Related papers: Efficient pattern matching in degenerate strings w…
We consider relativistic and non-relativistic particles and strings in spaces (or space-times) with a degenerate metric. We show that the resulting dynamics is described by a rich structure of constraints. All constraints are classified and…
The classic string indexing problem is to preprocess a string S into a compact data structure that supports efficient pattern matching queries. Typical queries include existential queries (decide if the pattern occurs in S), reporting…
In filtering, each output is produced by a certain number of different inputs. We explore the statistics of this degeneracy in an explicitly treatable filtering problem in which filtering performs the maximal compression of relevant…
The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…
Let $S_{T}(k)$ denote the set of distinct substrings of length $k$ in a string $T$, then the $k$-th substring complexity is defined by its cardinality $|S_{T}(k)|$. Recently, $\delta = \max \{ |S_{T}(k)| / k : k \ge 1 \}$ is shown to be a…
We extend the theory of minimal absent words to (rooted and unrooted) trees, having edges labeled by letters from an alphabet $\Sigma$ of cardinality $\sigma$. We show that the set $\text{MAW}(T)$ of minimal absent words of a rooted (resp.…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…
In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…
We consider the problem of indexing a string $t$ of length $n$ to report the occurrences of a query pattern $p$ containing $m$ characters and $j$ wildcards. Let $occ$ be the number of occurrences of $p$ in $t$, and $\sigma$ the size of the…
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…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
String matching is a fundamental problem in computer science, with critical applications in text retrieval, bioinformatics, and data analysis. Among the numerous solutions that have emerged for this problem in recent decades,…
In grammar-based compression a string is represented by a context-free grammar, also called a straight-line program (SLP), that generates only that string. We refine a recent balancing result stating that one can transform an SLP of size…
We introduce a novel chart-based algorithm for span-based parsing of discontinuous constituency trees of block degree two, including ill-nested structures. In particular, we show that we can build variants of our parser with smaller search…
Counting homomorphisms of a constant sized pattern graph $H$ in an input graph $G$ is a fundamental computational problem. There is a rich history of studying the complexity of this problem, under various constraints on the input $G$ and…
Sparse linear regression is a central problem in high-dimensional statistics. We study the correlated random design setting, where the covariates are drawn from a multivariate Gaussian $N(0,\Sigma)$, and we seek an estimator with small…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…
In this paper, we consider the problem of identifying patterns of interest in colored strings. A colored string is a string where each position is assigned one of a finite set of colors. Our task is to find substrings of the colored string…