Learning Over Molecular Conformer Ensembles: Datasets and Benchmarks

Y Zhu, J Hwang, K Adams, Z Liu, B Nan… - The Twelfth …, 2023 - openreview.net
Molecular Representation Learning (MRL) has proven impactful in numerous biochemical
applications such as drug discovery and enzyme design. While Graph Neural Networks …

Graph-based molecular representation learning

Z Guo, K Guo, B Nan, Y Tian, RG Iyer, Y Ma… - arXiv preprint arXiv …, 2022 - arxiv.org
Molecular representation learning (MRL) is a key step to build the connection between
machine learning and chemical science. In particular, it encodes molecules as numerical …

Molecular machine learning with conformer ensembles

S Axelrod, R Gomez-Bombarelli - Machine Learning: Science …, 2023 - iopscience.iop.org
Virtual screening can accelerate drug discovery by identifying promising candidates for
experimental evaluation. Machine learning is a powerful method for screening, as it can …

Molecular contrastive learning of representations via graph neural networks

Y Wang, J Wang, Z Cao… - Nature Machine …, 2022 - nature.com
Molecular machine learning bears promise for efficient molecular property prediction and
drug discovery. However, labelled molecule data can be expensive and time consuming to …

Molcpt: Molecule continuous prompt tuning to generalize molecular representation learning

C Diao, K Zhou, Z Liu, X Huang, X Hu - arXiv preprint arXiv:2212.10614, 2022 - arxiv.org
Molecular representation learning is crucial for the problem of molecular property prediction,
where graph neural networks (GNNs) serve as an effective solution due to their structure …

Smiclr: Contrastive learning on multiple molecular representations for semisupervised and unsupervised representation learning

GA Pinheiro, JLF Da Silva… - Journal of Chemical …, 2022 - ACS Publications
Machine learning as a tool for chemical space exploration broadens horizons to work with
known and unknown molecules. At its core lies molecular representation, an essential key to …

[HTML][HTML] Geometry-enhanced molecular representation learning for property prediction

X Fang, L Liu, J Lei, D He, S Zhang, J Zhou… - Nature Machine …, 2022 - nature.com
Effective molecular representation learning is of great importance to facilitate molecular
property prediction. Recent advances for molecular representation learning have shown …

A focus on molecular representation learning for the prediction of chemical properties

Y Harnik, A Milo - Chemical Science, 2024 - pubs.rsc.org
Molecular representation learning (MRL) is a specialized field in which deep-learning
models condense essential molecular information into a vectorized form. Whereas recent …

A Multi-view Molecular Pre-training with Generative Contrastive Learning

Y Liu, R Zhang, J Ma, T Li, Z Yu - … Sciences: Computational Life …, 2024 - Springer
Molecular representation learning can preserve meaningful molecular structures as
embedding vectors, which is a necessary prerequisite for molecular property prediction. Yet …

A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning

A Atsango, NL Diamant, Z Lu, T Biancalani… - arXiv preprint arXiv …, 2022 - arxiv.org
Molecular shape and geometry dictate key biophysical recognition processes, yet many
graph neural networks disregard 3D information for molecular property prediction. Here, we …