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Rapid advancements in machine learning (ML) are transforming materials science by significantly speeding up material property calculations. However, the proliferation of ML approaches has made it challenging for scientists to keep up with…

Geometric Graph Neural Networks (GNNs) and Transformers have become state-of-the-art for learning from 3D protein structures. However, their reliance on message passing prevents them from capturing the hierarchical interactions that govern…

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections,…

Many scientific problems require to process data in the form of geometric graphs. Unlike generic graph data, geometric graphs exhibit symmetries of translations, rotations, and/or reflections. Researchers have leveraged such inductive bias…

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

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…

The field of geometric deep learning has had a profound impact on the development of innovative and powerful graph neural network architectures. Disciplines such as computer vision and computational biology have benefited significantly from…

Graph neural networks (GNNs), which are capable of learning representations from graphical data, are naturally suitable for modeling molecular systems. This review introduces GNNs and their various applications for small organic molecules.…

Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material discovery. For these…

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new…

Constructing transferable descriptors for conformation representation of molecular and biological systems finds numerous applications in drug discovery, learning-based molecular dynamics, and protein mechanism analysis. Geometric graph…

Ground-state 3D geometries of molecules are essential for many molecular analysis tasks. Modern quantum mechanical methods can compute accurate 3D geometries but are computationally prohibitive. Currently, an efficient alternative to…

Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that…

We apply a temporal edge prediction model for weighted dynamic graphs to predict time-dependent changes in molecular structure. Each molecule is represented as a complete graph in which each atom is a vertex and all vertex pairs are…

Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive…

Effectively predicting molecular interactions has the potential to accelerate molecular dynamics by multiple orders of magnitude and thus revolutionize chemical simulations. Graph neural networks (GNNs) have recently shown great successes…

The fundamental laws of physics are intrinsically geometric, dictating the evolution of systems through principles of symmetry and conservation. While modern machine learning offers powerful tools for modeling complex dynamics from data,…

Graph Neural Networks (GNN) can capture the geometric properties of neural representations in EEG data. Here we utilise those to study how reinforcement-based motor learning affects neural activity patterns during motor planning, leveraging…

Graphs as a type of data structure have recently attracted significant attention. Representation learning of geometric graphs has achieved great success in many fields including molecular, social, and financial networks. It is natural to…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…