Related papers: BEETL-fastq: a searchable compressed archive for D…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
Open-domain Question Answering models which directly leverage question-answer (QA) pairs, such as closed-book QA (CBQA) models and QA-pair retrievers, show promise in terms of speed and memory compared to conventional models which retrieve…
With the rapid development of Natural Language Processing (NLP) technology, the accuracy and efficiency of machine translation have become hot topics of research. This paper proposes a novel Seq2Seq model aimed at improving translation…
The paper describes an algorithm to compute a consensus sequence from a set of DNA sequences of approximatively identical length generated by 3rd sequencing generation technologies. Its purpose targets DNA storage and is guided by specific…
Diffusion models have demonstrated remarkable capabilities in image synthesis and related generative tasks. Nevertheless, their practicality for real-world applications is constrained by substantial computational costs and latency issues.…
How does one search for a needle in a multi-dimensional haystack without knowing what a needle is and without knowing if there is one in the haystack? This kind of problem requires a paradigm shift - away from hypothesis driven searches of…
In large-scale recommender systems, ultra-long user behavior sequences encode rich signals of evolving interests. Extending sequence length generally improves accuracy, but directly modeling such sequences in production is infeasible due to…
We designed a fast similarity search engine for large molecular libraries: FPScreen. We downloaded 100 million molecules' structure files in PubChem with SDF extension, then applied a computational chemistry tool RDKit to convert each…
Data-free quantization aims to achieve model quantization without accessing any authentic sample. It is significant in an application-oriented context involving data privacy. Converting noise vectors into synthetic samples through a…
DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…
Efficient document retrieval heavily relies on the technique of semantic hashing, which learns a binary code for every document and employs Hamming distance to evaluate document distances. However, existing semantic hashing methods are…
Deep research requires reasoning over web evidence to answer open-ended questions, and it is a core capability for AI agents. Yet many deep research agents still rely on implicit, unstructured search behavior that causes redundant…
Recent studies in DNA sequence classification have leveraged sophisticated machine learning techniques, achieving notable accuracy in categorizing complex genomic data. Among these, methods such as k-mer counting have proven effective in…
We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…
Lookup tables are a fundamental structure in many data processing and systems applications. Examples include tokenized text in NLP, quantized embedding collections in recommendation systems, integer sketches for streaming data, and…
We describe FastCat Catalogues, a Web application that supports researchers studying archival material, such as historians, in exploring and quantitatively analysing the data (transcripts) of archival documents. The application was designed…
Technologies for sequencing (reading) and synthesizing (writing) DNA have progressed on a Moore's law-like trajectory over the last three decades. This has motivated the idea of using DNA for data storage. Theoretically, DNA-based storage…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
The Basic Local Alignment Search Tool (BLAST) is currently the most popular method for searching databases of biological sequences. BLAST compares sequences via similarity defined by a weighted edit distance, which results in it being…