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Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling…

Although algebraic graph theory based models have been widely applied in physical modeling and molecular studies, they are typically incompetent in the analysis and prediction of biomolecular properties when compared with other quantitative…

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…

Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful…

Machine learning on graphs has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually…

Large-eddy simulations (LES) require closures for filtered production rates because the resolved fields do not contain all correlations that govern chemical source terms. We develop a graph neural network (GNN) that predicts filtered…

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great…

Graphene is one of the most researched two dimensional (2D) material due to its unique combination of mechanical, thermal and electrical properties. Special 2D structure of graphene enables it to exhibit a wide range of peculiar material…

To enable heterogeneous computing systems with autonomous programming and optimization capabilities, we propose a unified, end-to-end, programmable graph representation learning (PGL) framework that is capable of mining the complexity of…

Graphs play an important role in representing complex relationships in various domains like social networks, knowledge graphs, and molecular discovery. With the advent of deep learning, Graph Neural Networks (GNNs) have emerged as a…

Accurate prediction of physical properties is critical for discovering and designing novel materials. Machine learning technologies have attracted significant attention in the materials science community for their potential for large-scale…

Recent progress in Graph Neural Networks (GNNs) has greatly enhanced the ability to model complex molecular structures for predicting properties. Nevertheless, molecular data encompasses more than just graph structures, including textual…

Background: Virtual Screening (VS) has become an essential tool in drug discovery, enabling the rapid and cost-effective identification of potential bioactive molecules. Among recent advancements, Graph Neural Networks (GNNs) have gained…

Machine learning (ML) methods have gained increasing popularity in exploring and developing new materials. More specifically, graph neural network (GNN) has been applied in predicting material properties. In this work, we develop a novel…

The aim of the inverse chemical design is to develop new molecules with given optimized molecular properties or objectives. Recently, generative deep learning (DL) networks are considered as the state-of-the-art in inverse chemical design…

Accurate and fast simulation of particle physics processes is crucial for the high-energy physics community. Simulating particle interactions with detectors is both time consuming and computationally expensive. With the proton-proton…

In the majority of molecular optimization tasks, predictive machine learning (ML) models are limited due to the unavailability and cost of generating big experimental datasets on the specific task. To circumvent this limitation, ML models…

Machine Learning (ML) potentials such as Gaussian Approximation Potential (GAP) have demonstrated impressive capabilities in mapping structure to properties across diverse systems. Here, we introduce a GAP model for low-dimensional Ni…

Geometric deep learning (GDL) has demonstrated huge power and enormous potential in molecular data analysis. However, a great challenge still remains for highly efficient molecular representations. Currently, covalent-bond-based molecular…

Recent research efforts have shown the possibility to discover anticancer drug-like molecules in food from their effect on protein-protein interaction networks, opening a potential pathway to disease-beating diet design. We formulate this…