Related papers: Even better correction of genome sequencing data
Scanning Electron Microscopy (SEM) is pivotal in revealing intricate micro- and nanoscale features across various research fields. However, obtaining high-resolution SEM images presents challenges, including prolonged scanning durations and…
In this article we show that the reconstructions of semiconductor surfaces can be determined using a genetic procedure. Coupled with highly optimized interatomic potentials, the present approach represents an efficient tool for finding and…
We develop an iterative refinement method that improves the accuracy of a user-chosen subset of $k$ eigenvectors ($k\ll n$) of an $n\times n$ real symmetric matrix. Using an orthogonal matrix represented in compact WY form, the method…
To address a looming crisis of unreproducible evaluation for named entity recognition, we propose guidelines and introduce SeqScore, a software package to improve reproducibility. The guidelines we propose are extremely simple and center…
A new algorithm is developed to jointly recover a temporal sequence of images from noisy and under-sampled Fourier data. Specifically, we consider the case where each data set is missing vital information that prevents its (individual)…
Sequencing by Emergence (SEQE) is a new single-molecule nucleic acid (DNA/RNA) sequencing technology that estimates sequence as an emergent property of the binding and localization of a repertoire of short oligonucleotide probes. SEQE…
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…
Recently, Transformer-based encoder-decoder models have demonstrated strong performance in multilingual speech recognition. However, the decoder's autoregressive nature and large size introduce significant bottlenecks during inference.…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
As genetic sequencing costs decrease, the lack of clinical interpretation of variants has become the bottleneck in using genetics data. A major rate limiting step in clinical interpretation is the manual curation of evidence in the genetic…
Motivation: As cancer researchers have come to appreciate the importance of intratumor heterogeneity, much attention has focused on the challenges of accurately profiling heterogeneity in individual patients. Experimental technologies for…
The biochemical processes underlying DNA data storage, including synthesis, amplification, and sequencing, are inherently noisy. Consequently, base-level insertion, deletion, and substitution (IDS) errors, as well as sequence-level…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
This paper presents RevOrder, a novel technique aimed at improving arithmetic operations in large language models (LLMs) by reversing the output digits in addition, subtraction, and n-digit by 1-digit (nD by 1D) multiplication tasks. Our…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Motivation :Reconstructing the topology of a gene regulatory network is one of the key tasks in systems biology. Despite of the wide variety of proposed methods, very little work has been dedicated to the assessment of their stability…
The advent of high-throughput sequencing technologies has revolutionized genome analysis by enabling the rapid and cost-effective sequencing of large genomes. Despite these advancements, the increasing complexity and volume of genomic data…
Domain specific accelerators present new challenges and opportunities for code generation onto novel instruction sets, communication fabrics, and memory architectures. In this paper we introduce an intermediate representation (IR) which…