Confidently Uncertain: Probabilistic Machine Learning to Predict Soil Biotransformation Half-Lives

Predicting environmental persistence of chemicals from molecular structure is an open challenge, yet indispensable in regulatory screenings for potentially harmful substances and to advance the development of safe-and-sustainable-by-design chemicals. Limited availability of biotransformation half-life data makes persistence prediction difficult, and models typically struggle to generalize beyond their training data. Therefore, reliable estimates of prediction confidence are key. Here, we propose a probabilistic model for the prediction of soil biotransformation half-lives. A Gaussian Process Regressor was trained on 867 mean pesticide half-lives with data uncertainty estimates. Instead of single half-life values, our model predicts well-calibrated probability distributions that can be used to calculate a compound's probability of being persistent. Although the overall model performance remains moderate, the predictions are reliable when the confidence in the prediction is high. We applied our model to pesticide transformation products with unknown half-lives, and to a database of globally marketed chemicals. We show that our model is able to identify chemicals that are known, or suspected to be, persistent in the environment. The model is available as an online app (https://pepper-app.streamlit.app/) and as a Python library (pepper-lab) to meet diverse user needs.