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The aim of plant breeding trials is often to identify germplasms that are well adapt to target environments. These germplasms are identified through genomic prediction from the analysis of multi-environmental field trial (MET) using linear…

Retrieval-augmented generation (RAG) can enhance the generation quality of large language models (LLMs) by incorporating external token databases. However, retrievals from large databases can constitute a substantial portion of the overall…

A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…

Modern information retrieval systems often employ a two-stage pipeline: an efficient initial retrieval stage followed by a computationally intensive reranking stage. Cross-encoders have shown strong effectiveness for reranking due to their…

While coarse-grained reconfigurable arrays (CGRAs) have emerged as promising programmable accelerator architectures, pipelining applications running on CGRAs is required to ensure high maximum clock frequencies. Current CGRA compilers…

The choice of convolutional routines (primitives) to implement neural networks has a tremendous impact on their inference performance (execution speed) on a given hardware platform. To optimise a neural network by primitive selection, the…

Achieving an accurate description of fermionic systems typically requires considerably many more orbitals than fermions. Previous resource analyses of quantum chemistry simulation often failed to exploit this low fermionic number…

Large Language Models (LLMs) have made query reformulation ubiquitous in modern retrieval and Retrieval-Augmented Generation (RAG) pipelines, enabling the generation of multiple semantically equivalent query variants. However, executing the…

Exponential increases in scientific experimental data are outstripping the rate of progress in silicon technology. As a result, heterogeneous combinations of architectures and process or device technologies are increasingly important to…

High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…

The marine environment is one of the most important sources for microbial biodiversity on the planet. These microbes are drivers for many biogeochemical processes, and their enormous genetic potential is still not fully explored or…

Genetic algorithms are heuristic optimization techniques inspired by Darwinian evolution, which are characterized by successfully finding robust solutions for optimization problems. Here, we propose a subroutine-based quantum genetic…

Global routing is a critical stage in electronic design automation (EDA) that enables early estimation and optimization of the routability of modern integrated circuits with respect to congestion, power dissipation, and design complexity.…

In kernel methods, temporal information on the data is commonly included by using time-delayed embeddings as inputs. Recently, an alternative formulation was proposed by defining a gamma-filter explicitly in a reproducing kernel Hilbert…

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline…

To address the challenge of scarce computational resources in genomic modeling, we introduce GERM, a genomic foundation model with strong compression performance and fast adaptability. GERM improves upon models like DNABERT-2 by eliminating…

We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially…

A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…

Heavily pre-trained transformers for language modelling, such as BERT, have shown to be remarkably effective for Information Retrieval (IR) tasks, typically applied to re-rank the results of a first-stage retrieval model. IR benchmarks…