[HTML][HTML] Graph neural networks: A review of methods and applications

J Zhou, G Cui, S Hu, Z Zhang, C Yang, Z Liu, L Wang… - AI open, 2020 - Elsevier
Lots of learning tasks require dealing with graph data which contains rich relation
information among elements. Modeling physics systems, learning molecular fingerprints …

E (n) equivariant graph neural networks

VG Satorras, E Hoogeboom… - … conference on machine …, 2021 - proceedings.mlr.press
This paper introduces a new model to learn graph neural networks equivariant to rotations,
translations, reflections and permutations called E (n)-Equivariant Graph Neural Networks …

A review on the recent applications of deep learning in predictive drug toxicological studies

K Sinha, N Ghosh, PC Sil - Chemical Research in Toxicology, 2023 - ACS Publications
Drug toxicity prediction is an important step in ensuring patient safety during drug design
studies. While traditional preclinical studies have historically relied on animal models to …

Training graph neural networks with 1000 layers

G Li, M Müller, B Ghanem… - … conference on machine …, 2021 - proceedings.mlr.press
Deep graph neural networks (GNNs) have achieved excellent results on various tasks on
increasingly large graph datasets with millions of nodes and edges. However, memory …

Graphaf: a flow-based autoregressive model for molecular graph generation

C Shi, M Xu, Z Zhu, W Zhang, M Zhang… - arxiv preprint arxiv …, 2020 - arxiv.org
Molecular graph generation is a fundamental problem for drug discovery and has been
attracting growing attention. The problem is challenging since it requires not only generating …

On the binding problem in artificial neural networks

K Greff, S Van Steenkiste, J Schmidhuber - arxiv preprint arxiv …, 2020 - arxiv.org
Contemporary neural networks still fall short of human-level generalization, which extends
far beyond our direct experiences. In this paper, we argue that the underlying cause for this …

Graph neural ordinary differential equations

M Poli, S Massaroli, J Park, A Yamashita… - arxiv preprint arxiv …, 2019 - arxiv.org
We introduce the framework of continuous--depth graph neural networks (GNNs). Graph
neural ordinary differential equations (GDEs) are formalized as the counterpart to GNNs …

E (n) equivariant normalizing flows

V Garcia Satorras, E Hoogeboom… - Advances in …, 2021 - proceedings.neurips.cc
This paper introduces a generative model equivariant to Euclidean symmetries: E (n)
Equivariant Normalizing Flows (E-NFs). To construct E-NFs, we take the discriminative E (n) …

Graphdf: A discrete flow model for molecular graph generation

Y Luo, K Yan, S Ji - International conference on machine …, 2021 - proceedings.mlr.press
We consider the problem of molecular graph generation using deep models. While graphs
are discrete, most existing methods use continuous latent variables, resulting in inaccurate …

Moflow: an invertible flow model for generating molecular graphs

C Zang, F Wang - Proceedings of the 26th ACM SIGKDD international …, 2020 - dl.acm.org
Generating molecular graphs with desired chemical properties driven by deep graph
generative models provides a very promising way to accelerate drug discovery process …