Related papers: Fast Exact String to D-Texts Alignments
In this paper we propose a novel approach to identify anomalies in DNS traffic. The traffic time-points data is transformed to a string, which is used by new fast appproximate string matching algorithm to detect anomalies. Our approach is…
Unsupervised domain adaptation (UDA) for semantic segmentation aims to adapt a segmentation model trained on the labeled source domain to the unlabeled target domain. Existing methods try to learn domain invariant features while suffering…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…
Speech tokenizers are a key building block of fully discrete Speech LLMs.Existing tokenizers either prioritize semantic encoding,fuse semantic content with acoustic style inseparably,or achieve incomplete semantic-acoustic…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
A weighted string over an alphabet of size $\sigma$ is a string in which a set of letters may occur at each position with respective occurrence probabilities. Weighted strings, also known as position weight matrices or uncertain sequences,…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
Semantic Textual Similarity (STS) is a crucial component of many Natural Language Processing (NLP) applications. However, existing approaches typically reduce semantic nuances to a single score, limiting interpretability. To address this,…
In computer vision, traditional ensemble learning methods exhibit either a low training efficiency or the limited performance to enhance the reliability of deep neural networks. In this paper, we propose a lightweight, loss-function-free,…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
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…
The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…
This paper presents a novel evaluation approach to text-based speaker diarization (SD), tackling the limitations of traditional metrics that do not account for any contextual information in text. Two new metrics are proposed, Text-based…
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 many applications, it is necessary to determine the string similarity. Edit distance[WF74] approach is a classic method to determine Field Similarity. A well known dynamic programming algorithm [GUS97] is used to calculate edit distance…
We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment introduced in the RNA-Seq context is suitable in the…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…