Related papers: BEETL-fastq: a searchable compressed archive for D…

Vector quantization (VQ) based ANN indexes, such as Inverted File System (IVF) and Product Quantization (PQ), have been widely applied to embedding based document retrieval thanks to the competitive time and memory efficiency. Originally,…

Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…

Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…

Web search and other large-scale web data analytics rely on processing archives of web pages stored in a standardized and efficient format. Since its introduction in 2008, the IIPC's Web ARCive (WARC) format has become the standard format…

The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics formats,…

Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of crucial details and…

In a private database query scheme (PDQ), a server maintains a database, and users send queries to retrieve records of interest from the server while keeping their queries private. A crucial step in PDQ protocols based on homomorphic…

Deoxyribonucleic Acid (DNA), with its high density and long durability, is a promising storage medium for long-term archival storage and has attracted much attention. Several studies have verified the feasibility of using DNA for archival…

DNA sequencing is revolutionising the field of medicine. DNA sequencers, the machines which perform DNA sequencing, have evolved from the size of a fridge to that of a mobile phone over the last two decades. The cost of sequencing a human…

With the explosive growth of multi-modal information on the Internet, unimodal search cannot satisfy the requirement of Internet applications. Text-image retrieval research is needed to realize high-quality and efficient retrieval between…

Deep neural network powered artificial intelligence has rapidly changed our daily life with various applications. However, as one of the essential steps of deep neural networks, training a heavily weighted network requires a tremendous…

Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional…

Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This…

Deep Neural Networks (DNNs) typically require massive amount of computation resource in inference tasks for computer vision applications. Quantization can significantly reduce DNN computation and storage by decreasing the bitwidth of…

We consider the problem of producing compact architectures for text classification, such that the full model fits in a limited amount of memory. After considering different solutions inspired by the hashing literature, we propose a method…

Multimodal encoders have pushed the boundaries of visual document retrieval, matching textual query tokens directly to image patches and achieving state-of-the-art performance on public benchmarks. Recent models relying on this paradigm…

DNA sequence classification requires not only high predictive accuracy but also the ability to uncover latent site interactions, combinatorial regulation, and epistasis-like higher-order dependencies. Although the standard Transformer…

The recent detection transformer (DETR) has advanced object detection, but its application on resource-constrained devices requires massive computation and memory resources. Quantization stands out as a solution by representing the network…

We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…

The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required…