Related papers: On Arithmetically Progressed Suffix Arrays and rel…
Let A be a finite alphabet and f: A^* --> A^* be a morphism with an iterative fixed point f^\omega(\alpha), where \alpha{} is in A. Consider the subshift (X, T), where X is the shift orbit closure of f^\omega(\alpha) and T: X --> X is the…
The suffix array is the key to efficient solutions for myriads of string processing problems in different applications domains, like data compression, data mining, or Bioinformatics. With the rapid growth of available data, suffix array…
The grammar representation of a narrowing tree for a syntactically deterministic conditional term rewriting system and a pair of terms is a regular tree grammar that generates expressions for substitutions obtained by all possible…
We prove that deciding whether a given input word contains as subsequence every possible permutation of integers $\{1,2,\ldots,n\}$ is coNP-complete. The coNP-completeness holds even when given the guarantee that the input word contains as…
In the present paper, we study the match test for extended regular expressions. We approach this NP-complete problem by introducing a novel variant of two-way multihead automata, which reveals that the complexity of the match test is…
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse…
Permutation tableaux are combinatorial objects related with permutations and various statistics on them. They appeared in connection with total positivity in Grassmannians, and stationary probabilities in a PASEP model. In particular they…
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…
We show that equivalence of deterministic top-down tree-to-string transducers is decidable, thus solving a long standing open problem in formal language theory. We also present efficient algorithms for subclasses: polynomial time for total…
We investigate the structural relationship between prefix-free codes over the binary alphabet and a class of unlabeled rooted trees, which we call \emph{symmetric} trees. We establish a canonical correspondence between prefix-free codes and…
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…
We introduce a novel model-theoretic framework inspired from graph modification and based on the interplay between model theory and algorithmic graph minors. The core of our framework is a new compound logic operating with two types of…
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string $w$ into another string $\mathsf{BWT}(w)$. The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
In this work, we completely characterize (i) permutation binomials of the form $x^{{{2^n -1}\over {2^t-1}}+1}+ ax \in \mathbb{F}_{2^n}[x], n = 2^st, a \in \mathbb{F}_{2^{2t}}^{*}$, and (ii) permutation trinomials of the form…
Given a countable set X (usually taken to be the natural numbers or the integers), an infinite permutation \pi of X is a linear ordering of X. This paper investigates the combinatorial complexity of the infinite permutation on the natural…
In this paper we study several variations of the \emph{pancake flipping problem}, which is also well known as the problem of \emph{sorting by prefix reversals}. We consider the variations in the sorting process by adding with prefix…
The parameterized matching problem is a variant of string matching, which is to search for all parameterized occurrences of a pattern $P$ in a text $T$. In considering matching algorithms, the combinatorial natures of strings, especially…
A permutation on an alphabet $ \Sigma $, is a sequence where every element in $ \Sigma $ occurs precisely once. Given a permutation $ \pi $= ($\pi_{1} $, $ \pi_{2} $, $ \pi_{3} $,....., $ \pi_{n} $) over the alphabet $ \Sigma $ =$\{ $0, 1,…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…