Optimal Ensemble Construction for Multi-Study Prediction with Applications to COVID-19 Excess Mortality Estimation

It is increasingly common to encounter prediction tasks in the biomedical sciences for which multiple datasets are available for model training. Common approaches such as pooling datasets and applying standard statistical learning methods can result in poor out-of-study prediction performance when datasets are heterogeneous. Theoretical and applied work has shown textitmulti-study ensembling to be a viable alternative that leverages the variability across datasets in a manner that promotes model generalizability. Multi-study ensembling uses a two-stage textitstacking strategy which fits study-specific models and estimates ensemble weights separately. This approach ignores, however, the ensemble properties at the model-fitting stage, potentially resulting in a loss of efficiency. We therefore propose textitoptimal ensemble construction, an textitall-in-one approach to multi-study stacking whereby we jointly estimate ensemble weights as well as parameters associated with each study-specific model. We prove that limiting cases of our approach yield existing methods such as multi-study stacking and pooling datasets before model fitting. We propose an efficient block coordinate descent algorithm to optimize the proposed loss function. We compare our approach to standard methods by applying it to a multi-country COVID-19 dataset for baseline mortality prediction. We show that when little data is available for a country before the onset of the pandemic, leveraging data from other countries can substantially improve prediction accuracy. Importantly, our approach outperforms multi-study stacking and other standard methods in this application. We further characterize the method's performance in simulations. Our method remains competitive with or outperforms multi-study stacking and other earlier methods across a range of between-study heterogeneity levels.