Related papers: MiMiC: A High-Performance Framework for Multiscale…
The trend towards highly parallel multi-processing is ubiquitous in all modern computer architectures, ranging from handheld devices to large-scale HPC systems; yet many applications are struggling to fully utilise the multiple levels of…
In multimodal sentiment analysis (MSA), the performance of a model highly depends on the quality of synthesized embeddings. These embeddings are generated from the upstream process called multimodal fusion, which aims to extract and combine…
Harnessing modern parallel computing resources to achieve complex multi-physics simulations is a daunting task. The Multiphysics Object Oriented Simulation Environment (MOOSE) aims to enable such development by providing simplified…
We present an end-to-end differentiable molecular simulation framework (DIMOS) for molecular dynamics and Monte Carlo simulations. DIMOS easily integrates machine-learning-based interatomic potentials and implements classical force fields…
As tools for designing multiple processor systems-on-chips (MPSoCs) continue to evolve to meet the demands of developers, there exist systematic gaps that must be bridged to provide a more cohesive hardware/software development environment.…
Multimodal semantic communication has great potential to enhance downstream task performance by integrating complementary information across modalities. This paper introduces ProMSC-MIS, a novel Prompt-based Multimodal Semantic…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…
Scaling up hardware systems has become an important tactic for improving performance as Moore's law fades. Unfortunately, simulations of large hardware systems are often a design bottleneck due to slow throughput and long build times. In…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
MGSim is an open source discrete event simulator for on-chip hardware components, developed at the University of Amsterdam. It is intended to be a research and teaching vehicle to study the fine-grained hardware/software interactions on…
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…
Model Predictive Control (MPC) is a computationally demanding control technique that allows dealing with multiple-input and multiple-output systems, while handling constraints in a systematic way. The necessity of solving an optimization…
Multimodal clinical prediction faces three challenges: multiple foundation models (FMs) with complementary strengths per modality, pervasive missing modalities at training and test time, and sample-specific variation in modality…
Manycore System-on-Chip include an increasing amount of processing elements and have become an important research topic for improvements of both hardware and software. While research can be conducted using system simulators, prototyping…
This article presents MuMFiM, an open source application for multiscale modeling of fibrous materials on massively parallel computers. MuMFiM uses two scales to represent fibrous materials such as biological network materials (extracellular…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
We discuss the computational bottlenecks in molecular dynamics (MD) and describe the challenges in parallelizing the computation intensive tasks. We present a hybrid algorithm using MPI (Message Passing Interface) with OpenMP threads for…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
In this paper, we present BIMS (Biomedical Information Management System). BIMS is a software architecture designed to provide a flexible computational framework to manage the information needs of a wide range of biomedical research…
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…