Related papers: Locally consistent decomposition of strings with a…

In natural speech, the speaker does not pause between words, yet a human listener somehow perceives this continuous stream of phonemes as a series of distinct words. The detection of boundaries between spoken words is an instance of a…

We formulate a bounded distance decoding strategy applicable to all stabilizer codes including both CSS and non-CSS code-families. The framework emerges out of the local Clifford equivalence between arbitrary stabilizer states and graph…

There are efficient dynamic programming solutions to the computation of the Edit Distance from $S\in[1..\sigma]^n$ to $T\in[1..\sigma]^m$, for many natural subsets of edit operations, typically in time within $O(nm)$ in the worst-case over…

Let $X$ be a set of $n$ points of norm at most $1$ in the Euclidean space $R^k$, and suppose $\varepsilon>0$. An $\varepsilon$-distance sketch for $X$ is a data structure that, given any two points of $X$ enables one to recover the square…

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…

We show that the edit distance between two run-length encoded strings of compressed lengths $m$ and $n$ respectively, can be computed in $\mathcal{O}(mn\log(mn))$ time. This improves the previous record by a factor of…

When a node in a distributed storage system fails, it needs to be promptly repaired to maintain system integrity. While typical erasure codes can provide a significant storage advantage over replication, they suffer from poor repair…

In this paper, we present an efficiently encodable and decodable code construction that is capable of correction a burst of deletions of length at most $k$. The redundancy of this code is $\log n + k(k+1)/2\log \log n+c_k$ for some constant…

Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…

We adapt a well known streaming algorithm for approximating item frequencies to the matrix sketching setting. The algorithm receives the rows of a large matrix $A \in \R^{n \times m}$ one after the other in a streaming fashion. It maintains…

We study codes that are list-decodable under insertions and deletions. Specifically, we consider the setting where a codeword over some finite alphabet of size $q$ may suffer from $\delta$ fraction of adversarial deletions and $\gamma$…

Edit distance, also known as Levenshtein distance, is an essential way to compare two strings that proved to be particularly useful in the analysis of genetic sequences and natural language processing. However, edit distance is a discrete…

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…

We show how to compute the edit distance between two strings of length n up to a factor of 2^{\~O(sqrt(log n))} in n^(1+o(1)) time. This is the first sub-polynomial approximation algorithm for this problem that runs in near-linear time,…

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…

We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a…

Locally repairable convolutional codes (LRCCs) for distributed storage systems (DSSs) are introduced in this work. They enable local repair, for a single node erasure (or more generally, $ \partial - 1 $ erasures per local group), and…

In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string…

We study the problem of edit similarity joins, where given a set of strings and a threshold value $K$, we want to output all pairs of strings whose edit distances are at most $K$. Edit similarity join is a fundamental problem in data…

Classic similarity measures of strings are longest common subsequence and Levenshtein distance (i.e., the classic edit distance). A classic similarity measure of curves is dynamic time warping. These measures can be computed by simple…