[HTML][HTML] Uncertainty quantification: Can we trust artificial intelligence in drug discovery?

J Yu, D Wang, M Zheng - Iscience, 2022 - cell.com
The problem of human trust is one of the most fundamental problems in applied artificial
intelligence in drug discovery. In silico models have been widely used to accelerate the …

[HTML][HTML] DeepDelta: predicting ADMET improvements of molecular derivatives with deep learning

Z Fralish, A Chen, P Skaluba, D Reker - Journal of Cheminformatics, 2023 - Springer
Established molecular machine learning models process individual molecules as inputs to
predict their biological, chemical, or physical properties. However, such algorithms require …

[HTML][HTML] Deep ensembles vs committees for uncertainty estimation in neural-network force fields: Comparison and application to active learning

J Carrete, H Montes-Campos, R Wanzenböck… - The Journal of …, 2023 - pubs.aip.org
ABSTRACT A reliable uncertainty estimator is a key ingredient in the successful use of
machine-learning force fields for predictive calculations. Important considerations are …

Datasets, tasks, and training methods for large-scale hypergraph learning

S Kim, D Lee, Y Kim, J Park, T Hwang… - Data Mining and …, 2023 - Springer
Relations among multiple entities are prevalent in many fields, and hypergraphs are widely
used to represent such group relations. Hence, machine learning on hypergraphs has …

[HTML][HTML] Uncertain of uncertainties? A comparison of uncertainty quantification metrics for chemical data sets

MH Rasmussen, C Duan, HJ Kulik… - Journal of Cheminformatics, 2023 - Springer
With the increasingly more important role of machine learning (ML) models in chemical
research, the need for putting a level of confidence to the model predictions naturally arises …

[HTML][HTML] Computing the relative binding affinity of ligands based on a pairwise binding comparison network

J Yu, Z Li, G Chen, X Kong, J Hu, D Wang… - Nature Computational …, 2023 - nature.com
Abstract Structure-based lead optimization is an open challenge in drug discovery, which is
still largely driven by hypotheses and depends on the experience of medicinal chemists …

Benchmark of general-purpose machine learning-based quantum mechanical method AIQM1 on reaction barrier heights

Y Chen, Y Ou, P Zheng, Y Huang, F Ge… - The Journal of Chemical …, 2023 - pubs.aip.org
Artificial intelligence-enhanced quantum mechanical method 1 (AIQM1) is a general-
purpose method that was shown to achieve high accuracy for many applications with a …

A bioactivity foundation model using pairwise meta-learning

B Feng, Z Liu, N Huang, Z Xiao, H Zhang… - Nature Machine …, 2024 - nature.com
The bioactivity of compounds plays an important role in drug development and discovery.
Existing machine learning approaches have poor generalizability in bioactivity prediction …

Prediction uncertainty validation for computational chemists

P Pernot - The Journal of Chemical Physics, 2022 - pubs.aip.org
Validation of prediction uncertainty (PU) is becoming an essential task for modern
computational chemistry. Designed to quantify the reliability of predictions in meteorology …

Physicochemical Responsive Integrated Similarity Measure (PRISM) for a Comprehensive Quantitative Perspective of Sample Similarity Dynamically Assessed with …

RC Spiers, C Norby, JH Kalivas - Analytical Chemistry, 2023 - ACS Publications
Determining sample similarity underlies many foundational principles in analytical
chemistry. For example, calibration models are unsuitable to predict outliers. Calibration …