Assigning confidence to molecular property prediction. (2nd September 2021)

• Record Type: Journal Article
• Authors: Nigam, AkshatKumar; Pollice, Robert; Hurley, Matthew F. D.; Hickman, Riley J.; Aldeghi, Matteo; Yoshikawa, Naruki; Chithrananda, Seyone; Voelz, Vincent A.; Aspuru-Guzik, Alán
• Is Part Of: Expert opinion on drug discovery. Volume 16:Number 9(2021)
• Page Start: 1009
• Page End: 1023
• Publication Date: 2021-09-02
• Subjects: Neural networks -- deep learning -- drug discovery -- generative models -- artificial intelligence -- model uncertainty estimation -- docking -- molecular dynamics; 615.1
• DOI: 10.1080/17460441.2021.1925247
• Languages: English
• ISSNs: 1746-0441

Abstract

ABSTRACT: Introduction : Computational modeling has rapidly advanced over the last decades. Recently, machine learning has emerged as a powerful and cost-effective strategy to learn from existing datasets and perform predictions on unseen molecules. Accordingly, the explosive rise of data-driven techniques raises an important question: What confidence can be assigned to molecular property predictions and what techniques can be used? Areas covered : The authors discuss popular strategies for predicting molecular properties, their corresponding uncertainty sources and methods to quantify uncertainty. First, the authors' considerations for assessing confidence begin with dataset bias and size, data-driven property prediction and feature design. Next, the authors discuss property simulation via computations of binding affinity in detail. Lastly, they investigate how these uncertainties propagate to generative models, as they are usually coupled with property predictors. Expert opinion : Computational techniques are paramount to reduce the prohibitive cost of brute-force experimentation during exploration. The authors believe that assessing uncertainty in property prediction models is essential whenever closed-loop drug design campaigns relying on high-throughput virtual screening are deployed. Accordingly, considering sources of uncertainty leads to better-informed validations, more reliable predictions and more realistic expectations of the entire workflow. Overall, this increases confidence in the predictions and, ultimately, accelerates drug design.