Pedro Seber

Pedro Seber, Richard D. Braatz

The LASSO-Clip-EN (LCEN) algorithm was previously introduced for nonlinear, interpretable feature selection and machine learning. However, its design and use was limited to regression tasks. In this work, we create a modified version of the LCEN algorithm that is suitable for classification tasks and maintains its desirable properties, such as interpretability. This modified LCEN algorithm is evaluated on four widely used binary and multiclass classification datasets. In these experiments, LCEN is compared against 10 other model types and consistently reaches high test-set macro F$_1$ score and Matthews correlation coefficient (MCC) metrics, higher than that of the majority of investigated models. LCEN models for classification remain sparse, eliminating an average of 56% of all input features in the experiments performed. Furthermore, LCEN-selected features are used to retrain all models using the same data, leading to statistically significant performance improvements in three of the experiments and insignificant differences in the fourth when compared to using all features or other feature selection methods. Simultaneously, the weighted focal differentiable MCC (diffMCC) loss function is evaluated on the same datasets. Models trained with the diffMCC loss function are always the best-performing methods in these experiments, and reach test-set macro F$_1$ scores that are, on average, 4.9% higher and MCCs that are 8.5% higher than those obtained by models trained with the weighted cross-entropy loss. These results highlight the performance of LCEN as a feature selection and machine learning algorithm also for classification tasks, and how the diffMCC loss function can train very accurate models, surpassing the weighted cross-entropy loss in the tasks investigated.

Pedro Seber, Richard D. Braatz

Interpretable architectures can have advantages over black-box architectures, and interpretability is essential for the application of machine learning in critical settings, such as aviation or medicine. However, the simplest, most commonly used interpretable architectures, such as LASSO or elastic net (EN), are limited to linear predictions and have poor feature selection capabilities. In this work, we introduce the LASSO-Clip-EN (LCEN) algorithm for the creation of nonlinear, interpretable machine learning models. LCEN is tested on a wide variety of artificial and empirical datasets, frequently creating more accurate, sparser models than other architectures, including those for building sparse, nonlinear models. LCEN is robust against many issues typically present in datasets and modeling, including noise, multicollinearity, data scarcity, and hyperparameter variance. LCEN is also able to rediscover multiple physical laws from empirical data and, for processes with no known physical laws, LCEN achieves better results than many other dense and sparse methods -- including using 10.8-fold fewer features than dense methods and 8.1-fold fewer features than EN on one dataset, and is comparable to or better than ANNs on multiple datasets.

Pedro Seber

O-GlcNAcylation, a subtype of glycosylation, has the potential to be an important target for therapeutics, but methods to reliably predict O-GlcNAcylation sites had not been available until 2023; a 2021 review correctly noted that published models were insufficient and failed to generalize. Moreover, many are no longer usable. In 2023, a considerably better recurrent neural network (RNN) model was published. This article creates improved models by using a new loss function, which we call the weighted focal differentiable MCC. RNN models trained with this new loss display superior performance to models trained using the weighted cross-entropy loss; this new function can also be used to fine-tune trained models. An RNN trained with this loss achieves state-of-the-art performance in O-GlcNAcylation site prediction with an F$_1$ score of 38.88% and an MCC of 38.20% on an independent test set from the largest dataset available.