Everything is connected: Graph neural networks

P Veličković - Current Opinion in Structural Biology, 2023 - Elsevier
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 …

Graph neural networks for materials science and chemistry

P Reiser, M Neubert, A Eberhard, L Torresi… - Communications …, 2022 - nature.com
Abstract Machine learning plays an increasingly important role in many areas of chemistry
and materials science, being used to predict materials properties, accelerate simulations …

Pure transformers are powerful graph learners

J Kim, D Nguyen, S Min, S Cho… - Advances in Neural …, 2022 - proceedings.neurips.cc
We show that standard Transformers without graph-specific modifications can lead to
promising results in graph learning both in theory and practice. Given a graph, we simply …

Graph inductive biases in transformers without message passing

L Ma, C Lin, D Lim, A Romero-Soriano… - International …, 2023 - proceedings.mlr.press
Transformers for graph data are increasingly widely studied and successful in numerous
learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous …

A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Equiformer: Equivariant graph attention transformer for 3d atomistic graphs

YL Liao, T Smidt - ar** molecular therapies require deciphering the
cell types in which proteins act as well as the interactions between proteins. However …

Superhypergraph neural networks and plithogenic graph neural networks: Theoretical foundations

T Fujita - arxiv preprint arxiv:2412.01176, 2024 - arxiv.org
Hypergraphs extend traditional graphs by allowing edges to connect multiple nodes, while
superhypergraphs further generalize this concept to represent even more complex …