STREAMLINE: A Simple, Transparent, End-To-End Automated Machine Learning Pipeline Facilitating Data Analysis and Algorithm Comparison

Machine learning (ML) offers powerful methods for detecting and modeling associations often in data with large feature spaces and complex associations. Many useful tools/packages (e.g. scikit-learn) have been developed to make the various elements of data handling, processing, modeling, and interpretation accessible. However, it is not trivial for most investigators to assemble these elements into a rigorous, replicatable, unbiased, and effective data analysis pipeline. Automated machine learning (AutoML) seeks to address these issues by simplifying the process of ML analysis for all. Here, we introduce STREAMLINE, a simple, transparent, end-to-end AutoML pipeline designed as a framework to easily conduct rigorous ML modeling and analysis (limited initially to binary classification). STREAMLINE is specifically designed to compare performance between datasets, ML algorithms, and other AutoML tools. It is unique among other autoML tools by offering a fully transparent and consistent baseline of comparison using a carefully designed series of pipeline elements including: (1) exploratory analysis, (2) basic data cleaning, (3) cross validation partitioning, (4) data scaling and imputation, (5) filter-based feature importance estimation, (6) collective feature selection, (7) ML modeling with `Optuna' hyperparameter optimization across 15 established algorithms (including less well-known Genetic Programming and rule-based ML), (8) evaluation across 16 classification metrics, (9) model feature importance estimation, (10) statistical significance comparisons, and (11) automatically exporting all results, plots, a PDF summary report, and models that can be easily applied to replication data.