Related papers: MD-Bench: A generic proxy-app toolbox for state-of…
Determinantal point processes (DPPs) have emerged as a kernelized alternative to vanilla independent sampling for generating efficient minibatches, coresets and other parsimonious representations of large-scale datasets. While theoretical…
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by high computational cost. We present ProTDyn, a foundation…
Large language model (LLM)-based mobile agents are increasingly popular due to their capability to interact directly with mobile phone Graphic User Interfaces (GUIs) and their potential to autonomously manage daily tasks. Despite their…
Machine learning-based modeling of physical systems has experienced increased interest in recent years. Despite some impressive progress, there is still a lack of benchmarks for Scientific ML that are easy to use but still challenging and…
The evaluation of large language models (LLMs) is crucial to assess their performance and mitigate potential security risks. In this paper, we introduce PromptBench, a unified library to evaluate LLMs. It consists of several key components…
Molecular dynamics (MD) simulations are widely used to study large-scale molecular systems. HPC systems are ideal platforms to run these studies, however, reaching the necessary simulation timescale to detect rare processes is challenging,…
Recently, extensive deep learning architectures and pretraining strategies have been explored to support downstream protein applications. Additionally, domain-specific models incorporating biological knowledge have been developed to enhance…
Matrix Distributed Processing (MDP) is a C++ library for fast development of efficient parallel algorithms. It constitues the core of FermiQCD. MDP enables programmers to focus on algorithms, while parallelization is dealt with…
Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…
This article introduces a benchmark application for seismic modeling using finite difference method, which is namedMiniMod, a mini application for seismic modeling. The purpose is to provide a benchmark suite that is, on one hand easy to…
This paper presents the first industry-standard open-source machine learning (ML) benchmark to allow perfor mance and accuracy evaluation of mobile devices with different AI chips and software stacks. The benchmark draws from the expertise…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
NLP Workbench is a web-based platform for text mining that allows non-expert users to obtain semantic understanding of large-scale corpora using state-of-the-art text mining models. The platform is built upon latest pre-trained models and…
Liquid Chromatography Mass Spectrometry (LC-MS) is an indispensable analytical technique in proteomics, metabolomics, and other life sciences. While OpenMS provides advanced open-source software for MS data analysis, its complexity can be…
Network latency in mobile software has a large impact on user experience, with potentially severe economic consequences. Prefetching and caching have been shown effective in reducing the latencies in browser-based systems. However, those…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
MFEM is an open-source, lightweight, flexible and scalable C++ library for modular finite element methods that features arbitrary high-order finite element meshes and spaces, support for a wide variety of discretization approaches and…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
We use the XSBench proxy application, a memory-intensive OpenMP program, to explore the source of on-node scalability degradation of a popular Monte Carlo (MC) reactor physics benchmark on non-uniform memory access (NUMA) systems. As…