Related papers: CIN++: Enhancing Topological Message Passing

The irreducible complexity of natural phenomena has led Graph Neural Networks to be employed as a standard model to perform representation learning tasks on graph-structured data. While their capacity to capture local and global patterns is…

We present a hierarchical neural message passing architecture for learning on molecular graphs. Our model takes in two complementary graph representations: the raw molecular graph representation and its associated junction tree, where nodes…

Graph Neural Networks (GNNs) have become a prominent approach to machine learning with graphs and have been increasingly applied in a multitude of domains. Nevertheless, since most existing GNN models are based on flat message-passing…

The standard cosmological model with cold dark matter posits a hierarchical formation of structures. We introduce topological neural networks (TNNs), implemented as message-passing neural networks on higher-order structures, to effectively…

Subgraph isomorphism counting is an important problem on graphs, as many graph-based tasks exploit recurring subgraph patterns. Classical methods usually boil down to a backtracking framework that needs to navigate a huge search space with…

The mechanism of message passing in graph neural networks (GNNs) is still mysterious. Apart from convolutional neural networks, no theoretical origin for GNNs has been proposed. To our surprise, message passing can be best understood in…

Graph Neural Networks (GNNs) are limited in their expressive power, struggle with long-range interactions and lack a principled way to model higher-order structures. These problems can be attributed to the strong coupling between the…

The message passing framework is the foundation of the immense success enjoyed by graph neural networks (GNNs) in recent years. In spite of its elegance, there exist many problems it provably cannot solve over given input graphs. This has…

Recent studies have highlighted the limitations of message-passing based graph neural networks (GNNs), e.g., limited model expressiveness, over-smoothing, over-squashing, etc. To alleviate these issues, Graph Transformers (GTs) have been…

Graph Neural Networks (GNNs) are key tools for graph representation learning, demonstrating strong results across diverse prediction tasks. In this paper, we present Convexified Message-Passing Graph Neural Networks (CGNNs), a novel and…

Message passing neural networks (MPNNs) learn the representation of graph-structured data based on graph original information, including node features and graph structures, and have shown astonishing improvement in node classification…

Message passing has evolved as an effective tool for designing Graph Neural Networks (GNNs). However, most existing methods for message passing simply sum or average all the neighboring features to update node representations. They are…

Graph Neural Networks (GNNs) have become essential in high-stakes domains such as drug discovery, yet their black-box nature remains a significant barrier to trustworthiness. While self-explainable GNNs attempt to bridge this gap, they…

Graph neural networks (GNNs) based on message passing between neighboring nodes are known to be insufficient for capturing long-range interactions in graphs. In this project we study hierarchical message passing models that leverage a…

Graph Neural Networks (GNNs) have demonstrated strong performance in graph mining tasks due to their message-passing mechanism, which is aligned with the homophily assumption that adjacent nodes exhibit similar behaviors. However, in many…

Graph neural networks (GNNs) have achieved state-of-the-art performance in graph representation learning. Message passing neural networks, which learn representations through recursively aggregating information from each node and its…

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…

Glycans are the most complex biological sequence, with monosaccharides forming extended, non-linear sequences. As post-translational modifications, they modulate protein structure, function, and interactions. Due to their diversity and…

Graph-based data present unique challenges and opportunities for machine learning. Graph Neural Networks (GNNs), and especially those algorithms that capture graph topology through message passing for neighborhood aggregation, have been a…

Graph neural networks (GNNs) have drawn increasing attention in recent years and achieved remarkable performance in many graph-based tasks, especially in semi-supervised learning on graphs. However, most existing GNNs are based on the…