Related papers: Single and multiple consecutive permutation motif …
The probability of finding a prime multiplet, i.e., a sequence of primes $p$ and $p+a_i$, $i=1... m$, being all primes where $p$ is some prime less than the integer $n$ is naively $1/log(n)^{m+1}$. It is shown that, in reality, it is…
We consider the problem of computing the Maximal Exact Matches (MEMs) of a given pattern $P[1 .. m]$ on a large repetitive text collection $T[1 .. n]$, which is represented as a (hopefully much smaller) run-length context-free grammar of…
The dictionary matching is a task to find all occurrences of patterns in a set $D$ (called a dictionary) on a text $T$. The Aho-Corasick-automaton (AC-automaton) is a data structure which enables us to solve the dictionary matching problem…
We survey permutation-based methods for approximate k-nearest neighbor search. In these methods, every data point is represented by a ranked list of pivots sorted by the distance to this point. Such ranked lists are called permutations. The…
The palindrome pattern matching (pal-matching) is a kind of generalized pattern matching, in which two strings $x$ and $y$ of same length are considered to match (pal-match) if they have the same palindromic structures, i.e., for any…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
We study the space requirements of a sorting algorithm where only items that at the end will be adjacent are kept together. This is equivalent to the following combinatorial problem: Consider a string of fixed length n that starts as a…
We address the problem of building an index for a set $D$ of $n$ strings, where each string location is a subset of some finite integer alphabet of size $\sigma$, so that we can answer efficiently if a given simple query string (where each…
Since Grover's seminal work, quantum search has been studied in great detail. In the usual search problem, we have a collection of n items and we would like to find a marked item. We consider a new variant of this problem in which…
Recent works put much effort into tensor network structure search (TN-SS), aiming to select suitable tensor network (TN) structures, involving the TN-ranks, formats, and so on, for the decomposition or learning tasks. In this paper, we…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
The aim of sequential pattern mining (SPM) is to discover potentially useful information from a given se-quence. Although various SPM methods have been investigated, most of these focus on mining all of the patterns. However, users…
Dokos et. al. studied the distribution of two statistics over permutations $\mathfrak{S}_n$ of $\{1,2,\dots, n\}$ that avoid one or more length three patterns. A permutation $\sigma\in\mathfrak{S}_n$ contains a pattern…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
We study $p$-Faulty Search, a variant of the classic cow-path optimization problem, where a unit speed robot searches the half-line (or $1$-ray) for a hidden item. The searcher is probabilistically faulty, and detection of the item with…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
It is widely assumed that $O(m+\lg \sigma)$ is the best one can do for finding a pattern of length $m$ in a compacted trie storing strings over an alphabet of size $\sigma$, if one insists on linear-size data structures and deterministic…
The dictionary matching with gaps problem is to preprocess a dictionary $D$ of $d$ gapped patterns $P_1,\ldots,P_d$ over alphabet $\Sigma$, where each gapped pattern $P_i$ is a sequence of subpatterns separated by bounded sequences of don't…
Sorting is a fundamental problem in computer science. In the classical setting, it is well-known that $(1\pm o(1)) n\log_2 n$ comparisons are both necessary and sufficient to sort a list of $n$ elements. In this paper, we study the Noisy…
Two recent lower bounds on the compressibility of repetitive sequences, $\delta \le \gamma$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $\sigma$ can be represented within the…