Machine learning methods for small data challenges in molecular science

B Dou, Z Zhu, E Merkurjev, L Ke, L Chen… - Chemical …, 2023 - ACS Publications
Small data are often used in scientific and engineering research due to the presence of
various constraints, such as time, cost, ethics, privacy, security, and technical limitations in …

Hit and lead discovery with explorative rl and fragment-based molecule generation

S Yang, D Hwang, S Lee, S Ryu… - Advances in Neural …, 2021 - proceedings.neurips.cc
Recently, utilizing reinforcement learning (RL) to generate molecules with desired properties
has been highlighted as a promising strategy for drug design. Molecular docking program--a …

Characterizing uncertainty in machine learning for chemistry

E Heid, CJ McGill, FH Vermeire… - Journal of Chemical …, 2023 - ACS Publications
Characterizing uncertainty in machine learning models has recently gained interest in the
context of machine learning reliability, robustness, safety, and active learning. Here, we …

HiGNN: A hierarchical informative graph neural network for molecular property prediction equipped with feature-wise attention

W Zhu, Y Zhang, D Zhao, J Xu… - Journal of Chemical …, 2022 - ACS Publications
Elucidating and accurately predicting the druggability and bioactivities of molecules plays a
pivotal role in drug design and discovery and remains an open challenge. Recently, graph …

Augmentations in graph contrastive learning: Current methodological flaws & towards better practices

P Trivedi, ES Lubana, Y Yan, Y Yang… - Proceedings of the ACM …, 2022 - dl.acm.org
Graph classification has a wide range of applications in bioinformatics, social sciences,
automated fake news detection, web document classification, and more. In many practical …

[HTML][HTML] Calibration and generalizability of probabilistic models on low-data chemical datasets with DIONYSUS

G Tom, RJ Hickman, A Zinzuwadia, A Mohajeri… - Digital …, 2023 - pubs.rsc.org
Deep learning models that leverage large datasets are often the state of the art for modelling
molecular properties. When the datasets are smaller (< 2000 molecules), it is not clear that …

[HTML][HTML] Large-scale evaluation of k-fold cross-validation ensembles for uncertainty estimation

TM Dutschmann, L Kinzel, A Ter Laak… - Journal of …, 2023 - Springer
It is insightful to report an estimator that describes how certain a model is in a prediction,
additionally to the prediction alone. For regression tasks, most approaches implement a …

Comprehensible artificial intelligence on knowledge graphs: A survey

S Schramm, C Wehner, U Schmid - Journal of Web Semantics, 2023 - Elsevier
Artificial Intelligence applications gradually move outside the safe walls of research labs and
invade our daily lives. This is also true for Machine Learning methods on Knowledge …

[HTML][HTML] DeepReac+: deep active learning for quantitative modeling of organic chemical reactions

Y Gong, D Xue, G Chuai, J Yu, Q Liu - Chemical Science, 2021 - pubs.rsc.org
Various computational methods have been developed for quantitative modeling of organic
chemical reactions; however, the lack of universality as well as the requirement of large …

[HTML][HTML] Drug-likeness scoring based on unsupervised learning

K Lee, J Jang, S Seo, J Lim, WY Kim - Chemical Science, 2022 - pubs.rsc.org
Drug-likeness prediction is important for the virtual screening of drug candidates. It is
challenging because the drug-likeness is presumably associated with the whole set of …