oculomix: Hierarchical Sampling for Retinal-Based Systemic Disease Prediction
This work addresses a specific bottleneck in oculomics for medical researchers by enhancing data augmentation to better retain patient characteristics, though it is incremental as it builds on existing transformer-based models.
The paper tackled the problem of preserving patient-specific attributes in retinal imaging for systemic disease prediction by proposing Oculomix, a hierarchical sampling strategy for mixed sample augmentations, which improved AUROC by up to 3% compared to existing methods.
Oculomics - the concept of predicting systemic diseases, such as cardiovascular disease and dementia, through retinal imaging - has advanced rapidly due to the data efficiency of transformer-based foundation models like RETFound. Image-level mixed sample data augmentations, such as CutMix and MixUp, are frequently used for training transformers, yet these techniques perturb patient-specific attributes, such as medical comorbidity and clinical factors, since they only account for images and labels. To address this limitation, we propose a hierarchical sampling strategy, Oculomix, for mixed sample augmentations. Our method is based on two clinical priors. First (exam level), images acquired from the same patient at the same time point share the same attributes. Second (patient level), images acquired from the same patient at different time points have a soft temporal trend, as morbidity generally increases over time. Guided by these priors, our method constrains the mixing space to the patient and exam levels to better preserve patient-specific characteristics and leverages their hierarchical relationships. The proposed method is validated using ViT models on a five-year prediction of major adverse cardiovascular events (MACE) in a large ethnically diverse population (Alzeye). We show that Oculomix consistently outperforms image-level CutMix and MixUp by up to 3% in AUROC, demonstrating the necessity and value of the proposed method in oculomics.