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Deep Learning-Based Conformal Prediction of Toxicity
Department of Drug Metabolism and Pharmacokinetics, Janssen Pharmaceutica NV, Beerse, Belgium.
Örebro University, School of Science and Technology. Department of Computer and Systems Sciences, Stockholm University, Kista, Sweden; Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden. (MTM Research Centre)ORCID iD: 0000-0003-3107-331X
The Alzheimer's Research UK University College London Drug Discovery Institute, The Cruciform Building, London, U.K.
2021 (English)In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 61, no 6, p. 2648-2657Article in journal (Refereed) Published
Abstract [en]

Predictive modeling for toxicity can help reduce risks in a range of applications and potentially serve as the basis for regulatory decisions. However, the utility of these predictions can be limited if the associated uncertainty is not adequately quantified. With recent studies showing great promise for deep learning-based models also for toxicity predictions, we investigate the combination of deep learning-based predictors with the conformal prediction framework to generate highly predictive models with well-defined uncertainties. We use a range of deep feedforward neural networks and graph neural networks in a conformal prediction setting and evaluate their performance on data from the Tox21 challenge. We also compare the results from the conformal predictors to those of the underlying machine learning models. The results indicate that highly predictive models can be obtained that result in very efficient conformal predictors even at high confidence levels. Taken together, our results highlight the utility of conformal predictors as a convenient way to deliver toxicity predictions with confidence, adding both statistical guarantees on the model performance as well as better predictions of the minority class compared to the underlying models.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2021. Vol. 61, no 6, p. 2648-2657
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:oru:diva-92041DOI: 10.1021/acs.jcim.1c00208ISI: 000669541400015PubMedID: 34043352Scopus ID: 2-s2.0-85108450331OAI: oai:DiVA.org:oru-92041DiVA, id: diva2:1558458
Note

Funding Agencies:

Alzheimer's Research UK (ARUK) 520909

NVIDIA Corporation 

Available from: 2021-05-31 Created: 2021-05-31 Last updated: 2024-01-16Bibliographically approved

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Norinder, Ulf

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