CDAWG: new repetition-aware indexing a…
We present a new semi-external algorithm that builds the Burrows--Wheeler transform variant of Bauer et al. (a.k.a., BCR BWT) in linear expected time. Our method uses compression techniques to reduce computational costs when the input is…
We study the task of conducting structured reasoning as generating a reasoning graph from natural language input using large language models (LLMs). Previous approaches have explored various prompting schemes, yet they suffer from error…
We introduce the first index that can be built in $o(n)$ time for a text of length $n$, and can also be queried in $o(q)$ time for a pattern of length $q$. On an alphabet of size $\sigma$, our index uses $O(n\sqrt{\log n\log\sigma})$ bits,…
Compressed suffix arrays (CSAs) index large repetitive collections and are key in many text applications. The r-index and its derivatives combine the run-length Burrows-Wheeler Transform (BWT) with suffix array sampling to achieve space…
Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…
In this paper we are interested in indexing texts for substring matching queries with one edit error. That is, given a text $T$ of $n$ characters over an alphabet of size $\sigma$, we are asked to build a data structure that answers the…
An L-system (for lossless compression) is a CPD0L-system extended with two parameters $d$ and $n$, which determines unambiguously a string $w = \tau(\varphi^d(s))[1:n]$, where $\varphi$ is the morphism of the system, $s$ is its axiom, and…
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…
The $k$-mappability problem has two integers parameters $m$ and $k$. For every subword of size $m$ in a text $S$, we wish to report the number of indices in $S$ in which the word occurs with at most $k$ mismatches. The problem was lately…
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…
Two strings $x$ and $y$ over $\Sigma \cup \Pi$ of equal length are said to \emph{parameterized match} (\emph{p-match}) if there is a renaming bijection $f:\Sigma \cup \Pi \rightarrow \Sigma \cup \Pi$ that is identity on $\Sigma$ and…
This paper uses the Minimum Description Length paradigm to model the complexity of CxGs (operationalized as the encoding size of a grammar) alongside their descriptive adequacy (operationalized as the encoding size of a corpus given a…
We study the problem of supporting queries on a string $S$ of length $n$ within a space bounded by the size $\gamma$ of a string attractor for $S$. Recent works showed that random access on $S$ can be supported in optimal…
We develop a new approach for distributed distance computation in planar graphs that is based on a variant of the metric compression problem recently introduced by Abboud et al. [SODA'18]. One of our key technical contributions is in…
Unsupervised spoken term discovery (UTD) aims at finding recurring segments of speech from a corpus of acoustic speech data. One potential approach to this problem is to use dynamic time warping (DTW) to find well-aligning patterns from the…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
The graph with complex annotations is the most potent data type, whose constantly evolving motivates further exploration of the unsupervised dynamic graph representation. One of the representative paradigms is graph contrastive learning. It…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
We examine the complexity of the online Dictionary Matching with One Gap Problem (DMOG) which is the following. Preprocess a dictionary $D$ of $d$ patterns, where each pattern contains a special gap symbol that can match any string, so that…