Validation Study of QSAR/DNN Models Using the Competition Datasets

Abstract

Since the QSAR/DNN model showed predominant predictive performance over other conventional methods in the Kaggle QSAR competition, many artificial neural network (ANN) methods have been applied to drug and material discovery. Appearance of artificial intelligence (AI), which is combined various general purpose ANN platforms with large-scale open access chemical databases, has attracting great interest and expectation in a wide range of molecular sciences. In this study, we investigate various DNN settings in order to reach a high-level of predictive performance comparable to the champion team of the competition, even with a general purpose ANN platform, and introduce the Meister setting for constructing a good QSAR/DNNs model.Here, we have used the most commonly available DNN model and constructed many QSAR/DNN models trained with various DNN settings by using the 15 datasets employed in the competition. As a result, it was confirmed that we can constructed the QSAR/DNN model that shows the same level of R2 performance as the champion team. The difference from the DNN setting recommended by the champion team was to reduce the mini-batch size. We have also explained that the R2 performance of each target depends on the molecular activity type, which is related to the complexity of biological mechanisms and chemical processes observed in molecular activity measurements.