Related papers: Accelerating Drug Discovery in AutoDock-GPU with T…

Molecular conformation generation (MCG) is a fundamental and important problem in drug discovery. Many traditional methods have been developed to solve the MCG problem, such as systematic searching, model-building, random searching,…

The global optimization of atomic clusters represents a fundamental challenge in computational chemistry and materials science due to the exponential growth of local minima with system size (i.e., the curse of dimensionality). We introduce…

We describe the use of Graphics Processing Units (GPUs) for speeding up the code NBODY6 which is widely used for direct $N$-body simulations. Over the years, the $N^2$ nature of the direct force calculation has proved a barrier for…

We accelerated an ab-initio molecular QMC calculation by using GPGPU. Only the bottle-neck part of the calculation is replaced by CUDA subroutine and performed on GPU. The performance on a (single core CPU + GPU) is compared with that on a…

We present a massively parallel Lagrange decomposition method for solving 0--1 integer linear programs occurring in structured prediction. We propose a new iterative update scheme for solving the Lagrangean dual and a perturbation technique…

Black-box optimization is essential for tuning complex machine learning algorithms which are easier to experiment with than to understand. In this paper, we show that a simple ensemble of black-box optimization algorithms can outperform any…

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data…

The complexity of combustion simulations demands the latest high-performance computing tools to accelerate its time-to-solution results. A current trend on HPC systems is the utilization of CPUs with SIMD or vector extensions to exploit…

The classical simulation of quantum algorithms is a crucial tool for circuit development, testing, and validation. Although acceleration using GPUs significantly reduces simulation time, most high-performance simulators rely on…

Scientific applications produce vast amounts of data, posing grand challenges in the underlying data management and analytic tasks. Progressive compression is a promising way to address this problem, as it allows for on-demand data…

We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…

Molecular docking is a cornerstone of drug discovery, relying on high-resolution ligand-bound structures to achieve accurate predictions. However, obtaining these structures is often costly and time-intensive, limiting their availability.…

The objective of our research is to demonstrate the practical usage and orders of magnitude speedup of real-world applications by using alternative technologies to support high performance computing. Currently, the main barrier to the…

The protein-protein interactions (PPIs) are crucial for understanding the majority of cellular processes. PPIs play important role in gene transcription regulation, cellular signaling, molecular basis of immune response and more. Moreover,…

Low-dose Proton Computed Tomography (pCT) is an evolving imaging modality that is used in proton therapy planning which addresses the range uncertainty problem. The goal of pCT is generating a 3D map of Relative Stopping Power (RSP)…

Machine learning based methods have shown potential for optimizing existing molecules with more desirable properties, a critical step towards accelerating new chemical discovery. Here we propose QMO, a generic query-based molecule…

Tucker decomposition is one of the most popular models for analyzing and compressing large-scale tensorial data. Existing Tucker decomposition algorithms usually rely on a single solver to compute the factor matrices and core tensor, and…

Protein interactions and assembly formation are fundamental to most biological processes. Predicting the assembly structure from constituent proteins -- referred to as the protein docking task -- is thus a crucial step in protein design…

Graph neural networks (GNNs) have seen extensive application in domains such as social networks, bioinformatics, and recommendation systems. However, the irregularity and sparsity of graph data challenge traditional computing methods, which…

Traditional drug discovery programs are being transformed by the advent of machine learning methods. Among these, Generative AI methods (GM) have gained attention due to their ability to design new molecules and enhance specific properties…