Pharm-AutoML: An open-source, end-to-end automated machine learning package for clinical outcome prediction

Although there is increased interest in utilizing machine learning (ML) to support drug development, technical hurdles associated with complex algorithms have limited widespread adoption. In response, we have developed Pharm-AutoML, an open-source Python package that enables users to automate the construction of ML models and predict clinical outcomes, especially in the context of pharmacological interventions. In particular, our approach streamlines tedious steps within the ML workflow, including data preprocessing, model tuning, model selection, results analysis, and model interpretation. Moreover, our open-source package helps to identify the most predictive ML pipeline among defined search spaces by selecting the best data preprocessing strategy and tuning the ML model hyperparameters. The package currently supports multiclass classification tasks, and additional functions are being developed. Using a set of five publicly available biomedical datasets, we show that our Pharm-AutoML outperforms other ML frameworks, including H2O with default settings, by demonstrating improved predictive accuracy of classification. We further illustrate how model interpretation methods can be utilized to help explain the fine-tuned ML pipeline to end users. Pharm-AutoML provides both novice and expert users improved clinical predictions and scientific insights.