Empirical investigation of multi-source cross-validation in clinical
  machine learning
Tuija Leinonen David Wong Ali Wahab Ramesh Nadarajah Matti Kaisti Antti Airola
Traditionally, machine learning-based clinical prediction models have been
trained and evaluated on patient data from a single source, such as a hospital.
Cross-validation methods can be used to estimate the accuracy of such models on
new patients originating from the same source, by repeated random splitting of
the data. However, such estimates tend to be highly overoptimistic when
compared to accuracy obtained from deploying models to sources not represented
in the dataset, such as a new hospital. The increasing availability of
multi-source medical datasets provides new opportunities for obtaining more
comprehensive and realistic evaluations of expected accuracy through
source-level cross-validation designs.
  In this study, we present a systematic empirical evaluation of standard
K-fold cross-validation and leave-source-out cross-validation methods in a
multi-source setting. We consider the task of electrocardiogram based
cardiovascular disease classification, combining and harmonizing the openly
available PhysioNet CinC Challenge 2021 and the Shandong Provincial Hospital
datasets for our study.
  Our results show that K-fold cross-validation, both on single-source and
multi-source data, systemically overestimates prediction performance when the
end goal is to generalize to new sources. Leave-source-out cross-validation
provides more reliable performance estimates, having close to zero bias though
larger variability. The evaluation highlights the dangers of obtaining
misleading cross-validation results on medical data and demonstrates how these
issues can be mitigated when having access to multi-source data.