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We introduce primed-PCA (pPCA), a two-step algorithm for speeding up the approximation of principal components. This algorithm first runs any approximate-PCA method to get an initial estimate of the principal components (priming), and then…

The rapid development of large language models (LLM) has greatly enhanced everyday applications. While many FPGA-based accelerators, with flexibility for fine-grained data control, exhibit superior speed and energy efficiency compared to…

The quantum kernel method has attracted considerable attention in the field of quantum machine learning. However, exploring the applicability of quantum kernels in more realistic settings has been hindered by the number of physical qubits…

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…

Open Modification Search (OMS) is a promising algorithm for mass spectrometry analysis that enables the discovery of modified peptides. However, OMS encounters challenges as it exponentially extends the search scope. Existing OMS…

Particle tracking in large-scale numerical simulations of turbulent flows presents one of the major bottlenecks in parallel performance and scaling efficiency. Here, we describe a particle tracking algorithm for large-scale parallel…

By providing highly efficient one-sided communication with globally shared memory space, Partitioned Global Address Space (PGAS) has become one of the most promising parallel computing models in high-performance computing (HPC). Meanwhile,…

The use of FPGAs for efficient graph processing has attracted significant interest. Recent memory subsystem upgrades including the introduction of HBM in FPGAs promise to further alleviate memory bottlenecks. However, modern multi-channel…

We implement two recently developed fast Coulomb solvers, HSMA3D [J. Chem. Phys. 149 (8) (2018) 084111] and HSMA2D [J. Chem. Phys. 152 (13) (2020) 134109], into a new user package HSMA for molecular dynamics simulation engine LAMMPS. The…

With the rapid development of in-depth learning, neural network and deep learning algorithms have been widely used in various fields, e.g., image, video and voice processing. However, the neural network model is getting larger and larger,…

Graphics processing units (GPU) had evolved from a specialized hardware capable to render high quality graphics in games to a commodity hardware for effective processing blocks of data in a parallel schema. This evolution is particularly…

Efficient quantum control is necessary for practical quantum computing implementations with current technologies. Conventional algorithms for determining optimal control parameters are computationally expensive, largely excluding them from…

Particle-in-Cell (PIC) methods are widely used computational tools for fluid and kinetic plasma modeling. While both the fluid and kinetic PIC approaches have been successfully used to target either kinetic or fluid simulations, little was…

Probabilistic graphical models (PGMs) serve as a powerful framework for modeling complex systems with uncertainty and extracting valuable insights from data. However, users face challenges when applying PGMs to their problems in terms of…

The Kernel Polynomial Method (KPM) is one of the fast diagonalization methods used for simulations of quantum systems in research fields of condensed matter physics and chemistry. The algorithm has a difficulty to be parallelized on a…

Stencil computation is one of the fundamental computing patterns in many application domains such as scientific computing and image processing. While there are promising studies that accelerate stencils on FPGAs, there lacks an automated…

This study presents advanced neural network architectures including Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN), Long Short-Term Memory Networks (LSTMs), and Deep Belief Networks (DBNs) for enhanced ECG signal…

In recent years, deep learning has become more and more mature, and as a commonly used algorithm in deep learning, convolutional neural networks have been widely used in various visual tasks. In the past, research based on deep learning…

Trends in hardware, the prevalence of the cloud, and the rise of highly demanding applications have ushered an era of specialization that quickly changes how data is processed at scale. These changes are likely to continue and accelerate in…

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…