Exploring the potential of in silico machine learning tools for the prediction of acute Daphnia magna nanotoxicity

Abstract

Engineered nanomaterials (ENMs) are ubiquitous nowadays, finding their application in different fields of technology and various consumer products. Virtually any chemical can be manipulated at the nano-scale to display unique characteristics which makes them appealing over larger sized materials. As the production and development of ENMs have increased considerably over time, so too have concerns regarding their adverse effects and environmental impacts. It is unfeasible to assess the risks associated with every single ENM through in vivo or in vitro experiments. As an alternative, in silico methods can be employed to evaluate ENMs. To perform such an evaluation, we collected data from databases and literature to create classification models based on machine learning algorithms in accordance with the principles laid out by the OECD for the creation of QSARs. The aim was to investigate the performance of various machine learning algorithms towards predicting a well-defined in vivo toxicity endpoint (Daphnia magna immobilization) and also to identify which features are important drivers of D. magna in vivo nanotoxicity. Results indicated highly comparable model performance between all algorithms and predictive performance exceeding ∼0.7 for all evaluated metrics (e.g. accuracy, sensitivity, specificity, balanced accuracy, Matthews correlation coefficient, area under the receiver operator characteristic curve). The random forest, artificial neural network, and k-nearest neighbor models displayed the best performance but this was only marginally better compared to the other models. Furthermore, the variable importance analysis indicated that molecular descriptors and physicochemical properties were generally important within most models, while features related to the exposure conditions produced slightly conflicting results. Lastly, results also indicate that reliable and robust machine learning models can be generated for in vivo endpoints with smaller datasets.