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The edit distance is a metric of dissimilarity between strings, widely applied in computational biology, speech recognition, and machine learning. Let $e_k(n)$ denote the average edit distance between random, independent strings of $n$…
Much research in stringology focuses on structures that can, in a way, ``grasp'' repeats (substrings that occur multiple times) as, for example, the so-called runs, a.k.a. maximal repetitions, compactly describe all tandem repeats. In this…
The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…
We study edit distance computation with preprocessing: the preprocessing algorithm acts on each string separately, and then the query algorithm takes as input the two preprocessed strings. This model is inspired by scenarios where we would…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
We propose the neural string edit distance model for string-pair matching and string transduction based on learnable string edit distance. We modify the original expectation-maximization learned edit distance algorithm into a differentiable…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
Error-correcting codes resilient to synchronization errors such as insertions and deletions are known as insdel codes. Due to their important applications in DNA storage and computational biology, insdel codes have recently become a focal…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
Nanopore sequencing, superior to other sequencing technologies for DNA storage in multiple aspects, has recently attracted considerable attention. Its high error rates, however, demand thorough research on practical and efficient coding…
Sidon sequences and their generalizations have found during the years and especially recently various applications in coding theory. One of the most important applications of these sequences is in the connection of synchronization patterns.…
The repetition threshold is the smallest real number $\alpha$ such that there exists an infinite word over a $k$-letter alphabet that avoids repetition of exponent strictly greater than $\alpha$. This notion can be generalized to graph…
In this paper, for any fixed positive integers $t$ and $q>2$, we construct $q$-ary codes correcting a burst of at most $t$ deletions with redundancy $\log n+8\log\log n+o(\log\log n)+\gamma_{q,t}$ bits and near-linear encoding/decoding…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
We present an efficient algorithm for finding all approximate occurrences of a given pattern $p$ of length $m$ in a text $t$ of length $n$ allowing for translocations of equal length adjacent factors and inversions of factors. The algorithm…
We introduce a new permutation statistic, namely, the number of cycles of length $q$ consisting of consecutive integers, and consider the distribution of this statistic among the permutations of $\{1,2,...,n\}$. We determine explicit…
Maximal repetition of a string is the maximal length of a repeated substring. This paper investigates maximal repetition of strings drawn from stochastic processes. Strengthening previous results, two new bounds for the almost sure growth…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…