Related papers: Fast Exact String to D-Texts Alignments
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
An elastic-degenerate (ED) string $T$ is a sequence of $n$ sets $T[1],\ldots,T[n]$ containing $m$ strings in total whose cumulative length is $N$. We call $n$, $m$, and $N$ the length, the cardinality and the size of $T$, respectively. The…
Modern neural networks have greatly improved performance across speech recognition benchmarks. However, gains are often driven by frequent words with limited semantic weight, which can obscure meaningful differences in word error rate, the…
The construction of high-quality parallel corpora for translation research has increasingly evolved from simple sentence alignment to complex, multi-layered annotation tasks. This methodological shift presents significant challenges for…
Cell counting remains a fundamental yet challenging task in medical and biological research due to the diverse morphology of cells, their dense distribution, and variations in image quality. We present DLA-Count, a breakthrough approach to…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We address the problem of building an index for a set $D$ of $n$ strings, where each string location is a subset of some finite integer alphabet of size $\sigma$, so that we can answer efficiently if a given simple query string (where each…
The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
String consensus problems aim at finding a string that minimizes some given distance with respect to an input set of strings. In particular, in the Closest string problem, we are given a set of strings of equal length and a radius $d$. The…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
Domain adaptation aims to bridge the domain shifts between the source and the target domain. These shifts may span different dimensions such as fog, rainfall, etc. However, recent methods typically do not consider explicit prior knowledge…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
Exact String Matching is an essential issue in many computer science applications. Unfortunately, the performance of Exact String Matching algorithms, namely, executing time, does not address the needs of these applications. This paper…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. Sampled string…
As alignment links are not given between English sentences and Abstract Meaning Representation (AMR) graphs in the AMR annotation, automatic alignment becomes indispensable for training an AMR parser. Previous studies formalize it as a…
The goal of this paper is to optimize the training process of diffusion-based text-to-speech models. While recent studies have achieved remarkable advancements, their training demands substantial time and computational costs, largely due to…
The Longest Common Subsequence (LCS) is the problem of finding a subsequence among a set of strings that has two properties of being common to all and is the longest. The LCS has applications in computational biology and text editing, among…