Fundus Retinal imaging is an easy-to-acquire modality typically used for monitoring eye health. Current evidence indicates that the retina, and its vasculature in particular, is associated with other disease processes making it an ideal candidate for biomarker discovery. The development of these biomarkers has typically relied on predefined measurements, which makes the development process slow. Recently, representation learning algorithms such as general purpose convolutional neural networks or vasculature embeddings have been proposed as an approach to learn imaging biomarkers directly from the data, hence greatly speeding up their discovery. In this work, we compare and contrast different state-of-the-art retina biomarker discovery methods to identify signs of past stroke in the retinas of a curated patient cohort of 2,472 subjects from the UK Biobank dataset. We investigate two convolutional neural networks previously used in retina biomarker discovery and directly trained on the stroke outcome, and an extension of the vasculature embedding approach which infers its feature representation from the vasculature and combines the information of retinal images from both eyes.In our experiments, we show that the pipeline based on vasculature embeddings has comparable or better performance than other methods with a much more compact feature representation and ease of training.Clinical Relevance—This study compares and contrasts three retinal biomarker discovery strategies, using a curated dataset of subject evidence, for the analysis of the retina as a proxy in the assessment of clinical outcomes, such as stroke risk.