Amesformer: a graph transformer neural network for mutagenicity prediction

The Ames mutagenicity test is a gold standard assay for the safety assessment of new chemicals. However, many in silico models rely on challenging-to-interpret ensemble strategies and molecular fingerprint data which neglects gestalt molecular structure. To improve upon these models, we propose AmesFormer, a graph transformer neural network which shows state-of-the-art performance when paired with our new Ames dataset. We briefly review the current state of Ames modelling with a focus on graph neural networks. We then benchmark AmesFormer on a standardised test dataset against 22 other Ames models, achieving state of the art (SOTA) performance. We then uniquely report the calibration performance of our model and attempts to improve it using temperature scaling. We support our findings with reference to other models from the literature and with developments in machine learning (ML) and graph theory. Overall, we present a high-performance, accessible, and open-source computational model for Ames mutagenicity, with significant potential for regulatory and drug development applications