Related papers: Small Space Encoding and Recognition of $k$-Palind…

We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…

In this paper we consider several variants of the pattern matching problem. In particular, we investigate the following problems: 1) Pattern matching with k mismatches; 2) Approximate counting of mismatches; and 3) Pattern matching with…

We study the problem of finding all $k$-periods of a length-$n$ string $S$, presented as a data stream. $S$ is said to have $k$-period $p$ if its prefix of length $n-p$ differs from its suffix of length $n-p$ in at most $k$ locations. We…

We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…

Let $n$ and $k$ be positive integers, and let $F$ be an alphabet of size $n$. A sequence over $F$ of length $m$ is a \emph{$k$-radius sequence} if any two distinct elements of $F$ occur within distance $k$ of each other somewhere in the…

We study the classification performance of Kronecker-structured models in two asymptotic regimes and developed an algorithm for separable, fast and compact K-S dictionary learning for better classification and representation of…

This paper addresses the problem of identifying palindromic factors in texts that include wildcards -- special characters that match all others. These symbols challenge many classical algorithms, as numerous combinatorial properties are not…

An unweighted, undirected graph $G$ on $n$ nodes is said to have \emph{bandwidth} at most $k$ if its nodes can be labelled from $0$ to $n - 1$ such that no two adjacent nodes have labels that differ by more than $k$. It is known that one…

The k-spectrum of a string is the set of all distinct substrings of length k occurring in the string. K-spectra have many applications in bioinformatics including pseudoalignment and genome assembly. The Spectral Burrows-Wheeler Transform…

The palindromic tree (a.k.a. eertree) is a data structure that provides access to all palindromic substrings of a string. In this paper, we propose a dynamic version of eertree, called double-ended eertree, which supports online operations…

Given a nonempty finite word $v$, let $PL(v)$ be the palindromic length of $v$; it means the minimal number of palindromes whose concatenation is equal to $v$. Let $v^R$ denote the reversal of $v$. Given a finite or infinite word $y$, let…

We consider the problem of counting the copies of a length-$k$ pattern $\sigma$ in a sequence $f \colon [n] \to \mathbb{R}$, where a copy is a subset of indices $i_1 < \ldots < i_k \in [n]$ such that $f(i_j) < f(i_\ell)$ if and only if…

Pattern matching is a fundamental process in almost every scientific domain. The problem involves finding the positions of a given pattern (usually of short length) in a reference stream of data (usually of large length). The matching can…

We present space efficient Monte Carlo algorithms that solve Subset Sum and Knapsack instances with $n$ items using $O^*(2^{0.86n})$ time and polynomial space, where the $O^*(\cdot)$ notation suppresses factors polynomial in the input size.…

The Fibonacci word $W$ on an infinite alphabet was introduced in [Zhang et al., Electronic J. Combinatorics 2017 24(2), 2-52] as a fixed point of the morphism $2i\rightarrow (2i)(2i+1)$, $(2i+1) \rightarrow (2i+2)$, $i\geq 0$. Here, for any…

We study the problem of finding small trees. Classical network design problems are considered with the additional constraint that only a specified number $k$ of nodes are required to be connected in the solution. A prototypical example is…

We study algorithms for solving three problems on strings. The first one is the Most Frequently String Search Problem. The problem is the following. Assume that we have a sequence of $n$ strings of length $k$. The problem is finding the…

An integer $n\geq 1$ is a $v$-palindrome if it is not a multiple of $10$, nor a decimal palindrome, and such that the sum of the prime factors and corresponding exponents larger than $1$ in the prime factorization of $n$ is equal to that of…

In this thesis, we consider the problem of characterizing and enumerating sets of polyominoes described in terms of some constraints, defined either by convexity or by pattern containment. We are interested in a well known subclass of…

We present a novel bit-parallel representation, based on the run-length encoding, of the nondeterministic KMP and suffix automata for a string $P$ with at least two distinct symbols. Our method is targeted to the case of long strings over…