Related papers: Pairwise sequence alignment with block and charact…
Automated Program Repair (APR) helps improve the efficiency of software development and maintenance. Recent APR techniques use deep learning, particularly the encoder-decoder architecture, to generate patches. Though existing DL-based APR…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Suppose that we have two parties that possess each a binary string. Suppose that the length of the first string (document) is $n$ and that the two strings (documents) have edit distance (minimal number of deletes, inserts and substitutions…
Text similarity calculation is a fundamental problem in natural language processing and related fields. In recent years, deep neural networks have been developed to perform the task and high performances have been achieved. The neural…
A matching cut is a partition of the vertex set of a graph into two sets $A$ and $B$ such that each vertex has at most one neighbor in the other side of the cut. The MATCHING CUT problem asks whether a graph has a matching cut, and has been…
We consider the classical tree edit distance between ordered labeled trees, which is defined as the minimum-cost sequence of node edit operations that transform one tree into another. The state-of-the-art solutions for the tree edit…
We study the problem of approximating edit distance in sublinear time. This is formalized as the $(k,k^c)$-Gap Edit Distance problem, where the input is a pair of strings $X,Y$ and parameters $k,c>1$, and the goal is to return YES if…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
Transformer-based pre-trained language models such as BERT have achieved remarkable results in Semantic Sentence Matching. However, existing models still suffer from insufficient ability to capture subtle differences. Minor noise like word…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…
Document exchange and error correcting codes are two fundamental problems regarding communications. In the first problem, Alice and Bob each holds a string, and the goal is for Alice to send a short sketch to Bob, so that Bob can recover…
The unordered tree edit distance is a natural metric to compute distances between trees without intrinsic child order, such as representations of chemical molecules. While the unordered tree edit distance is MAX SNP-hard in principle, it is…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model,…
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine,…
Kondo et al. (DS 2014) proposed methods for computing distances between unordered rooted trees by transforming an instance of the distance computing problem into an instance of the integer programming problem. They showed that the tree edit…
Randomized smoothing is a leading approach for constructing classifiers that are certifiably robust against adversarial examples. Existing work on randomized smoothing has focused on classifiers with continuous inputs, such as images, where…
In the field of automated program repair, the redundancy assumption claims large programs contain the seeds of their own repair. However, most redundancy-based program repair techniques do not reason about the repair ingredients---the code…