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Deep learning (DL) has been widely investigated in a vast majority of applications in electroencephalography (EEG)-based brain-computer interfaces (BCIs), especially for motor imagery (MI) classification in the past five years. The…

A graph is a powerful concept for representation of relations between pairs of entities. Data with underlying graph structure can be found across many disciplines and there is a natural desire for understanding such data better. Deep…

Here, we develop a framework for the prediction and screening of native defects and functional impurities in a chemical space of Group IV, III-V, and II-VI zinc blende (ZB) semiconductors, powered by crystal Graph-based Neural Networks…

Electron density $\rho(\vec{r})$ is the fundamental variable in the calculation of ground state energy with density functional theory (DFT). Beyond total energy, features and changes in $\rho(\vec{r})$ distributions are often used to…

Graph Convolutional Neural Network (GCNN) is a popular class of deep learning (DL) models in material science to predict material properties from the graph representation of molecular structures. Training an accurate and comprehensive GCNN…

Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…

Explainable Graph Neural Networks (GNNs) have been developed and applied to drug-protein binding prediction to identify the key chemical structures in a drug that have active interactions with the target proteins. However, the key…

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these…

Modern laboratory techniques like ultrafast laser excitation and shock compression can bring matter into highly nonequilibrium states with complex structural transformation, metallization and dissociation dynamics. To understand and model…

We address the efficiency issue for the construction of a deep graph neural network (GNN). The approach exploits the idea of representing each input graph as a fixed point of a dynamical system (implemented through a recurrent neural…

Graph neural networks are attractive for learning properties of atomic structures thanks to their intuitive graph encoding of atoms and bonds. However, conventional encoding does not include angular information, which is critical for…

Equivariant graph neural networks force fields (EGraFFs) have shown great promise in modelling complex interactions in atomic systems by exploiting the graphs' inherent symmetries. Recent works have led to a surge in the development of…

Electrocardiogram (ECG) detection and delineation are key steps for numerous tasks in clinical practice, as ECG is the most performed non-invasive test for assessing cardiac condition. State-of-the-art algorithms employ digital signal…

Atom segmentation and localization, noise reduction and deblurring of atomic-resolution scanning transmission electron microscopy (STEM) images with high precision and robustness is a challenging task. Although several conventional…

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…

Radio-Frequency (RF) imaging concerns the digital recreation of the surfaces of scene objects based on the scattered field at distributed receivers. To solve this difficult inverse scattering problems, data-driven methods are often employed…

Graph neural networks (GNN) are very popular methods in machine learning and have been applied very successfully to the prediction of the properties of molecules and materials. First-order GNNs are well known to be incomplete, i.e., there…

Incorporating Euclidean symmetries (e.g. rotation equivariance) as inductive biases into graph neural networks has improved their generalization ability and data efficiency in unbounded physical dynamics modeling. However, in various…

In the past decades, many graph drawing techniques have been proposed for generating aesthetically pleasing graph layouts. However, it remains a challenging task since different layout methods tend to highlight different characteristics of…

Pre-trained models have been successful in many protein engineering tasks. Most notably, sequence-based models have achieved state-of-the-art performance on protein fitness prediction while structure-based models have been used…