FragNet: A Graph Neural Network for Molecular Property Prediction with Four Layers of Interpretability

Molecular property prediction is a crucial step in many modern-day scientific applications including drug discovery and energy storage material design. Despite the availability of numerous machine learning models for this task, we are lacking in models that provide both high accuracies and interpretability of the predictions. We introduce the FragNet architecture, a graph neural network not only capable of achieving prediction accuracies comparable to the current state-of-the-art models, but also able to provide insight on four levels of molecular substructures. This model enables understanding of which atoms, bonds, molecular fragments, and molecular fragment connections are critical in the prediction of a given molecular property. The ability to interpret the importance of connections between fragments is of particular interest for molecules which have substructures that are not connected with regular covalent bonds. The interpretable capabilities of FragNet are key to gaining scientific insights from the model's learned patterns between molecular structure and molecular properties.