Exposing the limitations of molecular machine learning with activity cliffs

D van Tilborg, A Alenicheva… - Journal of chemical …, 2022 - ACS Publications
Machine learning has become a crucial tool in drug discovery and chemistry at large, eg, to
predict molecular properties, such as bioactivity, with high accuracy. However, activity …

Explainability and white box in drug discovery

KK Kırboğa, S Abbasi… - Chemical Biology & Drug …, 2023 - Wiley Online Library
Recently, artificial intelligence (AI) techniques have been increasingly used to overcome the
challenges in drug discovery. Although traditional AI techniques generally have high …

Explainable artificial intelligence: A taxonomy and guidelines for its application to drug discovery

I Ponzoni, JA Páez Prosper… - Wiley Interdisciplinary …, 2023 - Wiley Online Library
Artificial intelligence (AI) is having a growing impact in many areas related to drug discovery.
However, it is still critical for their adoption by the medicinal chemistry community to achieve …

Integrating explainability into graph neural network models for the prediction of X-ray absorption spectra

A Kotobi, K Singh, D Höche, S Bari… - Journal of the …, 2023 - ACS Publications
The use of sophisticated machine learning (ML) models, such as graph neural networks
(GNNs), to predict complex molecular properties or all kinds of spectra has grown rapidly …

[HTML][HTML] Machine learning for small molecule drug discovery in academia and industry

A Volkamer, S Riniker, E Nittinger, J Lanini… - Artificial Intelligence in …, 2023 - Elsevier
Academic and pharmaceutical industry research are both key for progresses in the field of
molecular machine learning. Despite common open research questions and long-term …

[PDF][PDF] Quantitative evaluation of explainable graph neural networks for molecular property prediction

J Rao, S Zheng, Y Lu, Y Yang - Patterns, 2022 - cell.com
Graph neural networks (GNNs) have received increasing attention because of their
expressive power on topological data, but they are still criticized for their lack of …

[PDF][PDF] EdgeSHAPer: Bond-centric Shapley value-based explanation method for graph neural networks

A Mastropietro, G Pasculli, C Feldmann… - Iscience, 2022 - cell.com
Graph neural networks (GNNs) recursively propagate signals along the edges of an input
graph, integrate node feature information with graph structure, and learn object …

[HTML][HTML] Large-scale prediction of activity cliffs using machine and deep learning methods of increasing complexity

S Tamura, T Miyao, J Bajorath - Journal of Cheminformatics, 2023 - Springer
Activity cliffs (AC) are formed by pairs of structural analogues that are active against the
same target but have a large difference in potency. While much of our knowledge about ACs …

[HTML][HTML] DeepAC–conditional transformer-based chemical language model for the prediction of activity cliffs formed by bioactive compounds

H Chen, M Vogt, J Bajorath - Digital Discovery, 2022 - pubs.rsc.org
Activity cliffs (ACs) are formed by pairs of structurally similar or analogous active small
molecules with large differences in potency. In medicinal chemistry, ACs are of high interest …

Unlocking the potential of generative AI in drug discovery

A Gangwal, A Lavecchia - Drug Discovery Today, 2024 - Elsevier
Highlights•Artificial intelligence (AI) is transforming the drug discovery process by providing
actionable insights from huge amount of data.•Deep-learning models, especially generative …