Addressing Imbalanced Classification Problems in Drug Discovery and Development Using Random Forest, Support Vector Machine, AutoGluon-Tabular, and H2O AutoML

The classification models built on class imbalanced data sets tend to prioritize the accuracy of the majority class, and thus, the minority class generally has a higher misclassification rate. Different techniques are available to address the class imbalance in classification models and can be categorized as data-level, algorithm-level, and hybrid methods. But to the best of our knowledge, an in-depth analysis of the performance of these techniques against the class ratio is not available in the literature. We have addressed these shortcomings in this study and have performed a detailed analysis of the performance of four different techniques to address imbalanced class distribution using machine learning (ML) methods and AutoML tools. To carry out our study, we have selected four such techniques─(a) threshold optimization using (i) GHOST and (ii) the area under the precision-recall curve (AUPR) curve, (b) internal balancing method of AutoML and class-weight of machine learning methods, and (c) data balancing using SMOTETomek─and generated 27 data sets considering nine different class ratios (i.e., the ratio of the positive class and total samples) from three data sets that belong to the drug discovery and development field. We have employed random forest (RF) and support vector machine (SVM) as representatives of ML classifier and AutoGluon-Tabular (version 0.6.1) and H2O AutoML (version 3.40.0.4) as representatives of AutoML tools. The important findings of our studies are as follows: (i) there is no effect of threshold optimization on ranking metrics such as AUC and AUPR, but AUC and AUPR get affected by class-weighting and SMOTTomek; (ii) for ML methods RF and SVM, significant percentage improvement up to 375, 33.33, and 450 over all the data sets can be achieved, respectively, for F1 score, MCC, and balanced accuracy, which are suitable for performance evaluation of imbalanced data sets; (iii) for AutoML libraries AutoGluon-Tabular and H2O AutoML, significant percentage improvement up to 383.33, 37.25, and 533.33 over all the data sets can be achieved, respectively, for F1 score, MCC, and balanced accuracy; (iv) the general pattern of percentage improvement in balanced accuracy is that the percentage improvement increases when the class ratio is systematically decreased from 0.5 to 0.1; in the case of F1 score and MCC, maximum improvement is achieved at the class ratio of 0.3; (v) for both ML and AutoML with balancing, it is observed that any individual class-balancing technique does not outperform all other methods on a significantly higher number of data sets based on F1 score; (vi) the three external balancing techniques combined outperformed the internal balancing methods of the ML and AutoML; (vii) AutoML tools perform as good as the ML models and in some cases perform even better for handling imbalanced classification when applied with imbalance handling techniques. In summary, exploration of multiple data balancing techniques is recommended for classifying imbalanced data sets to achieve optimal performance as neither of the external techniques nor the internal techniques outperform others significantly. The results are specific to the ML methods and AutoML libraries used in this study, and for generalization, a study can be carried out considering a sizable number of ML methods and AutoML libraries.