Related papers: Using GNN property predictors as molecule generato…
Graph neural networks (GNN) represent an emerging line of deep learning models that operate on graph structures. It is becoming more and more popular due to its high accuracy achieved in many graph-related tasks. However, GNN is not as well…
Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework…
In this study, we present a framework aimed at enhancing molecular property prediction through the integration of local descriptors obtained from large-scale pretrained machine learning potentials into three-dimensional graph neural…
We study how to generate molecule conformations (i.e., 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning…
Graph Neural Networks (GNNs) have gained popularity in various learning tasks, with successful applications in fields like molecular biology, transportation systems, and electrical grids. These fields naturally use graph data, benefiting…
Graph neural networks (GNNs) have been shown to be astonishingly capable models for molecular property prediction, particularly as surrogates for expensive density functional theory calculations of relaxed energy for novel material…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Graph generation has emerged as a crucial task in machine learning, with significant challenges in generating graphs that accurately reflect specific properties. Existing methods often fall short in efficiently addressing this need as they…
Unraveling the complexities of Gene Regulatory Networks (GRNs) is crucial for understanding cellular processes and disease mechanisms. Traditional computational methods often struggle with the dynamic nature of these networks. This study…
Graph neural networks (GNNs) are a well-regarded tool for learned control of networked dynamical systems due to their ability to be deployed in a distributed manner. However, current distributed GNN architectures assume that all nodes in…
Learning expressive molecular representations is crucial to facilitate the accurate prediction of molecular properties. Despite the significant advancement of graph neural networks (GNNs) in molecular representation learning, they generally…
Learning from graph-structured data is an important task in machine learning and artificial intelligence, for which Graph Neural Networks (GNNs) have shown great promise. Motivated by recent advances in geometric representation learning, we…
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…
Graph Neural Networks (GNNs) is an architecture for structural data, and has been adopted in a mass of tasks and achieved fabulous results, such as link prediction, node classification, graph classification and so on. Generally, for a…
Graph Neural Networks (GNNs) have emerged as a flexible and powerful approach for learning over graphs. Despite this success, existing GNNs are constrained by their local message-passing architecture and are provably limited in their…
This study presents a Graph Neural Networks (GNNs)-based approach for predicting the effective elastic moduli of rocks from their digital CT-scan images. We use the Mapper algorithm to transform 3D digital rock images into graph datasets,…
Graphs are a powerful data structure to represent relational data and are widely used to describe complex real-world data structures. Probabilistic Graphical Models (PGMs) have been well-developed in the past years to mathematically model…
Graph neural networks (GNNs) have been successfully applied in many structured data domains, with applications ranging from molecular property prediction to the analysis of social networks. Motivated by the broad applicability of GNNs, we…
Generating graph structures is a challenging problem due to the diverse representations and complex dependencies among nodes. In this paper, we introduce Graph Variational Recurrent Neural Network (GraphVRNN), a probabilistic autoregressive…
Graphs are ubiquitous in social networks and biochemistry, where Graph Neural Networks (GNN) are the state-of-the-art models for prediction. Graphs can be evolving and it is vital to formally model and understand how a trained GNN responds…