Related papers: String Representation in Suffixient Set Size Space
Covers are a kind of quasiperiodicity in strings. A string $C$ is a cover of another string $T$ if any position of $T$ is inside some occurrence of $C$ in $T$. The shortest and longest cover arrays of $T$ have the lengths of the shortest…
Given a string $S$ over an alphabet $\Sigma$, the 'string indexing problem' is to preprocess $S$ to subsequently support efficient pattern matching queries, i.e., given a pattern string $P$ report all the occurrences of $P$ in $S$. In this…
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,…
In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the…
Given a finite word $w$ over a finite alphabet $V$, consider the graph with vertex set $V$ and with an edge between two elements of $V$ if and only if the two elements alternate in the word $w$. Such a graph is said to be word-representable…
A {\it superpattern} is a string of characters of length $n$ that contains as a subsequence, and in a sense that depends on the context, all the smaller strings of length $k$ in a certain class. We prove structural and probabilistic results…
A string attractor of a string $T[1..|T|]$ is a set of positions $\Gamma$ of $T$ such that any substring $w$ of $T$ has an occurrence that crosses a position in $\Gamma$, i.e., there is a position $i$ such that $w = T[i..i+|w|-1]$ and the…
A string is closed if it has length 1 or has a nonempty border without internal occurrences. In this paper we introduce the definition of a \emph{maximal closed substring} (MCS), which is an occurrence of a closed substring that cannot be…
Minimizers are sampling schemes with numerous applications in computational biology. Assuming a fixed alphabet of size $\sigma$, a minimizer is defined by two integers $k,w\ge2$ and a linear order $\rho$ on strings of length $k$ (also…
We show that if DTIME[2^{O(n)}] is not included in DSPACE[2^{o(n)}], then, for every set B in PSPACE, all strings x in B of length n can be represented by a string compressed(x) of length at most log (|B^{=n}|) + O(log n), such that a…
We study the maximum size of a set system on $n$ elements whose trace on any $b$ elements has size at most $k$. We show that if for some $b \ge i \ge 0$ the shatter function $f_R$ of a set system $([n],R)$ satisfies $f_R(b) < 2^i(b-i+1)$…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Suppose we are asked to preprocess a string \(s [1..n]\) such that later, given a substring's endpoints, we can quickly count how many distinct characters it contains. In this paper we give a data structure for this problem that takes \(n…
Sequence representations supporting not only direct access to their symbols, but also rank/select operations, are a fundamental building block in many compressed data structures. Several recent applications need to represent highly…
We present a compressed representation of tries based on top tree compression [ICALP 2013] that works on a standard, comparison-based, pointer machine model of computation and supports efficient prefix search queries. Namely, we show how to…
The problem of guessing a random string is revisited. A close relation between guessing and compression is first established. Then it is shown that if the sequence of distributions of the information spectrum satisfies the large deviation…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
Given a regular language L over an ordered alphabet $\Sigma$, the set of lexicographically smallest (resp., largest) words of each length is itself regular. Moreover, there exists an unambiguous finite-state transducer that, on a given word…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…