Related papers: String Matching with Wildcards in the Massively Pa…
We study the fully dynamic pattern matching problem where the pattern may contain up to kwildcard symbols, each matching any symbol of the alphabet. Both the text and the pattern are subject to updates (insert, delete, change). We design an…
In this work, we consider the problem of pattern matching under the dynamic time warping (DTW) distance motivated by potential applications in the analysis of biological data produced by the third generation sequencing. To measure the DTW…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
We consider the problem of identifying tandem scattered subsequences within a string. Our algorithm identifies a longest subsequence which occurs twice without overlap in a string. This algorithm is based on the Hunt-Szymanski algorithm,…
Given a string $S$ over an alphabet $\Sigma$, the 'string indexing problem' is to preprocess $S$ to subsequently support efficient pattern matching queries, i.e., given a pattern string $P$ report all the occurrences of $P$ in $S$. In this…
We generalise a multiple string pattern matching algorithm, recently proposed by Fredriksson and Grabowski [J. Discr. Alg. 7, 2009], to deal with arbitrary dictionaries on an alphabet of size $s$. If $r_m$ is the number of words of length…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
We study fundamental graph problems such as graph connectivity, minimum spanning forest (MSF), and approximate maximum (weight) matching in a distributed setting. In particular, we focus on the Adaptive Massively Parallel Computation (AMPC)…
Widespread use of string solvers in formal analysis of string-heavy programs has led to a growing demand for more efficient and reliable techniques which can be applied in this context, especially for real-world cases. Designing an…
In this paper we describe a data structure that supports pattern matching queries on a dynamically arriving text over an alphabet ofconstant size. Each new symbol can be prepended to $T$ in O(1) worst-case time. At any moment, we can report…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
Biclustering algorithms play a central role in the biotechnological and biomedical domains. The knowledge extracted supports the extraction of putative regulatory modules, essential to understanding diseases, aiding therapy research, and…
Recently, studying fundamental graph problems in the \emph{Massively Parallel Computation (MPC) framework, inspired by the MapReduce paradigm, has gained a lot of attention. An assumption common to a vast majority of approaches is to allow…
There has been surprisingly little work on algorithms for sorting strings on distributed-memory parallel machines. We develop efficient algorithms for this problem based on the multi-way merging principle. These algorithms inspect only…