Related papers: HQAlign: Aligning nanopore reads for SV detection …
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Incorporating heterogeneous representations from different architectures has facilitated various vision tasks, e.g., some hybrid networks combine transformers and convolutions. However, complementarity between such heterogeneous…
Sequence alignments are fundamental to bioinformatics which has resulted in a variety of optimized implementations. Unfortunately, the vast majority of them are hand-tuned and specific to certain architectures and execution models. This not…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Change detection (CD) is a fundamental and important task for monitoring the land surface dynamics in the earth observation field. Existing deep learning-based CD methods typically extract bi-temporal image features using a weight-sharing…
Super-resolution (SR) aims to increase the resolution of imagery. Applications include security, medical imaging, and object recognition. We propose a deep learning-based SR system that takes a hexagonally sampled low-resolution image as an…
Document parsing has garnered widespread attention as vision-language models (VLMs) advance OCR capabilities. However, the field remains fragmented across dozens of specialized models with varying strengths, forcing users to navigate…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Motivation: The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate. In this paper, we…
Heterogeneous domain adaptation (HDA) transfers knowledge across source and target domains that present heterogeneities e.g., distinct domain distributions and difference in feature type or dimension. Most previous HDA methods tackle this…
Large vision-language models (VLMs) frequently suffer from hallucinations, generating content that is inconsistent with visual inputs. Existing methods typically address this problem through post-hoc filtering, additional training…
Fake news detection remains a challenging problem due to the complex interplay between textual misinformation, manipulated images, and external knowledge reasoning. While existing approaches have achieved notable results in verifying…
Vector comparison in high dimensions is a fundamental task in NLP, yet it is dominated by two baselines: the raw dot product, which is unbounded and sensitive to vector norms, and the cosine similarity, which discards magnitude information…
Early detection and characterization of coronavirus disease (COVID-19), caused by SARS-CoV-2, remain critical for effective clinical response and public-health planning. The global availability of large-scale viral sequence data presents…
Sequencing a genome to determine an individual's DNA produces an enormous number of short nucleotide subsequences known as reads, which must be reassembled to reconstruct the full genome. We present a method for analyzing this type of data…
Predicting the consensus structure of a set of aligned RNA homologs is a convenient method to find conserved structures in an RNA genome, which has many applications including viral diagnostics and therapeutics. However, the most commonly…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identification of RBPs is complicated by their extreme sequence…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…