Related papers: A New Algebraic Approach for String Reconstruction…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…
Given a string $T$ of length $N$, the goal of grammar compression is to construct a small context-free grammar generating only $T$. Among existing grammar compression methods, RePair (recursive paring) [Larsson and Moffat, 1999] is notable…
We revisit two well-known algorithmic problems on strings: computing a shortest unique substring (SUS) and a shortest absent substring (SAS) of a string $S$ of length $n$. Both problems admit folklore $\mathcal{O}(n)$-time solutions using…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
Algorithmic statistics considers the following problem: given a binary string $x$ (e.g., some experimental data), find a "good" explanation of this data. It uses algorithmic information theory to define formally what is a good explanation.…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
In this paper we address the constrained longest common subsequence problem. Given two sequences $X$, $Y$ and a constrained sequence $P$, a sequence $Z$ is a constrained longest common subsequence for $X$ and $Y$ with respect to $P$ if $Z$…
We investigate the fine-grained and the parameterized complexity of several generalizations of binary constraint satisfaction problems (BINARY-CSPs), that subsume variants of graph colouring problems. Our starting point is the observation…
In this paper, we propose a novel binary-based cost computation and aggregation approach for stereo matching problem. The cost volume is constructed through bitwise operations on a series of binary strings. Then this approach is combined…
In this paper, we consider the satisfiability problem for string logic with equations, regular membership and Presburger constraints over length functions. The difficulty comes from multiple occurrences of string variables making…
The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$…
String constraint solving refers to solving combinatorial problems involving constraints over string variables. String solving approaches have become popular over the last years given the massive use of strings in different application…
The most disappointing aspect of $\W$-strings is probably the fact that at least for the known models one does not recover a physical spectrum that differs much from that of ordinary string theory. It is hoped that this is not an intrinsic…
Two decades ago, a breakthrough in indexing string collections made it possible to represent them within their compressed space while at the same time offering indexed search functionalities. As this new technology permeated through…
It is shown that from two strings that are partially random and independent (in the sense of Kolmogorov complexity) it is possible to effectively construct polynomially many strings that are random and pairwise independent. If the two…
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…
We provide a randomized linear time approximation scheme for a generic problem about clustering of binary vectors subject to additional constrains. The new constrained clustering problem encompasses a number of problems and by solving it,…
The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…