Related papers: Boundary Graph Neural Networks for 3D Simulations

As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…

Graph are a ubiquitous data representation, as they represent a flexible and compact representation. For instance, the 3D structure of RNA can be efficiently represented as $\textit{2.5D graphs}$, graphs whose nodes are nucleotides and…

Accurately simulating physics is crucial across scientific domains, with applications spanning from robotics to materials science. While traditional mesh-based simulations are precise, they are often computationally expensive and require…

Graph Neural Networks (GNNs) are an emerging research field. This specialized Deep Neural Network (DNN) architecture is capable of processing graph structured data and bridges the gap between graph processing and Deep Learning (DL). As…

This paper studies the relationship between a graph neural network (GNN) and a manifold neural network (MNN) when the graph is constructed from a set of points sampled from the manifold, thus encoding geometric information. We consider…

Neural-symbolic computing has now become the subject of interest of both academic and industry research laboratories. Graph Neural Networks (GNN) have been widely used in relational and symbolic domains, with widespread application of GNNs…

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…

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…

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.…

Recent developments in Machine Learning approaches for modelling physical systems have begun to mirror the past development of numerical methods in the computational sciences. In this survey, we begin by providing an example of this with…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

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…

Porous media is widely distributed in nature, found in environments such as soil, rock formations, and plant tissues, and is crucial in applications like subsurface oil and gas extraction, medical drug delivery, and filtration systems.…

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…

Recent advancements in graph learning have revolutionized the way to understand and analyze data with complex structures. Notably, Graph Neural Networks (GNNs), i.e. neural network architectures designed for learning graph representations,…

Many interesting datasets ubiquitous in machine learning and deep learning can be described via graphs. As the scale and complexity of graph-structured datasets increase, such as in expansive social networks, protein folding, chemical…

Graph Neural Networks (GNNs) are a promising deep learning approach for circumventing many real-world problems on graph-structured data. However, these models usually have at least one of four fundamental limitations: over-smoothing,…

Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this…

Surface meshes are widely used shape representations and capture finer geometry data than point clouds or volumetric grids, but are challenging to apply CNNs directly due to their non-Euclidean structure. We use parallel frames on surface…

Networks are a powerful tool to model complex systems, and the definition of many Graph Neural Networks (GNN), Deep Learning algorithms that can handle networks, has opened a new way to approach many real-world problems that would be hardly…