Related papers: Fast Exact String to D-Texts Alignments
Accurate alignment of dysfluent speech with intended text is crucial for automating the diagnosis of neurodegenerative speech disorders. Traditional methods often fail to model phoneme similarities effectively, limiting their performance.…
Motivation: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over ten years ago and did not incorporate the latest advances in…
We study the problem of recognition of fingerspelled letter sequences in American Sign Language in a signer-independent setting. Fingerspelled sequences are both challenging and important to recognize, as they are used for many content…
Detection transformers have recently shown promising object detection results and attracted increasing attention. However, how to develop effective domain adaptation techniques to improve its cross-domain performance remains unexplored and…
Drug-target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common…
New exact string solutions in non-constant background fields are found and it is shown that some of them are compatible with the boundary conditions for the open string - D-brane system. Extension of the constraint algebra is proposed and…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
Time Series Alignment is a critical task in signal processing with numerous real-world applications. In practice, signals often exhibit temporal shifts and scaling, making classification on raw data prone to errors. This paper introduces a…
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…
We study the complexity of approximating solution structure of the bijective weighted sentence alignment problem of DeNero and Klein (2008). In particular, we consider the complexity of finding an alignment that has a significant overlap…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
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…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
The Data-to-Text task aims to generate human-readable text for describing some given structured data enabling more interpretability. However, the typical generation task is confined to a few particular domains since it requires well-aligned…
Genome sequence analysis has enabled significant advancements in medical and scientific areas such as personalized medicine, outbreak tracing, and the understanding of evolution. Unfortunately, it is currently bottlenecked by the…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
Motivation: The pan-genome can be stored as elastic-degenerate (ED) string, a recently introduced compact representation of multiple overlapping sequences. However, a search over the ED string does not indicate which individuals (if any)…
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores…