Building of Robust and Interpretable QSAR Classification Models by Means of the Rivality Index

Prototype Selection Method Based on the Rivality and Reliability Indexes for the Improvement of the Classification Models and External Predictions

Prototype or instance selection techniques is an important field of research in knowledge discovery, data mining, and machine learning. In QSAR, the use of prototype selection techniques in the preprocessing stage of the construction of the QSAR models favors the data set curation, improving the interpretability and accuracy of the models as well as the performance of the algorithms. In this paper, we propose an efficient method for prototype selection to be used in the preprocessing stage of the construction of QSAR classification models. The proposed method is able to generate very high reduction rates in the cardinality of the training set while maintaining or even increasing the accuracy of the classification models. The validation of the method has been carried out by means of the prediction of external molecules, demonstrating that the prediction of new molecules is also maintained or even improved. The method has been tested using 40 benchmark data sets of different sizes and balancing ratios; the results of the tests have demonstrated the wide applicability domain of the proposed method.

Experimental Error, Kurtosis, Activity Cliffs, and Methodology: What Limits the Predictivity of Quantitative Structure-Activity Relationship Models?

Given a particular descriptor/method combination, some quantitative structure-activity relationship (QSAR) datasets are very predictive by random-split cross-validation while others are not. Recent literature in modelability suggests that the limiting issue for predictivity is in the data, not the QSAR methodology, and the limits are due to activity cliffs. Here, we investigate, on in-house data, the relative usefulness of experimental error, distribution of the activities, and activity cliff metrics in determining how predictive a dataset is likely to be. We include unmodified in-house datasets, datasets that should be perfectly predictive based only on the chemical structure, datasets where the distribution of activities is manipulated, and datasets that include a known amount of added noise. We find that activity cliff metrics determine predictivity better than the other metrics we investigated, whatever the type of dataset, consistent with the modelability literature. However, such metrics cannot distinguish real activity cliffs due to large uncertainties in the activities. We also show that a number of modern QSAR methods, and some alternative descriptors, are equally bad at predicting the activities of compounds on activity cliffs, consistent with the assumptions behind "modelability." Finally, we relate time-split predictivity with random-split predictivity and show that different coverages of chemical space are at least as important as uncertainty in activity and/or activity cliffs in limiting predictivity.

Prediction Model of Aryl Hydrocarbon Receptor Activation by a Novel QSAR Approach, DeepSnap-Deep Learning

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that senses environmental exogenous and endogenous ligands or xenobiotic chemicals. In particular, exposure of the liver to environmental metabolism-disrupting chemicals contributes to the development and propagation of steatosis and hepatotoxicity. However, the mechanisms for AhR-induced hepatotoxicity and tumor propagation in the liver remain to be revealed, due to the wide variety of AhR ligands. Recently, quantitative structure–activity relationship (QSAR) analysis using deep neural network (DNN) has shown superior performance for the prediction of chemical compounds. Therefore, this study proposes a novel QSAR analysis using deep learning (DL), called the DeepSnap–DL method, to construct prediction models of chemical activation of AhR. Compared with conventional machine learning (ML) techniques, such as the random forest, XGBoost, LightGBM, and CatBoost, the proposed method achieves high-performance prediction of AhR activation. Thus, the DeepSnap–DL method may be considered a useful tool for achieving high-throughput in silico evaluation of AhR-induced hepatotoxicity.

Rivality index neighbourhood algorithm with density and distances weighted schemes for the building of robust QSAR classification models with high reliable applicability domain

The rivality index (RI) is a normalized distance measurement between a molecule and their first nearest neighbours providing a robust prediction of the activity of a molecule based on the known activity of their nearest neighbours. Negative values of the RI describe molecules that would be correctly classified by a statistic algorithm and, vice versa, positive values of this index describe those molecules detected as outliers by the classification algorithms. In this paper, we have described a classification algorithm based on the RI and we have proposed four weighted schemes (kernels) for its calculation based on the measuring of different characteristics of the neighbourhood of molecules for each molecule of the dataset at established values of the threshold of neighbours. The results obtained have demonstrated that the proposed classification algorithm, based on the RI, generates more reliable and robust classification models than many of the more used and well-known machine learning algorithms. These results have been validated and corroborated by using 20 balanced and unbalanced benchmark datasets of different sizes and modelability. The classification models generated provide valuable information about the molecules of the dataset, the applicability domain of the models and the reliability of the predictions.