neural networks

Machine learning interatomic potentials (MLIPs) have emerged as powerful tools for investigating atomistic systems with high accuracy and a relatively low computational cost. However, a common and unaddressed challenge with many current neural network (NN) MLIP models is their limited ability to accurately predict the relative energies of systems containing isolated or nearly isolated atoms, which appear in various reactive processes. To address this limitation, we present a mathematical technique for modifying any existing atom-centered NN architecture to account for the energies of isolated atoms. The result produces a consistent prediction of the atomization energy (AE) of a system using minimal constraints on the model. Using this technique, we build a model architecture that we call hierarchically interacting particle neural network (HIP-NN)-AE, an AE-constrained version of the HIP-NN, as well as ANI-AE, the AE-constrained version of the accurate NN engine for molecular energies (ANI). Our results demonstrate AE consistency of AE-constrained models, which drastically improves the AE predictions for the models. We compare the AE-constrained approach to unconstrained models as well as models from the literature in other scenarios, such as bond dissociation energies, bond dissociation pathways, and extensibility tests. These results show that the constraints improve the model performance in some of these tasks and do not negatively affect the performance on any tasks. The AE constraint approach thus offers a robust solution to the challenges posed by isolated atoms in energy prediction tasks.

Quantitative structure-activity relationship (QSAR) modelling, an approach that was introduced 60 years ago, is widely used in computer-aided drug design. In recent years, progress in artificial intelligence techniques, such as deep learning, the rapid growth of databases of molecules for virtual screening and dramatic improvements in computational power have supported the emergence of a new field of QSAR applications that we term 'deep QSAR'. Marking a decade from the pioneering applications of deep QSAR to tasks involved in small-molecule drug discovery, we herein describe key advances in the field, including deep generative and reinforcement learning approaches in molecular design, deep learning models for synthetic planning and the application of deep QSAR models in structure-based virtual screening. We also reflect on the emergence of quantum computing, which promises to further accelerate deep QSAR applications and the need for open-source and democratized resources to support computer-aided drug design.

This themed collection includes a collection of articles on Insightful Machine Learning for Physical Chemistry.