Related papers: GraphiT: Encoding Graph Structure in Transformers

There has been a surge of recent interest in learning representations for graph-structured data. Graph representation learning methods have generally fallen into three main categories, based on the availability of labeled data. The first,…

The (variational) graph auto-encoder and its variants have been popularly used for representation learning on graph-structured data. While the encoder is often a powerful graph convolutional network, the decoder reconstructs the graph…

Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder…

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…

This work focuses on training graph foundation models (GFMs) that have strong generalization ability in graph-level tasks such as graph classification. Effective GFM training requires capturing information consistent across different…

In many ways, graphs are the main modality of data we receive from nature. This is due to the fact that most of the patterns we see, both in natural and artificial systems, are elegantly representable using the language of graph structures.…

Graph Neural Networks (GNNs) have gained momentum in graph representation learning and boosted the state of the art in a variety of areas, such as data mining (\emph{e.g.,} social network analysis and recommender systems), computer vision…

Graph neural networks (GNNs) are designed to extract latent patterns from graph-structured data, making them particularly well suited for crystal representation learning. Here, we propose a GNN model tailored for estimating electronic…

Graph neural networks are deep neural networks designed for graphs with attributes attached to nodes or edges. The number of research papers in the literature concerning these models is growing rapidly due to their impressive performance on…

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns,…

The inference of gene regulatory networks (GRNs) is a foundational stride towards deciphering the fundamentals of complex biological systems. Inferring a possible regulatory link between two genes can be formulated as a link prediction…

Today we have a good theoretical understanding of the representational power of Graph Neural Networks (GNNs). For example, their limitations have been characterized in relation to a hierarchy of Weisfeiler-Lehman (WL) isomorphism tests.…

We introduce Quantum Graph Attention Networks (QGATs) as trainable quantum encoders for inductive learning on graphs, extending the Quantum Graph Neural Networks (QGNN) framework. QGATs leverage parameterized quantum circuits to encode node…

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize…

Graph link prediction has long been a central problem in graph representation learning in both network analysis and generative modeling. Recent progress in deep learning has introduced increasingly sophisticated architectures for capturing…

Graph Neural Networks (GNNs) are widely used in graph data mining tasks. Traditional GNNs follow a message passing scheme that can effectively utilize local and structural information. However, the phenomena of over-smoothing and…

Most Graph Neural Networks (GNNs) cannot distinguish some graphs or indeed some pairs of nodes within a graph. This makes it impossible to solve certain classification tasks. However, adding additional node features to these models can…

Graph machine learning, particularly using graph neural networks, heavily relies on node features. However, many real-world systems, such as social and biological networks, lack node features due to privacy concerns, incomplete data, or…

Graph Neural Networks (GNNs) are a powerful representational tool for solving problems on graph-structured inputs. In almost all cases so far, however, they have been applied to directly recovering a final solution from raw inputs, without…

Transformers have achieved remarkable success in time series modeling, yet their internal mechanisms remain opaque. This work demystifies the Transformer encoder by establishing its fundamental equivalence to a Graph Convolutional Network…