Related papers: Accurate selfcorrection of errors in long reads us…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
Fine-tuning helps large language models (LLM) recover degraded information and enhance task performance. Although Low-Rank Adaptation (LoRA) is widely used and effective for fine-tuning, we have observed that its scaling factor can limit or…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
A new method to identify all sufficiently long repeating substrings in one or several symbol sequences is proposed. The method is based on a specific gauge applied to symbol sequences that guarantees identification of the repeating…
Transformer-based pre-trained models, such as BERT, have achieved remarkable results on machine reading comprehension. However, due to the constraint of encoding length (e.g., 512 WordPiece tokens), a long document is usually split into…
Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for…
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…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Motivation: Detection of structural variants (SV) from the alignment of sample DNA reads to the reference genome is an important problem in understanding human diseases. Long reads that can span repeat regions, along with an accurate…
Low-Rank Adaptation (LoRA) is the prevailing approach for efficient large language model (LLM) fine-tuning. Building on this paradigm, recent studies have proposed alternative initialization strategies, architectural modifications, and…
A common approach for improving OCR quality is a post-processing step based on models correcting misdetected characters and tokens. These models are typically trained on aligned pairs of OCR read text and their manually corrected…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Long-read sequencing has enabled the de novo assembly of several mammalian genomes, but with high cost in computing. Here, we demonstrated de novo assembly of mammalian genome using long reads in an efficient and inexpensive workstation.
Currently, third-generation sequencing techniques, which allow to obtain much longer DNA reads compared to the next-generation sequencing technologies, are becoming more and more popular. There are many possibilities to combine data from…
Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…
Previous approaches for blind image super-resolution (SR) have relied on degradation estimation to restore high-resolution (HR) images from their low-resolution (LR) counterparts. However, accurate degradation estimation poses significant…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
We study weighted pseudorandom generators (WPRGs) and derandomizations for read-once branching programs (ROBPs). Denote $n$ and $w$ as the length and the width of a ROBP. We have the following results. For standard ROBPs, we give an…
Full-text error correction with Large Language Models (LLMs) for Automatic Speech Recognition (ASR) is attracting increased attention for its ability to address a wide range of error types, such as punctuation restoration and inverse text…