Related papers: Mapache: a flexible pipeline to map ancient DNA
Recent advances in language models opened new opportunities to address complex schema matching tasks. Schema matching approaches have been proposed that demonstrate the usefulness of language models, but they have also uncovered important…
Multi-task model training has been adopted to enable a single deep neural network model (often a large language model) to handle multiple tasks (e.g., question answering and text summarization). Multi-task training commonly receives input…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Search systems often employ a re-ranking pipeline, wherein documents (or passages) from an initial pool of candidates are assigned new ranking scores. The process enables the use of highly-effective but expensive scoring functions that are…
DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…
We introduce a decentralized replication strategy for peer-to-peer file exchange based on exhaustive exploration of the neighborhood of any node in the network. The replication scheme lets the replicas evenly populate the network mesh,…
Achieving faster execution with shorter compilation time can foster further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…
Motivation: 3D structures of proteins provide rich information for understanding their biochemical roles. Identifying the representative protein structures for protein sequences is essential for analysis of proteins at proteome scale.…
DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media.…
This paper presents an efficient method to perform Structured Matrix Approximation by Separation and Hierarchy (SMASH), when the original dense matrix is associated with a kernel function. Given points in a domain, a tree structure is first…
Deep generative models show promise for $\textit{de novo}$ protein design, yet reliably producing designs that are geometrically plausible, evolutionarily consistent, functionally relevant, and dynamically stable remains challenging. We…
Machine intelligence, especially using convolutional neural networks (CNNs), has become a large area of research over the past years. Increasingly sophisticated hardware accelerators are proposed that exploit e.g. the sparsity in…
With the recent growth of Deep Learning for AI, there is a need for tools to meet the demand of data flowing into those models. In some cases, source data may exist in multiple formats, and therefore the source data must be investigated and…
Retrieval-augmented generation over semi-structured sources such as HTML is constrained by a mismatch between document structure and the flat, sequence-based interfaces of today's embedding and generative models. Retrieval pipelines often…
De novo assembly enables investigations of unknown genomes, paving the way for personalized medicine and disease management. However, it faces immense computational challenges arising from the excessive data volumes and algorithmic…
We propose a simple extension of residual networks that works simultaneously in multiple resolutions. Our network design is inspired by the iterative back-projection algorithm but seeks the more difficult task of learning how to enhance…
Efficiently optimizing multi-model inference pipelines for fast, accurate, and cost-effective inference is a crucial challenge in machine learning production systems, given their tight end-to-end latency requirements. To simplify the…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…