Related papers: BEETL-fastq: a searchable compressed archive for D…
RNA sequencing (RNA-seq) has been rapidly adopted for the profiling of transcriptomes in many areas of biology, including studies into gene regulation, development and disease. Of particular interest is the discovery of differentially…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Genome sequences contain hundreds of millions of DNA base pairs. Finding the degree of similarity between two genomes requires executing a compute-intensive dynamic programming algorithm, such as Smith-Waterman. Traditional von Neumann…
Since most analysis software for genome-wide association studies (GWAS) currently exploit only unrelated individuals, there is a need for efficient applications that can handle general pedigree data or mixtures of both population and…
This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…
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…
Ultra-fine entity typing plays a crucial role in information extraction by predicting fine-grained semantic types for entity mentions in text. However, this task poses significant challenges due to the massive number of entity types in the…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
We present APQ for efficient deep learning inference on resource-constrained hardware. Unlike previous methods that separately search the neural architecture, pruning policy, and quantization policy, we optimize them in a joint manner. To…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
This paper proposes a novel approach for storing and retrieving massive DNA sequences.. The method is based on a perceptual hash function, commonly used to determine the similarity between digital images, that we adapted for DNA sequences.…
Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a high-throughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
Retrieval augmentation is a powerful but expensive method to make language models more knowledgeable about the world. Memory-based methods like LUMEN pre-compute token representations for retrieved passages to drastically speed up…
Traditional lossless text compression preserves every byte, but its gains on natural language are often modest in realistic operating regimes. We study \emph{lossy semantic text compression}, where the encoder strategically deletes parts of…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Code retrieval, which retrieves code snippets based on users' natural language descriptions, is widely used by developers and plays a pivotal role in real-world software development. The advent of deep learning has shifted the retrieval…
In a dynamic retrieval system, documents must be ingested as they arrive, and be immediately findable by queries. Our purpose in this paper is to describe an index structure and processing regime that accommodates that requirement for…
Publicly available information contains valuable information for Cyber Threat Intelligence (CTI). This can be used to prevent attacks that have already taken place on other systems. Ideally, only the initial attack succeeds and all…
Electronic health record (EHR) data is an essential data source for machine learning for health, but researchers and clinicians face steep barriers in extracting and validating EHR data for modeling. Existing tools incur trade-offs between…