Related papers: The complexity of string partitioning
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
In this paper we consider two problems concerning string factorisation. Specifically given a string $w$ and an integer $k$ find a factorisation of $w$ where each factor has length bounded by $k$ and has the minimum (the FmD problem) or the…
Word Break is a prototypical factorization problem in string processing: Given a word $w$ of length $N$ and a dictionary $\mathcal{D} = \{d_1, d_2, \ldots, d_{K}\}$ of $K$ strings, determine whether we can partition $w$ into words from…
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…
Let $W$ be a string of length $n$ over an alphabet $\Sigma$, $k$ be a positive integer, and $\mathcal{S}$ be a set of length-$k$ substrings of $W$. The ETFS problem asks us to construct a string $X_{\mathrm{ED}}$ such that: (i) no string of…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…
We consider the problem of computing a shortest solid cover of an indeterminate string. An indeterminate string may contain non-solid symbols, each of which specifies a subset of the alphabet that could be present at the corresponding…
We show that Closest Substring, one of the most important problems in the field of biological sequence analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This problem is…
Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…
Given a set of integers W, the Partition problem determines whether W can be divided into two disjoint subsets with equal sums. We model the Partition problem as a system of polynomial equations, and then investigate the complexity of a…
In this paper we show that the following problem is NP-complete: Given an alphabet $\Sigma$ and two strings over $\Sigma$, the question is whether there exists a permutation of $\Sigma$ which is a subsequence of both of the given strings.
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
String matching is the problem of deciding whether a given $n$-bit string contains a given $k$-bit pattern. We study the complexity of this problem in three settings. Communication complexity. For small $k$, we provide near-optimal upper…
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…
The NP-hard Minimum Common String Partition problem asks whether two strings $x$ and $y$ can each be partitioned into at most $k$ substrings, called blocks, such that both partitions use exactly the same blocks in a different order. We…
Motivated by the study of genome rearrangements, the NP-hard Minimum Common String Partition problems asks, given two strings, to split both strings into an identical set of blocks. We consider an extension of this problem to unbalanced…
The Satisfactory Partition problem consists in deciding if the set of vertices of a given undirected graph can be partitioned into two nonempty parts such that each vertex has at least as many neighbours in its part as in the other part.…
String matching is one of the most fundamental problems in computer science. A natural problem is to determine the number of characters that need to be queried (i.e. the decision tree complexity) in a string in order to decide whether this…