Analysis of uncertainty of neural fingerprint-based models

Machine learning has gained popularity for predicting molecular properties based on molecular structure. This study explores the uncertainty estimates of neural fingerprint-based models by comparing pure graph neural networks (GNN) to classical machine learning algorithms combined with neural fingerprints. We investigate the advantage of extracting the neural fingerprint from the GNN and integrating it into a method known for producing better-calibrated probability estimates. Comparisons are made using three classical machine learning methods and the Chemprop model, considering different molecular representations and calibration techniques. We utilize 19 datasets from Toxcast, reflecting real-world scenarios with balanced accuracies ranging from 0.6 to 0.8. Results demonstrate that neural fingerprints combined with classical machine learning methods exhibit a slight decrease in prediction performance compared to the native Chemprop model. However, these models provide significantly improved uncertainty estimates. Notably, uncertainty estimates of neural fingerprint-based methods remain relatively robust for molecules dissimilar to the training set. This suggests that methods like random forest with neural fingerprints can deliver strong prediction performance and reliable uncertainty estimates. When considering both performance and uncertainty, the calibrated Chemprop model and the combination of neural fingerprints with random forest or support vector classifier (SVC) yield comparable results. Surprisingly, the SVC method shows promising performance when combined with neural or count fingerprints. These findings are particularly relevant in real-world industrial projects where accurate predictions and reliable uncertainty estimates are crucial.