[HTML][HTML] MoleculeNet: a benchmark for molecular machine learning

Z Wu, B Ramsundar, EN Feinberg, J Gomes… - Chemical …, 2018 - pubs.rsc.org
Molecular machine learning has been maturing rapidly over the last few years. Improved
methods and the presence of larger datasets have enabled machine learning algorithms to …

A systematic survey of chemical pre-trained models

J Xia, Y Zhu, Y Du, SZ Li - arXiv preprint arXiv:2210.16484, 2022 - arxiv.org
Deep learning has achieved remarkable success in learning representations for molecules,
which is crucial for various biochemical applications, ranging from property prediction to …

[HTML][HTML] Retrospective on a decade of machine learning for chemical discovery

OA von Lilienfeld, K Burke - Nature communications, 2020 - nature.com
Standfirst Over the last decade, we have witnessed the emergence of ever more machine
learning applications in all aspects of the chemical sciences. Here, we highlight specific …

ChemBERTa: large-scale self-supervised pretraining for molecular property prediction

S Chithrananda, G Grand, B Ramsundar - arXiv preprint arXiv:2010.09885, 2020 - arxiv.org
GNNs and chemical fingerprints are the predominant approaches to representing molecules
for property prediction. However, in NLP, transformers have become the de-facto standard …

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 …

Graseq: graph and sequence fusion learning for molecular property prediction

Z Guo, W Yu, C Zhang, M Jiang… - Proceedings of the 29th …, 2020 - dl.acm.org
With the recent advancement of deep learning, molecular representation learning--
automating the discovery of feature representation of molecular structure, has attracted …

Understanding the limitations of deep models for molecular property prediction: Insights and solutions

J Xia, L Zhang, X Zhu, Y Liu, Z Gao… - Advances in …, 2024 - proceedings.neurips.cc
Abstract Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug
Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to …

Chemical-reaction-aware molecule representation learning

H Wang, W Li, X Jin, K Cho, H Ji, J Han… - arXiv preprint arXiv …, 2021 - arxiv.org
Molecule representation learning (MRL) methods aim to embed molecules into a real vector
space. However, existing SMILES-based (Simplified Molecular-Input Line-Entry System) or …

A review of molecular representation in the age of machine learning

DS Wigh, JM Goodman… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Research in chemistry increasingly requires interdisciplinary work prompted by, among
other things, advances in computing, machine learning, and artificial intelligence. Everyone …

[HTML][HTML] Learning continuous and data-driven molecular descriptors by translating equivalent chemical representations

R Winter, F Montanari, F Noé, DA Clevert - Chemical science, 2019 - pubs.rsc.org
There has been a recent surge of interest in using machine learning across chemical space
in order to predict properties of molecules or design molecules and materials with the …