Current Methods for Drug Property Prediction in the Real World

TL;DR

This comprehensive empirical study evaluates various machine learning methods for drug property prediction, highlighting dataset-specific best practices and emphasizing the need for standardized benchmarks for practical application.

Contribution

It links multiple datasets and methods to provide a clear overview, emphasizing the importance of uncertainty quantification and dataset-specific method selection.

Findings

Classical ML methods often outperform deep learning on QSAR datasets.

Gaussian Processes are effective for QSAR datasets.

Trees and deep learning models like GNNs excel on ADMET datasets.

Abstract

Predicting drug properties is key in drug discovery to enable de-risking of assets before expensive clinical trials, and to find highly active compounds faster. Interest from the Machine Learning community has led to the release of a variety of benchmark datasets and proposed methods. However, it remains unclear for practitioners which method or approach is most suitable, as different papers benchmark on different datasets and methods, leading to varying conclusions that are not easily compared. Our large-scale empirical study links together numerous earlier works on different datasets and methods; thus offering a comprehensive overview of the existing property classes, datasets, and their interactions with different methods. We emphasise the importance of uncertainty quantification and the time and therefore cost of applying these methods in the drug development decision-making cycle. We discover that the best method depends on the dataset, and that engineered features with classical ML methods often outperform deep learning. Specifically, QSAR datasets are typically best analysed with classical methods such as Gaussian Processes while ADMET datasets are sometimes better described by Trees or Deep Learning methods such as Graph Neural Networks or language models. Our work highlights that practitioners do not yet have a straightforward, black-box procedure to rely on, and sets the precedent for creating practitioner-relevant benchmarks. Deep learning approaches must be proven on these benchmarks to become the practical method of choice in drug property prediction.