相关论文: ppsim: A software package for efficiently simulati…
Processing-in-memory architectures have been regarded as a promising solution for CNN acceleration. Existing PIM accelerator designs rely heavily on the experience of experts and require significant manual design overhead. Manual design…
We discuss R package SQUAREM for accelerating iterative algorithms which exhibit slow, monotone convergence. These include the well-known expectation-maximization algorithm, majorize-minimize (MM), and other EM-like algorithms such as…
We have developed a gravity solver based on combining the well developed Particle-Mesh (PM) method and TREE methods. It is designed for and has been implemented on parallel computer architectures. The new code can deal with tens of millions…
Time-domain simulations are crucial for ensuring power system stability and avoiding critical scenarios that could lead to blackouts. The next-generation power systems require a significant increase in the computational cost and complexity…
Background: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main…
Computing long-timescale kinetics of biomolecular processes remains a major challenge for atomistic simulations. A way out is to exploit local kinetic information to construct the global stationary flux across the reaction space. The…
We present an open-source software for the simulation of observables in magnetic resonance experiments, including nuclear magnetic/quadrupole resonance NMR/NQR and electron spin resonance (ESR), developed to assist experimental research in…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
We present our latest advancements of machine-learned potentials (MLPs) based on the neuroevolution potential (NEP) framework introduced in [Fan et al., Phys. Rev. B 104, 104309 (2021)] and their implementation in the open-source package…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Physics-Informed Neural Networks (PINNs) have become a popular way to infer interpretable interaction parameters from noisy microbial time series, but practitioners face many tunable design choices (loss weights, regularisers, scaling,…
Integrating population genetics into community ecology theory is a major goal in ecology and evolution, but analyzing the resulting models is computationally daunting. Here we describe sPEGG ($\underline{\textrm{s}}\textrm{imulating}$…
Several manufacturers have already started to commercialize near-bank Processing-In-Memory (PIM) architectures. Near-bank PIM architectures place simple cores close to DRAM banks and can yield significant performance and energy improvements…
The constant potential molecular dynamics simulation method proposed by Siepmann and Sprik and reformulated later by Reed (SR-CPM) has been widely employed to investigate the metallic electrolyte/electrode interfaces, especially for…
Convolutional neural networks (CNN) have become a ubiquitous algorithm with growing applications in mobile and edge settings. We describe a compute-in-memory (CIM) technique called FPIRM using Racetrack Memory (RM) to accelerate CNNs for…
The model of population protocols provides a universal platform to study distributed processes driven by pairwise interactions of anonymous agents. While population protocols present an elegant and robust model for randomized distributed…
The Energy Conserving semi-implicit method (ECsim), presented by Lapenta in 2017, is a Particle in Cell (PIC) algorithm for the simulation of plasmas. Energy conservation is achieved within a semi-implicit formulation that does not require…
The constrained nature of synthesizable chemical space poses a significant challenge for sampling molecules that are both synthetically accessible and possess desired properties. In this work, we present PrexSyn, an efficient and…
Several manufacturers have already started to commercialize near-bank Processing-In-Memory (PIM) architectures. Near-bank PIM architectures place simple cores close to DRAM banks and can yield significant performance and energy improvements…
Numerous algorithms and parallelisations have been developed for short-range particle simulations; however, none are optimally performant for all scenarios. Such a concept led to the prior development of the particle simulation library…