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Diffusion generative models have emerged as a powerful framework for addressing problems in structural biology and structure-based drug design. These models operate directly on 3D molecular structures. Due to the unfavorable scaling of…

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…

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating…

Given graphs as input, Graph Neural Networks (GNNs) support the inference of nodes, edges, attributes, or graph properties. Graph Rewriting investigates the rule-based manipulation of graphs to model complex graph transformations. We…

Graph data, with its structurally variable nature, represents complex real-world phenomena like chemical compounds, protein structures, and social networks. Traditional Graph Neural Networks (GNNs) primarily utilize the message-passing…

Subgraph GNNs enhance message-passing GNNs expressivity by representing graphs as sets of subgraphs, demonstrating impressive performance across various tasks. However, their scalability is hindered by the need to process large numbers of…

This study analyzes Graph Neural Networks (GNNs) for distribution system state estimation (DSSE) by employing an interpretable Graph Neural Additive Network (GNAN) and by utilizing an edge-conditioned message-passing mechanism. The…

Subgraph GNNs are a recent class of expressive Graph Neural Networks (GNNs) which model graphs as collections of subgraphs. So far, the design space of possible Subgraph GNN architectures as well as their basic theoretical properties are…

Graph Neural Networks (GNNs) are routinely used in molecular physics, social sciences, and economics to model many-body interactions in graph-like systems. However, GNNs are inherently local and can suffer from information flow bottlenecks.…

Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…

Graph Neural Networks (GNNs) have emerged as the leading paradigm for solving graph analytical problems in various real-world applications. Nevertheless, GNNs could potentially render biased predictions towards certain demographic…

We consider the explanation problem of Graph Neural Networks (GNNs). Most existing GNN explanation methods identify the most important edges or nodes but fail to consider substructures, which are more important for graph data. The only…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Graph Neural Networks (GNNs) have become increasingly ubiquitous in numerous applications and systems, necessitating explanations of their predictions, especially when making critical decisions. However, explaining GNNs is challenging due…

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…

Graph Neural Networks (GNNs) have achieved remarkable performance in a wide range of graph-related learning tasks. However, explaining their predictions remains a challenging problem, especially due to the mismatch between the graphs used…

Graph-based neural network models are gaining traction in the field of representation learning due to their ability to uncover latent topological relationships between entities that are otherwise challenging to identify. These models have…

Modeling molecular potential energy surface is of pivotal importance in science. Graph Neural Networks have shown great success in this field. However, their message passing schemes need special designs to capture geometric information and…

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this…

The geometry of three-dimensional (3D) graphs, consisting of nodes and edges, plays a crucial role in many important applications. An excellent example is molecular graphs, whose geometry influences important properties of a molecule…