Related papers: Hardness Results on Characteristics for Elastic-De…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
An elastic-degenerate (ED) string $T$ is a sequence of $n$ sets $T[1],\ldots,T[n]$ containing $m$ strings in total whose cumulative length is $N$. We call $n$, $m$, and $N$ the length, the cardinality and the size of $T$, respectively. The…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
A 'degenerate string' is a sequence of subsets of some alphabet; it represents any string obtainable by selecting one character from each set from left to right. Recently, Alanko et al. generalized the rank-select problem to degenerate…
Consensus problems for strings and sequences appear in numerous application contexts, ranging from bioinformatics over data mining to machine learning. Closing some gaps in the literature, we show that several fundamental problems in this…
We revisit the complexity of approximate pattern matching in an elastic-degenerate string. Such a string is a sequence of $n$ finite sets of strings of total length $N$, and compactly describes a collection of strings obtained by first…
In this paper we propose a new, more appropriate definition of regular and indeterminate strings. A regular string is one that is "isomorphic" to a string whose entries all consist of a single letter, but which nevertheless may itself…
Given a set of strings, the shortest common superstring problem is to find the shortest possible string that contains all the input strings. The problem is NP-hard, but a lot of work has gone into designing approximation algorithms for…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
Cadences are structurally maximal arithmetic progressions of indices corresponding to equal characters in an underlying string. This paper provides a polynomial time detection algorithm for 3-cadences in grammar-compressed binary strings.…
We relate the computational complexity of finite strings to universal representations of their underlying symmetries. First, Boolean functions are classified using the universal covering topologies of the circuits which enumerate them. A…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…
Generalization problems in languages with binders involve computing the most common structure between expressions while respecting bound variable renaming and freshness constraints. These problems often lack a least general solution.…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
Query evaluation over probabilistic databases is known to be intractable in many cases, even in data complexity, i.e., when the query is fixed. Although some restrictions of the queries [19] and instances [4] have been proposed to lower the…
Recently, deep neural networks (DNNs) have achieved great success in semantically challenging NLP tasks, yet it remains unclear whether DNN models can capture compositional meanings, those aspects of meaning that have been long studied in…
Deep Neural Networks (DNNs) generalize well despite their massive size and capability of memorizing all examples. There is a hypothesis that DNNs start learning from simple patterns and the hypothesis is based on the existence of examples…