Graph representation learning in biomedicine and healthcare

MM Li, K Huang, M Zitnik - Nature Biomedical Engineering, 2022 - nature.com
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

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 …

Deep learning in drug discovery: an integrative review and future challenges

H Askr, E Elgeldawi, H Aboul Ella… - Artificial Intelligence …, 2023 - Springer
Recently, using artificial intelligence (AI) in drug discovery has received much attention
since it significantly shortens the time and cost of develo** new drugs. Deep learning (DL) …

Machine learning for high-entropy alloys: Progress, challenges and opportunities

X Liu, J Zhang, Z Pei - Progress in Materials Science, 2023 - Elsevier
High-entropy alloys (HEAs) have attracted extensive interest due to their exceptional
mechanical properties and the vast compositional space for new HEAs. However …

Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models

D Jiang, Z Wu, CY Hsieh, G Chen, B Liao… - Journal of …, 2021 - Springer
Graph neural networks (GNN) has been considered as an attractive modelling method for
molecular property prediction, and numerous studies have shown that GNN could yield …

Graph neural networks and their current applications in bioinformatics

XM Zhang, L Liang, L Liu, MJ Tang - Frontiers in genetics, 2021 - frontiersin.org
Graph neural networks (GNNs), as a branch of deep learning in non-Euclidean space,
perform particularly well in various tasks that process graph structure data. With the rapid …

Interactiongraphnet: A novel and efficient deep graph representation learning framework for accurate protein–ligand interaction predictions

D Jiang, CY Hsieh, Z Wu, Y Kang, J Wang… - Journal of medicinal …, 2021 - ACS Publications
Accurate quantification of protein–ligand interactions remains a key challenge to structure-
based drug design. However, traditional machine learning (ML)-based methods based on …

[HTML][HTML] A review on machine learning approaches and trends in drug discovery

P Carracedo-Reboredo, J Liñares-Blanco… - Computational and …, 2021 - Elsevier
Drug discovery aims at finding new compounds with specific chemical properties for the
treatment of diseases. In the last years, the approach used in this search presents an …

GraphDTA: predicting drug–target binding affinity with graph neural networks

T Nguyen, H Le, TP Quinn, T Nguyen, TD Le… - …, 2021 - academic.oup.com
The development of new drugs is costly, time consuming and often accompanied with safety
issues. Drug repurposing can avoid the expensive and lengthy process of drug development …

Advances in de novo drug design: from conventional to machine learning methods

VD Mouchlis, A Afantitis, A Serra, M Fratello… - International journal of …, 2021 - mdpi.com
De novo drug design is a computational approach that generates novel molecular structures
from atomic building blocks with no a priori relationships. Conventional methods include …