A Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) Binary Classification Platform for Tabular Data

Abstract

Therapeutic resistance continues to impede overall survival rates for those affected by cancer. Although driver genes are associated with diverse cancer types, a scarcity of instrumental methods for predicting therapy response or resistance persists. Therefore, the impetus for designing predictive tools for therapeutic response is crucial and tools based on machine learning open new opportunities. Here, we present an easily accessible platform dedicated to Clear, Legible, Explainable, Transparent, and Elucidative (CLETE) yet wholly modifiable binary classification models. Our platform encompasses both unsupervised and supervised feature selection options, hyperparameter search methodologies, under-sampling and over-sampling methods, and normalization methods, along with fifteen machine learning algorithms. The platform furnishes a k-fold receiver operating curve (ROC) - area under the curve (AUC) and accuracy plots, permutation feature importance, SHapley Additive exPlanations (SHAP) plots, and Local Interpretable Model-agnostic Explanations (LIME) plots to interpret the model and individual predictions. We have deployed a unique custom metric for hyperparameter search, which considers both training and validation scores, thus ensuring a check on under or over-fitting. Moreover, we introduce an innovative scoring method, NegLog2RMSL, which incorporates both training and test scores for model evaluation that facilitates the evaluation of models via multiple parameters. In a bid to simplify the user interface, we provide a graphical interface that sidesteps programming expertise and is compatible with both Windows and Mac OS. Platform robustness has been validated using pharmacogenomic data for 23 drugs across four diseases and holds the potential for utilization with any form of tabular data.