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Leveraging domain knowledge including fingerprints and functional groups in molecular representation learning is crucial for chemical property prediction and drug discovery. When modeling the relation between graph structure and molecular…

Understanding Deep Neural Network (DNN) performance in changing conditions is essential for deploying DNNs in safety critical applications with unconstrained environments, e.g., perception for self-driving vehicles or medical image…

Recent advances in molecular representation learning have produced highly effective encodings of molecules for numerous cheminformatics and bioinformatics tasks. However, extracting general chemical insight while balancing predictive…

Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D…

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However,…

Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must respect the rotational symmetries inherent in physics. These…

Quadratic programming (QP) is the most widely applied category of problems in nonlinear programming. Many applications require real-time/fast solutions, though not necessarily with high precision. Existing methods either involve matrix…

This paper presents $\mathrm{E}(n)$ Equivariant Message Passing Simplicial Networks (EMPSNs), a novel approach to learning on geometric graphs and point clouds that is equivariant to rotations, translations, and reflections. EMPSNs can…

Accurate quantification of both aleatoric and epistemic uncertainties is essential when deploying Graph Neural Networks (GNNs) in high-stakes applications such as drug discovery and financial fraud detection, where reliable predictions are…

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,…

Accurate modelling and quantification of predictive uncertainty is crucial in deep learning since it allows a model to make safer decisions when the data is ambiguous and facilitates the users' understanding of the model's confidence in its…

Deep neural networks (NNs) are considered a powerful tool for balancing the performance and complexity of multiple-input multiple-output (MIMO) receivers due to their accurate feature extraction, high parallelism, and excellent inference…

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual…

Message-passing neural networks (MPNNs) are the leading architecture for deep learning on graph-structured data, in large part due to their simplicity and scalability. Unfortunately, it was shown that these architectures are limited in…

Molecular interactions often involve high-order relationships that cannot be fully captured by traditional graph-based models limited to pairwise connections. Hypergraphs naturally extend graphs by enabling multi-way interactions, making…

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and…

Recently, the study of graph neural network (GNN) has attracted much attention and achieved promising performance in molecular property prediction. Most GNNs for molecular property prediction are proposed based on the idea of learning the…

Equivariant Graph Neural Networks (EGNNs) have emerged as a promising approach in Multi-Agent Reinforcement Learning (MARL), leveraging symmetry guarantees to greatly improve sample efficiency and generalization. However, real-world…

Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…

Extracting informative representations of molecules using Graph neural networks (GNNs) is crucial in AI-driven drug discovery. Recently, the graph research community has been trying to replicate the success of self-supervised pretraining in…