Related papers: Pairwise sequence alignment with block and charact…
In this paper, we present a novel heuristic algorithm for the stable but NP-complete deformation-based edit distance on merge trees. Our key contribution is the introduction of a user-controlled look-ahead parameter that allows to trade off…
We initiate the theoretical study of directory reconciliation, a generalization of document exchange, in which Alice and Bob each have different versions of a set of documents that they wish to synchronize. This problem is designed to…
BERT (Devlin et al., 2018) and RoBERTa (Liu et al., 2019) has set a new state-of-the-art performance on sentence-pair regression tasks like semantic textual similarity (STS). However, it requires that both sentences are fed into the…
The edit distance (ED) and longest common subsequence (LCS) are two fundamental problems which quantify how similar two strings are to one another. In this paper, we consider these problems in the asymmetric streaming model introduced by…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
Many modern data-intensive computational problems either require, or benefit from distance or similarity data that adhere to a metric. The algorithms run faster or have better performance guarantees. Unfortunately, in real applications, the…
Given a text and a pattern over an alphabet, the pattern matching problem searches for all occurrences of the pattern in the text. An equivalence relation $\approx$ is called a substring consistent equivalence relation (SCER), if for two…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
Text compression has diverse applications such as Summarization, Reading Comprehension and Text Editing. However, almost all existing approaches require either hand-crafted features, syntactic labels or parallel data. Even for one that…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
The Word Error Rate (WER) is the common measure of accuracy for Automatic Speech Recognition (ASR). Transcripts are usually pre-processed by substituting specific characters to account for non-semantic differences. As a result of this…
Computing the similarity between two DNA sequences is of vital importance in bioscience, yet it can be computationally expensive on classical hardware. For example, the edit distance with move operations (EDM), a DNA similarity measure of…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Storing digital data in synthetic DNA faces challenges in ensuring data reliability in the presence of edit errors--deletions, insertions, and substitutions--that occur randomly during various stages of the storage process. Current…
The graph traversal edit distance (GTED), introduced by Ebrahimpour Boroojeny et al.~(2018), is an elegant distance measure defined as the minimum edit distance between strings reconstructed from Eulerian trails in two edge-labeled graphs.…
In this paper, we design new sublinear-time algorithms for solving the gap edit distance problem and for embedding edit distance to Hamming distance. For the gap edit distance problem, we give an $\tilde{O}(\frac{n}{k}+k^2)$-time greedy…
The edit distance under the DCJ model can be computed in linear time for genomes with equal content or with Indels. But it becomes NP-Hard in the presence of duplications, a problem largely unsolved especially when Indels are considered. In…