Compatibility of Missing Data Handling Methods across the Stages of Producing Clinical Prediction Models

Antonia Tsvetanova; Matthew Sperrin; David A. Jenkins; Niels Peek; Iain Buchan; Stephanie Hyland; Marcus Taylor; Angela Wood; Richard D. Riley; Glen P. Martin

arXiv · 2504.06799

Compatibility of Missing Data Handling Methods across the Stages of Producing Clinical Prediction Models

Antonia Tsvetanova·Matthew Sperrin·David A. Jenkins·Niels Peek·Iain Buchan·Stephanie Hyland·Marcus Taylor·Angela Wood·Richard D. Riley·Glen P. Martin

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Abstract

Missing data is a challenge when developing, validating and deploying clinical prediction models (CPMs). Traditionally, decisions concerning missing data handling during CPM development and validation havent accounted for whether missingness is allowed at deployment. We hypothesised that the missing data approach used during model development should optimise model performance upon deployment, whilst the approach used during model validation should yield unbiased predictive performance estimates upon deployment; we term this compatibility. We aimed to determine which combinations of missing data handling methods across the CPM life cycle are compatible. We considered scenarios where CPMs are intended to be deployed with missing data allowed or not, and we evaluated the impact of that choice on earlier modelling decisions. Through a simulation study and an empirical analysis of thoracic surgery data, we compared CPMs developed and validated using combinations of complete case analysis, mean imputation, single regression imputation, multiple imputation, and pattern sub-modelling. If planning to deploy a CPM without allowing missing data, then development and validation should use multiple imputation when required. Where missingness is allowed at deployment, the same imputation method must be used during development and validation. Commonly used combinations of missing data handling methods result in biased predictive performance estimates.

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Antonia Tsvetanova, Matthew Sperrin, David A. Jenkins, Niels Peek, Iain Buchan, Stephanie Hyland, Marcus Taylor, Angela Wood, Richard D. Riley, Glen P. Martin. 2025-04-09. Compatibility of Missing Data Handling Methods across the Stages of Producing Clinical Prediction Models. https://arxiv.org/abs/2504.06799

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