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 …

AI in drug discovery and its clinical relevance

R Qureshi, M Irfan, TM Gondal, S Khan, J Wu, MU Hadi… - Heliyon, 2023 - cell.com
The COVID-19 pandemic has emphasized the need for novel drug discovery process.
However, the journey from conceptualizing a drug to its eventual implementation in clinical …

A systematic study of key elements underlying molecular property prediction

J Deng, Z Yang, H Wang, I Ojima, D Samaras… - Nature …, 2023 - nature.com
Artificial intelligence (AI) has been widely applied in drug discovery with a major task as
molecular property prediction. Despite booming techniques in molecular representation …

Artificial intelligence for drug discovery: are we there yet?

C Hasselgren, TI Oprea - Annual Review of Pharmacology and …, 2024 - annualreviews.org
Drug discovery is adapting to novel technologies such as data science, informatics, and
artificial intelligence (AI) to accelerate effective treatment development while reducing costs …

Pre-training molecular graph representation with 3d geometry

S Liu, H Wang, W Liu, J Lasenby, H Guo… - arxiv preprint arxiv …, 2021 - arxiv.org
Molecular graph representation learning is a fundamental problem in modern drug and
material discovery. Molecular graphs are typically modeled by their 2D topological …

Exposing the limitations of molecular machine learning with activity cliffs

D Van Tilborg, A Alenicheva… - Journal of chemical …, 2022 - ACS Publications
Machine learning has become a crucial tool in drug discovery and chemistry at large, eg, to
predict molecular properties, such as bioactivity, with high accuracy. However, activity …

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 …

Hopfield networks is all you need

H Ramsauer, B Schäfl, J Lehner, P Seidl… - arxiv preprint arxiv …, 2020 - arxiv.org
We introduce a modern Hopfield network with continuous states and a corresponding
update rule. The new Hopfield network can store exponentially (with the dimension of the …

A knowledge-guided pre-training framework for improving molecular representation learning

H Li, R Zhang, Y Min, D Ma, D Zhao, J Zeng - Nature Communications, 2023 - nature.com
Learning effective molecular feature representation to facilitate molecular property prediction
is of great significance for drug discovery. Recently, there has been a surge of interest in pre …