Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
Given a string $w$ over a finite alphabet $\Sigma$ and an integer $K$, can $w$ be partitioned into strings of length at most $K$, such that there are no \emph{collisions}? We refer to this question as the \emph{string partition} problem and…
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
The stabilization of a quantum computer by repeated error correction can be reduced almost entirely to repeated preparation of blocks of qubits in quantum codeword states. These are multi-particle entangled states with a high degree of…
We study the problems of covering or partitioning a polygon $P$ (possibly with holes) using a minimum number of small pieces, where a small piece is a connected sub-polygon contained in an axis-aligned unit square. For covering, we seek to…
Minimizers sampling is one of the most widely-used mechanisms for sampling strings [Roberts et al., Bioinformatics 2004]. Let $S=S[1]\ldots S[n]$ be a string over a totally ordered alphabet $\Sigma$. Further let $w\geq 2$ and $k\geq 1$ be…
The problem is considered of arranging symbols around a cycle, in such a way that distances between different instances of a same symbol be as uniformly distributed as possible. A sequence of moments is defined for cycles, similarly to the…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
We consider the problems of finding a maximum clique in a graph and finding a maximum-edge biclique in a bipartite graph. Both problems are NP-hard. We write both problems as matrix-rank minimization and then relax them using the nuclear…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
We study fundamental clustering problems for incomplete data. Specifically, given a set of incomplete d-dimensional vectors (representing rows of a matrix), the goal is to complete the missing vector entries in a way that admits a…
We study the problem of edge partitioning, where the goal is to partition the edge set of a graph into several parts. The replication factor of a vertex $v$ is the number of parts that contain edges incident to $v$. The goal is to minimize…
We obtain exact expressions for the asymptotic behaviour of the average probability of the block decoding error for ensembles of regular low density parity check error correcting codes, by employing diagrammatic techniques. Furthermore, we…
In energy-time entanglement Quantum Key Distribution (QKD), two users extract a shared secret key from the arrival times (discretized as symbols) of entangled photon pairs. In prior work, Zhou et al. proposed a multi-level coding (MLC)…
We study regular expression membership testing: Given a regular expression of size $m$ and a string of size $n$, decide whether the string is in the language described by the regular expression. Its classic $O(nm)$ algorithm is one of the…
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…
We consider the Minimum Coverage Kernel problem: given a set $B$ of $d$-dimensional boxes, find a subset of $B$ of minimum size covering the same region as $B$. This problem is $\mathsf{NP}$-hard, but as for many $\mathsf{NP}$-hard problems…
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…