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 …
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 …
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 …
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
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 …
(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
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 …
molecular machine learning. Despite common open research questions and long-term …
[PDF][PDF] Quantitative evaluation of explainable graph neural networks for molecular property prediction
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 …
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 …
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 …
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 …
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 …
actionable insights from huge amount of data.•Deep-learning models, especially generative …