Uncertainty quantification: Can we trust artificial intelligence in drug discovery?
Open accessAbstract
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 process of drug discovery in recent years. However, most of these models can only give reliable predictions within a limited chemical space that the training set covers (applicability domain). Predictions of samples falling outside the applicability domain are unreliable and sometimes dangerous for the drug-design decision-making process. Uncertainty quantification accordingly has drawn great attention to enable autonomous drug designing. By quantifying the confidence level of model predictions, the reliability of the predictions can be quantitatively represented to assist researchers in their molecular reasoning and experimental design. Here we summarize the state-of-the-art approaches to uncertainty quantification and underline how they can be used for drug design and discovery projects. Furthermore, we also outline four representative application scenarios of uncertainty quantification in drug discovery.
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Most AI/ML models do not assign a confidence interval to the predictions.
“Another limitation of most AI/ML models is that they do not assign a confidence interval to the predictions.277,278”
From Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence (2023) · cites this paper as [277]
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- Authors
- Yu, J., Wang, D., & Zheng, M.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Zheng, Mingyue
- Venue
- iScience
- Publisher
- Elsevier BV
- Published
- 2022-08
- Volume
- 25
- Issue
- 8
- Pages
- 104814
- ISSN
- 2589-0042 (ISSN-L)
- PMC
- PMC9391523
- OpenAlex
- W4286508612
- Cited by
- 59
- References
- 79
- Citations by year
- 2026: 13 · 2025: 21 · 2024: 17 · 2023: 7 · 2022: 1
- FWCI
- 0.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- iScience (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- National Natural Science Foundation of China (81903639)
- Science and Technology Commission of Shanghai Municipality
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Keywords
- uncertainty quantification, drug discovery, artificial intelligence, applicability domain, prediction confidence, in silico models, model reliability, trust in AI
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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