Tapping on the Black Box: How Is the Scoring Power of a Machine-Learning Scoring Function Dependent on the Training Set?

In recent years, protein–ligand interaction scoring functions derived through machine-learning are repeatedly reported to outperform conventional scoring functions. However, several published studies have questioned that the superior performance of machine-learning scoring functions is dependent on the overlap between the training set and the test set. In order to examine the true power of machine-learning algorithms in scoring function formulation, we have conducted a systematic study of six off-the-shelf machine-learning algorithms, including Bayesian Ridge Regression (BRR), Decision Tree (DT), K-Nearest Neighbors (KNN), Multilayer Perceptron (MLP), Linear Support Vector Regression (L-SVR), and Random Forest (RF). Model scoring functions were derived with these machine-learning algorithms on various training sets selected from over 3700 protein–ligand complexes in the PDBbind refined set (version 2016). All resulting scoring functions were then applied to the CASF-2016 test set to validate their scoring power. In our first series of trial, the size of the training set was fixed; while the overall similarity between the training set and the test set was varied systematically. In our second series of trial, the overall similarity between the training set and the test set was fixed, while the size of the training set was varied. Our results indicate that the performance of those machine-learning models are more or less dependent on the contents or the size of the training set, where the RF model demonstrates the best learning capability. In contrast, the performance of three conventional scoring functions (i.e., ChemScore, ASP, and X-Score) is basically insensitive to the use of different training sets. Therefore, one has to consider not only “hard overlap” but also “soft overlap” between the training set and the test set in order to evaluate machine-learning scoring functions. In this spirit, we have complied data sets based on the PDBbind refined set by removing redundant samples under several similarity thresholds. Scoring functions developers are encouraged to employ them as standard training sets if they want to evaluate their new models on the CASF-2016 benchmark.