Related papers: Image-Like Graph Representations for Improved Mole…
Logical query answering over Knowledge Graphs (KGs) is a fundamental yet complex task. A promising approach to achieve this is to embed queries and entities jointly into the same embedding space. Research along this line suggests that using…
Molecular dynamics simulations can generate atomically detailed trajectories of complex systems, but analyzing these dynamics can be challenging when systems lack well-established quantitative descriptors (features). Graph neural networks…
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…
In this paper, we review recent developments and the role of Graph Neural Networks (GNNs) in computational drug discovery, including molecule generation, molecular property prediction, and drug-drug interaction prediction. By summarizing…
Learning to optimize is a rapidly growing area that aims to solve optimization problems or improve existing optimization algorithms using machine learning (ML). In particular, the graph neural network (GNN) is considered a suitable ML model…
Graph Neural Networks (GNNs) are the dominant architecture for molecular machine learning, particularly for molecular property prediction and machine learning interatomic potentials (MLIPs). GNNs perform message passing on predefined graphs…
Molecular property prediction is gaining increasing attention due to its diverse applications. One task of particular interests and importance is to predict quantum chemical properties without 3D equilibrium structures. This is practically…
Graph neural networks (GNNs) have become the standard learning architectures for graphs. GNNs have been applied to numerous domains ranging from quantum chemistry, recommender systems to knowledge graphs and natural language processing. A…
Designing molecules with specific properties is a long-lasting research problem and is central to advancing crucial domains such as drug discovery and material science. Recent advances in deep graph generative models treat molecule design…
The majority of model-based learned image reconstruction methods in medical imaging have been limited to uniform domains, such as pixelated images. If the underlying model is solved on nonuniform meshes, arising from a finite element method…
Graph Neural Networks (GNNs) have paved the way for being a cornerstone in graph-related learning tasks. Yet, the ability of GNNs to capture structural interactions within graphs remains under-explored. In this work, we address this gap by…
Deep generative models have emerged as a powerful tool for learning useful molecular representations and designing novel molecules with desired properties, with applications in drug discovery and material design. However, most existing deep…
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…
Recently, subgraphs-enhanced Graph Neural Networks (SGNNs) have been introduced to enhance the expressive power of Graph Neural Networks (GNNs), which was proved to be not higher than the 1-dimensional Weisfeiler-Leman isomorphism test. The…
Drug Discovery is a fundamental and ever-evolving field of research. The design of new candidate molecules requires large amounts of time and money, and computational methods are being increasingly employed to cut these costs. Machine…
Graph Neural Networks (GNNs) have become a prevailing tool for learning physical dynamics. However, they still encounter several challenges: 1) Physical laws abide by symmetry, which is a vital inductive bias accounting for model…
The network embedding problem that maps nodes in a graph to vectors in Euclidean space can be very useful for addressing several important tasks on a graph. Recently, graph neural networks (GNNs) have been proposed for solving such a…
Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…
Graph neural network (GNN) is a popular tool to learn the lower-dimensional representation of a graph. It facilitates the applicability of machine learning tasks on graphs by incorporating domain-specific features. There are various options…
In this study, we present the Graph Sub-Graph Network (GSN), a novel hybrid image classification model merging the strengths of Convolutional Neural Networks (CNNs) for feature extraction and Graph Neural Networks (GNNs) for structural…