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arXiv · 2201.03291

A novel interpretable machine learning system to generate clinical risk scores: An application for predicting early mortality or unplanned readmission in a retrospective cohort study

Yilin Ning·Siqi Li·Marcus Eng Hock Ong·Feng Xie·Bibhas Chakraborty·Daniel Shu Wei Ting·Nan Liu
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Abstract

Risk scores are widely used for clinical decision making and commonly generated from logistic regression models. Machine-learning-based methods may work well for identifying important predictors, but such 'black box' variable selection limits interpretability, and variable importance evaluated from a single model can be biased. We propose a robust and interpretable variable selection approach using the recently developed Shapley variable importance cloud (ShapleyVIC) that accounts for variability across models. Our approach evaluates and visualizes overall variable contributions for in-depth inference and transparent variable selection, and filters out non-significant contributors to simplify model building steps. We derive an ensemble variable ranking from variable contributions, which is easily integrated with an automated and modularized risk score generator, AutoScore, for convenient implementation. In a study of early death or unplanned readmission, ShapleyVIC selected 6 of 41 candidate variables to create a well-performing model, which had similar performance to a 16-variable model from machine-learning-based ranking.

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Yilin Ning, Siqi Li, Marcus Eng Hock Ong, Feng Xie, Bibhas Chakraborty, Daniel Shu Wei Ting, Nan Liu. 2022-01-10. A novel interpretable machine learning system to generate clinical risk scores: An application for predicting early mortality or unplanned readmission in a retrospective cohort study. https://doi.org/10.1371/journal.pdig.0000062

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