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 …

Multimodal learning with graphs

Y Ektefaie, G Dasoulas, A Noori, M Farhat… - Nature Machine …, 2023 - nature.com
Artificial intelligence for graphs has achieved remarkable success in modelling complex
systems, ranging from dynamic networks in biology to interacting particle systems in physics …

Recipe for a general, powerful, scalable graph transformer

L Rampášek, M Galkin, VP Dwivedi… - Advances in …, 2022 - proceedings.neurips.cc
We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer
with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph …

Do transformers really perform badly for graph representation?

C Ying, T Cai, S Luo, S Zheng, G Ke… - Advances in neural …, 2021 - proceedings.neurips.cc
The Transformer architecture has become a dominant choice in many domains, such as
natural language processing and computer vision. Yet, it has not achieved competitive …

Diffdock: Diffusion steps, twists, and turns for molecular docking

G Corso, H Stärk, B **g, R Barzilay… - arxiv preprint arxiv …, 2022 - arxiv.org
Predicting the binding structure of a small molecule ligand to a protein--a task known as
molecular docking--is critical to drug design. Recent deep learning methods that treat …

Rethinking graph transformers with spectral attention

D Kreuzer, D Beaini, W Hamilton… - Advances in …, 2021 - proceedings.neurips.cc
In recent years, the Transformer architecture has proven to be very successful in sequence
processing, but its application to other data structures, such as graphs, has remained limited …

Structure-aware transformer for graph representation learning

D Chen, L O'Bray, K Borgwardt - … Conference on Machine …, 2022 - proceedings.mlr.press
The Transformer architecture has gained growing attention in graph representation learning
recently, as it naturally overcomes several limitations of graph neural networks (GNNs) by …

Benchmarking graph neural networks

VP Dwivedi, CK Joshi, AT Luu, T Laurent… - Journal of Machine …, 2023 - jmlr.org
In the last few years, graph neural networks (GNNs) have become the standard toolkit for
analyzing and learning from data on graphs. This emerging field has witnessed an extensive …

Representing long-range context for graph neural networks with global attention

Z Wu, P Jain, M Wright, A Mirhoseini… - Advances in …, 2021 - proceedings.neurips.cc
Graph neural networks are powerful architectures for structured datasets. However, current
methods struggle to represent long-range dependencies. Scaling the depth or width of …

Combinatorial optimization and reasoning with graph neural networks

Q Cappart, D Chételat, EB Khalil, A Lodi… - Journal of Machine …, 2023 - jmlr.org
Combinatorial optimization is a well-established area in operations research and computer
science. Until recently, its methods have focused on solving problem instances in isolation …