Related papers: LISA: Towards Learned DNA Sequence Search
This paper summarizes the idea of Low-Cost Interlinked Subarrays (LISA), which was published in HPCA 2016, and examines the work's significance and future potential. Contemporary systems perform bulk data movement movement inefficiently, by…
A new LISA simulator (LISACode) is presented. Its ambition is to achieve a new degree of sophistication allowing to map, as closely as possible, the impact of the different sub-systems on the measurements. LISACode is not a detailed…
Index is an important component in database systems. Learned indexes have been shown to outperform traditional tree-based index structures for fixed-sized integer or floating point keys. However, the application of the learned solution to…
DNA storage is now being considered as a new archival storage method for its durability and high information density, but still facing some challenges like high costs and low throughput. By reducing sequencing sample size for decoding…
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…
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…
High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…
Although DNA foundation models have advanced the understanding of genomes, they still face significant challenges in the limited scale and diversity of genomic data. This limitation starkly contrasts with the success of natural language…
Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to…
The explosive growth in big data has attracted much attention in designing efficient indexing and search methods recently. In many critical applications such as large-scale search and pattern matching, finding the nearest neighbors to a…
Under normality and homoscedasticity assumptions, Linear Discriminant Analysis (LDA) is known to be optimal in terms of minimising the Bayes error for binary classification. In the heteroscedastic case, LDA is not guaranteed to minimise…
The Laser Interferometer Space Antenna (LISA) is a planned space-based gravitational wave telescope with the goal of measuring gravitational waves in the milli-Hertz frequency band, which is dominated by millions of Galactic binaries. While…
A new statistical technique for constructing linear latent structure (LLS) models from available data, supported by well established theoretical results and an efficient algorithm, is presented. The method reduces the problem of estimating…
This paper presents an accurate short-read mapper for next-generation sequencing data which is widely used in the 1000 Genomes Project, and human clinical and other species genome studies.
We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps…
Storing and archiving data produced by next-generation sequencing (NGS) is a huge burden for research institutions. Reference-based compression algorithms are effective in dealing with these data. Our work focuses on compressing FASTQ…
Approximating the recent phylogeny of $N$ phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…
Instruction tuning has unlocked powerful capabilities in large language models (LLMs), effectively using combined datasets to develop generalpurpose chatbots. However, real-world applications often require a specialized suite of skills…