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

Part of the Genetic and Evolutionary Computation book series (GEVO)


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.

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The study was supported by the following NIH grants: R01s LM010098 and AG066833. STREAMLINE development benefited from multiple biomedical research collaborators at the University of Pennsylvania, Fox Chase Cancer Center, Cedars Sinai Medical Center, and the University of Kansas Medical Center. Special thanks to Patryk Orzechowski, Trang Le, Sy Hwang, Richard Zhang, Wilson Zhang, and Pedro Ribeiro for their code contributions and feedback. We also thank the following collaborators for their feedback on the application of the pipeline during development: Shannon Lynch, Rachael Stolzenberg-Solomon, Ulysses Magalang, Allan Pack, Brendan Keenan, Danielle Mowery, Jason Moore, and Diego Mazzotti.

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Urbanowicz, R., Zhang, R., Cui, Y., Suri, P. (2023). STREAMLINE: A Simple, Transparent, End-To-End Automated Machine Learning Pipeline Facilitating Data Analysis and Algorithm Comparison. In: Trujillo, L., Winkler, S.M., Silva, S., Banzhaf, W. (eds) Genetic Programming Theory and Practice XIX. Genetic and Evolutionary Computation. Springer, Singapore.

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